phdthesis.bib

@article{3dligandsite,
  doi = {10.1093/nar/gkq406},
  url = {https://doi.org/10.1093/nar/gkq406},
  year = {2010},
  month = may,
  publisher = {Oxford University Press ({OUP})},
  volume = {38},
  number = {suppl{\_}2},
  pages = {W469--W473},
  author = {Mark N. Wass and Lawrence A. Kelley and Michael J. E. Sternberg},
  title = {3DLigandSite: predicting ligand-binding sites using similar structures},
  journal = {Nucleic Acids Research}
}

@article{3v,
  doi = {10.1093/nar/gkq395},
  url = {https://doi.org/10.1093/nar/gkq395},
  year = {2010},
  month = may,
  publisher = {Oxford University Press ({OUP})},
  volume = {38},
  number = {Web Server},
  pages = {W555--W562},
  author = {N. R. Voss and M. Gerstein},
  title = {3V: cavity,  channel and cleft volume calculator and extractor},
  journal = {Nucleic Acids Research}
}

@article{amber,
  author = {Case, David A. and Cheatham III, Thomas E. and Darden, Tom and Gohlke, Holger and Luo, Ray and Merz Jr., Kenneth M. and Onufriev, Alexey and Simmerling, Carlos and Wang, Bing and Woods, Robert J.},
  title = {The Amber biomolecular simulation programs},
  journal = {Journal of Computational Chemistry},
  volume = {26},
  number = {16},
  pages = {1668-1688},
  keywords = {Amber, biomolecular simulation programs},
  doi = {https://doi.org/10.1002/jcc.20290},
  url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20290},
  eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20290},
  abstract = {Abstract We describe the development, current features, and some directions for future development of the Amber package of computer programs. This package evolved from a program that was constructed in the late 1970s to do Assisted Model Building with Energy Refinement, and now contains a group of programs embodying a number of powerful tools of modern computational chemistry, focused on molecular dynamics and free energy calculations of proteins, nucleic acids, and carbohydrates. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1668-1688, 2005},
  year = {2005}
}

@inproceedings{amdahl1967,
  doi = {10.1145/1465482.1465560},
  url = {https://doi.org/10.1145/1465482.1465560},
  year = {1967},
  publisher = {{ACM} Press},
  author = {Gene M. Amdahl},
  title = {Validity of the single processor approach to achieving large scale computing capabilities},
  booktitle = {Proceedings of the April 18-20,  1967,  spring joint computer conference on - {AFIPS} {\textquotesingle}67 (Spring)}
}

@article{apropos,
  title={The automatic search for ligand binding sites in proteins of known three-dimensional structure using only geometric criteria},
  author={Peters, Klaus P and Fauck, Jana and Fr{\"o}mmel, Cornelius},
  journal={Journal of molecular biology},
  volume={256},
  number={1},
  pages={201--213},
  year={1996},
  publisher={Elsevier}
}

@article{baek2021,
  doi = {10.1126/science.abj8754},
  url = {https://doi.org/10.1126/science.abj8754},
  year = {2021},
  month = aug,
  publisher = {American Association for the Advancement of Science ({AAAS})},
  volume = {373},
  number = {6557},
  pages = {871--876},
  author = {Minkyung Baek and Frank DiMaio and Ivan Anishchenko and Justas Dauparas and Sergey Ovchinnikov and Gyu Rie Lee and Jue Wang and Qian Cong and Lisa N. Kinch and R. Dustin Schaeffer and Claudia Mill{\'{a}}n and Hahnbeom Park and Carson Adams and Caleb R. Glassman and Andy DeGiovanni and Jose H. Pereira and Andria V. Rodrigues and Alberdina A. van Dijk and Ana C. Ebrecht and Diederik J. Opperman and Theo Sagmeister and Christoph Buhlheller and Tea Pavkov-Keller and Manoj K. Rathinaswamy and Udit Dalwadi and Calvin K. Yip and John E. Burke and K. Christopher Garcia and Nick V. Grishin and Paul D. Adams and Randy J. Read and David Baker},
  title = {Accurate prediction of protein structures and interactions using a three-track neural network},
  journal = {Science}
}

@article{biobbvs,
  doi = {10.1038/s41597-019-0177-4},
  url = {https://doi.org/10.1038/s41597-019-0177-4},
  year = {2019},
  month = sep,
  publisher = {Springer Science and Business Media {LLC}},
  volume = {6},
  number = {1},
  author = {Pau Andrio and Adam Hospital and Javier Conejero and Luis Jord{\'{a}} and Marc Del Pino and Laia Codo and Stian Soiland-Reyes and Carole Goble and Daniele Lezzi and Rosa M. Badia and Modesto Orozco and Josep Ll. Gelpi},
  title = {{BioExcel} Building Blocks,  a software library for interoperable biomolecular simulation workflows},
  journal = {Scientific Data}
}

@techreport{black2020,
  doi = {10.6028/nist.ir.8318},
  url = {https://doi.org/10.6028/nist.ir.8318},
  year = {2020},
  month = sep,
  publisher = {National Institute of Standards and Technology},
  author = {Paul E Black},
  title = {DADS: The On-Line Dictionary of Algorithms and Data Structures}
}

@article{bohacek1997,
  doi = {10.1016/s1367-5931(97)80004-x},
  url = {https://doi.org/10.1016/s1367-5931(97)80004-x},
  year = {1997},
  month = aug,
  publisher = {Elsevier {BV}},
  volume = {1},
  number = {2},
  pages = {157--161},
  author = {Regine S Bohacek and Colin McMartin},
  title = {Modern computational chemistry and drug discovery: structure generating programs},
  journal = {Current Opinion in Chemical Biology}
}

@book{bondy1976,
  address = {New York},
  author = {Bondy, J. A. and Murty, U. S. R.},
  biburl = {https://www.zib.de/groetschel/teaching/WS1314/BondyMurtyGTWA.pdf},
  keywords = {networks graphs},
  publisher = {Elsevier},
  timestamp = {2011-08-28T03:04:05.000+0200},
  title = {Graph Theory with Applications},
  year = 1976
}

@article{brik2002,
  doi = {10.1039/b208248a},
  url = {https://doi.org/10.1039/b208248a},
  year = {2002},
  month = nov,
  publisher = {Royal Society of Chemistry ({RSC})},
  volume = {1},
  number = {1},
  pages = {5--14},
  author = {Ashraf Brik and Chi-Huey Wong},
  title = {{HIV}-1 protease: mechanism and drug discovery},
  journal = {Organic {\&}amp$\mathsemicolon$  Biomolecular Chemistry}
}

@article{brosey2021,
  doi = {10.1016/j.pbiomolbio.2021.02.002},
  url = {https://doi.org/10.1016/j.pbiomolbio.2021.02.002},
  year = {2021},
  month = aug,
  publisher = {Elsevier {BV}},
  volume = {163},
  pages = {171--186},
  author = {Chris A. Brosey and Jerry H. Houl and Panagiotis Katsonis and Lakshitha P.F. Balapiti-Modarage and Shobanbabu Bommagani and Andy Arvai and Davide Moiani and Albino Bacolla and Todd Link and Leslie S. Warden and Olivier Lichtarge and Darin E. Jones and Zamal Ahmed and John A. Tainer},
  title = {Targeting {SARS}-{CoV}-2 Nsp3 macrodomain structure with insights from human poly({ADP}-ribose) glycohydrolase ({PARG}) structures with inhibitors},
  journal = {Progress in Biophysics and Molecular Biology}
}

@article{burley2018,
  doi = {10.1093/nar/gky1004},
  url = {https://doi.org/10.1093/nar/gky1004},
  year = {2018},
  month = oct,
  publisher = {Oxford University Press ({OUP})},
  volume = {47},
  number = {D1},
  pages = {D464--D474},
  author = {Stephen K Burley and Helen M Berman and Charmi Bhikadiya and Chunxiao Bi and Li Chen and Luigi Di~Costanzo and Cole Christie and Ken Dalenberg and Jose M Duarte and Shuchismita Dutta and Zukang Feng and Sutapa Ghosh and David S Goodsell and Rachel K Green and Vladimir Guranovi{\'{c}} and Dmytro Guzenko and Brian P Hudson and Tara Kalro and Yuhe Liang and Robert Lowe and Harry Namkoong and Ezra Peisach and Irina Periskova and Andreas Prli{\'{c}} and Chris Randle and Alexander Rose and Peter Rose and Raul Sala and Monica Sekharan and Chenghua Shao and Lihua Tan and Yi-Ping Tao and Yana Valasatava and Maria Voigt and John Westbrook and Jesse Woo and Huanwang Yang and Jasmine Young and Marina Zhuravleva and Christine Zardecki},
  title = {{RCSB} Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology,  biomedicine,  biotechnology and energy},
  journal = {Nucleic Acids Research}
}

@article{capri,
  author = {Janin, J. and Henrick, K. and Moult, J. and Eyck, L. T. and Sternberg, M. J. and Vajda, S. and Vakser, I. A. and Wodak, S. J.},
  title = {Capri: a critical assessment of predicted interactions},
  journal = {Proteins: Structure, Function, and Bioinformatics},
  year = {2003},
  volume = {52},
  issue = {1},
  pages = {2-9},
  doi = {10.1002/prot.10381}
}

@article{carlson2008,
  doi = {10.1021/jm8006504},
  url = {https://doi.org/10.1021/jm8006504},
  year = {2008},
  month = oct,
  publisher = {American Chemical Society ({ACS})},
  volume = {51},
  number = {20},
  pages = {6432--6441},
  author = {Heather A. Carlson and Richard D. Smith and Nickolay A. Khazanov and Paul D. Kirchhoff and James B. Dunbar and Mark L. Benson},
  title = {Differences between High- and Low-Affinity Complexes of Enzymes and Nonenzymes},
  journal = {Journal of Medicinal Chemistry}
}

@article{caulder1998,
author = {Caulder, Dana L. and Powers, Ryan E. and Parac, Tatjana N. and Raymond, Kenneth N.},
title = {The Self-Assembly of a Predesigned Tetrahedral M4L6 Supramolecular Cluster},
journal = {Angewandte Chemie International Edition},
volume = {37},
number = {13-14},
pages = {1840-1843},
keywords = {Cage compounds, Clusters, Host-guest chemistry, O ligands, Self-organization},
doi = {https://doi.org/10.1002/(SICI)1521-3773(19980803)37:13/14<1840::AID-ANIE1840>3.0.CO;2-D},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291521-3773%2819980803%2937%3A13/14%3C1840%3A%3AAID-ANIE1840%3E3.0.CO%3B2-D},
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/%28SICI%291521-3773%2819980803%2937%3A13/14%3C1840%3A%3AAID-ANIE1840%3E3.0.CO%3B2-D},
abstract = {Abstract A remarkable selectivity on the basis of size is observed for the encapsulation of Et4N+ in the presence of Me4N+ and Pr4N+ by a predesigned [Ga4L6]12-- homochiral tetrahedral cluster (L=bis-bidentate ligand). Immediate and quantitative stepwise replacement of R4N+ counterions in the cluster cavity is observed by 1H NMR spectroscopy (see below). The encapsulation of Et4N+ is also observed in the solid state.},
year = {1998}
}

@article{caver,
  doi = {10.1186/1471-2105-7-316},
  url = {https://doi.org/10.1186/1471-2105-7-316},
  year = {2006},
  month = jun,
  publisher = {Springer Science and Business Media {LLC}},
  volume = {7},
  number = {1},
  author = {Martin Pet{\v{r}}ek and Michal Otyepka and Pavel Ban{\'{a}}{\v{s}} and Pavl{\'{\i}}na Ko{\v{s}}inov{\'{a}} and Jaroslav Ko{\v{c}}a and Ji{\v{r}}{\'{\i}} Damborsk{\'{y}}},
  title = {{CAVER}: a new tool to explore routes from protein clefts,  pockets and cavities},
  journal = {{BMC} Bioinformatics}
}

@article{caver3,
  doi = {10.1371/journal.pcbi.1002708},
  author = {Chovancova, Eva AND Pavelka, Antonin AND Benes, Petr AND Strnad, Ondrej AND Brezovsky, Jan AND Kozlikova, Barbora AND Gora, Artur AND Sustr, Vilem AND Klvana, Martin AND Medek, Petr AND Biedermannova, Lada AND Sochor, Jiri AND Damborsky, Jiri},
  journal = {PLOS Computational Biology},
  publisher = {Public Library of Science},
  title = {CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures},
  year = {2012},
  month = {10},
  volume = {8},
  url = {https://doi.org/10.1371/journal.pcbi.1002708},
  pages = {1-12},
  abstract = {Tunnels and channels facilitate the transport of small molecules, ions and water solvent in a large variety of proteins. Characteristics of individual transport pathways, including their geometry, physico-chemical properties and dynamics are instrumental for understanding of structure-function relationships of these proteins, for the design of new inhibitors and construction of improved biocatalysts. CAVER is a software tool widely used for the identification and characterization of transport pathways in static macromolecular structures. Herein we present a new version of CAVER enabling automatic analysis of tunnels and channels in large ensembles of protein conformations. CAVER 3.0 implements new algorithms for the calculation and clustering of pathways. A trajectory from a molecular dynamics simulation serves as the typical input, while detailed characteristics and summary statistics of the time evolution of individual pathways are provided in the outputs. To illustrate the capabilities of CAVER 3.0, the tool was applied for the analysis of molecular dynamics simulation of the microbial enzyme haloalkane dehalogenase DhaA. CAVER 3.0 safely identified and reliably estimated the importance of all previously published DhaA tunnels, including the tunnels closed in DhaA crystal structures. Obtained results clearly demonstrate that analysis of molecular dynamics simulation is essential for the estimation of pathway characteristics and elucidation of the structural basis of the tunnel gating. CAVER 3.0 paves the way for the study of important biochemical phenomena in the area of molecular transport, molecular recognition and enzymatic catalysis. The software is freely available as a multiplatform command-line application at http://www.caver.cz.},
  number = {10},
}

@article{caveranalyst2,
  doi = {10.1093/bioinformatics/bty386},
  url = {https://doi.org/10.1093/bioinformatics/bty386},
  year = {2018},
  month = may,
  publisher = {Oxford University Press ({OUP})},
  volume = {34},
  number = {20},
  pages = {3586--3588},
  author = {Adam Jurcik and David Bednar and Jan Byska and Sergio M Marques and Katarina Furmanova and Lukas Daniel and Piia Kokkonen and Jan Brezovsky and Ondrej Strnad and Jan Stourac and Antonin Pavelka and Martin Manak and Jiri Damborsky and Barbora Kozlikova},
  editor = {Alfonso Valencia},
  title = {{CAVER} Analyst 2.0: analysis and visualization of channels and tunnels in protein structures and molecular dynamics trajectories},
  journal = {Bioinformatics}
}

@article{caverweb,
  doi = {10.1093/nar/gkz378},
  url = {https://doi.org/10.1093/nar/gkz378},
  year = {2019},
  month = may,
  publisher = {Oxford University Press ({OUP})},
  volume = {47},
  number = {W1},
  pages = {W414--W422},
  author = {Jan Stourac and Ondrej Vavra and Piia Kokkonen and Jiri Filipovic and Gaspar Pinto and Jan Brezovsky and Jiri Damborsky and David Bednar},
  title = {Caver Web 1.0: identification of tunnels and channels in proteins and analysis of ligand transport},
  journal = {Nucleic Acids Research}
}

@article{cavitysearch,
  title={Cavity search: an algorithm for the isolation and display of cavity-like binding regions},
  author={Ho, Chris MW and Marshall, Garland R},
  journal={Journal of computer-aided molecular design},
  volume={4},
  pages={337--354},
  year={1990},
  publisher={Springer}
}

@article{cavvis,
  doi = {10.1021/acs.jcim.8b00572},
  url = {https://doi.org/10.1021/acs.jcim.8b00572},
  year = {2019},
  month = jan,
  publisher = {American Chemical Society ({ACS})},
  volume = {59},
  number = {2},
  pages = {786--796},
  author = {Tiago M. C. Sim{\~{o}}es and Abel J. P. Gomes},
  title = {{CavVis}{\textemdash}A Field-of-View Geometric Algorithm for Protein Cavity Detection},
  journal = {Journal of Chemical Information and Modeling}
}

@article{chen2018,
  doi = {10.1038/s41467-018-07704-x},
  url = {https://doi.org/10.1038/s41467-018-07704-x},
  year = {2018},
  month = dec,
  publisher = {Springer Science and Business Media {LLC}},
  volume = {9},
  number = {1},
  author = {Lihong Chen and Ming Wang and Dongjie Zhu and Zhenzhao Sun and Jun Ma and Jinglin Wang and Lingfei Kong and Shida Wang and Zaisi Liu and Lili Wei and Yuwen He and Jingfei Wang and Xinzheng Zhang},
  title = {Implication for alphavirus host-cell entry and assembly indicated by a 3.5{\{AA}} resolution cryo-{EM} structure},
  journal = {Nature Communications}
}

@article{chen2023,
  title = {Cryo-EM structures of human SPCA1a reveal the mechanism of Ca
            2+
            /Mn
            2+
            transport into the Golgi apparatus},
  volume = {9},
  ISSN = {2375-2548},
  url = {http://dx.doi.org/10.1126/sciadv.add9742},
  DOI = {10.1126/sciadv.add9742},
  number = {9},
  journal = {Science Advances},
  publisher = {American Association for the Advancement of Science (AAAS)},
  author = {Chen,  Zhenghao and Watanabe,  Satoshi and Hashida,  Hironori and Inoue,  Michio and Daigaku,  Yasukazu and Kikkawa,  Masahide and Inaba,  Kenji},
  year = {2023},
  month = mar 
}

@article{chimerax,
  doi = {10.1002/pro.3943},
  url = {https://doi.org/10.1002/pro.3943},
  year = {2020},
  month = oct,
  publisher = {Wiley},
  volume = {30},
  number = {1},
  pages = {70--82},
  author = {Eric F. Pettersen and Thomas D. Goddard and Conrad C. Huang and Elaine C. Meng and Gregory S. Couch and Tristan I. Croll and John H. Morris and Thomas E. Ferrin},
  title = {UCSF ChimeraX: Structure visualization for researchers,  educators,  and developers},
  journal = {Protein Science}
}

@article{claverie2020,
  doi = {10.3390/v12060646},
  url = {https://doi.org/10.3390/v12060646},
  year = {2020},
  month = jun,
  publisher = {{MDPI} {AG}},
  volume = {12},
  number = {6},
  pages = {646},
  author = {Jean-Michel Claverie},
  title = {A Putative Role of de-Mono-{ADP}-Ribosylation of {STAT}1 by the {SARS}-{CoV}-2 Nsp3 Protein in the Cytokine Storm Syndrome of {COVID}-19},
  journal = {Viruses}
}

@article{coleman2006,
  title = {Structure-Based Identification of Small Molecule Binding Sites Using a Free Energy Model},
  volume = {46},
  ISSN = {1549-960X},
  url = {http://dx.doi.org/10.1021/ci600229z},
  DOI = {10.1021/ci600229z},
  number = {6},
  journal = {Journal of Chemical Information and Modeling},
  publisher = {American Chemical Society (ACS)},
  author = {Coleman,  Ryan G. and Salzberg,  Anna C. and Cheng,  Alan C.},
  year = {2006},
  month = nov,
  pages = {2631–2637}
}

@article{csd,
  author = "Groom, Colin R. and Bruno, Ian J. and Lightfoot, Matthew P. and Ward, Suzanna C.",
  title = "{The Cambridge Structural Database}",
  journal = "Acta Crystallographica Section B",
  year = "2016",
  volume = "72",
  number = "2",
  pages = "171--179",
  month = "Apr",
  doi = {10.1107/S2052520616003954},
  url = {https://doi.org/10.1107/S2052520616003954},
  abstract = {The Cambridge Structural Database (CSD) contains a complete record of all published organic and metal{--}organic small-molecule crystal structures. The database has been in operation for over 50years and continues to be the primary means of sharing structural chemistry data and knowledge across disciplines. As well as structures that are made public to support scientific articles, it includes many structures published directly as CSD Communications. All structures are processed both computationally and by expert structural chemistry editors prior to entering the database. A key component of this processing is the reliable association of the chemical identity of the structure studied with the experimental data. This important step helps ensure that data is widely discoverable and readily reusable. Content is further enriched through selective inclusion of additional experimental data. Entries are available to anyone through free CSD community web services. Linking services developed and maintained by the CCDC, combined with the use of standard identifiers, facilitate discovery from other resources. Data can also be accessed through CCDC and third party software applications and through an application programming interface.},
  keywords = {Cambridge Structural Database, CIF archive, open data, crystal structure database},
}

@article{cullen2016,
  title = {Highly efficient catalysis of the Kemp elimination in the cavity of a cubic coordination cage},
  volume = {8},
  ISSN = {1755-4349},
  url = {http://dx.doi.org/10.1038/nchem.2452},
  DOI = {10.1038/nchem.2452},
  number = {3},
  journal = {Nature Chemistry},
  publisher = {Springer Science and Business Media LLC},
  author = {Cullen,  William and Misuraca,  M. Cristina and Hunter,  Christopher A. and Williams,  Nicholas H. and Ward,  Michael D.},
  year = {2016},
  month = feb,
  pages = {231–236}
}

@article{dali,
  doi = {10.1093/nar/gkq366},
  url = {https://doi.org/10.1093/nar/gkq366},
  year = {2010},
  month = may,
  publisher = {Oxford University Press ({OUP})},
  volume = {38},
  number = {suppl{\_}2},
  pages = {W545--W549},
  author = {Liisa Holm and Päivi Rosenström},
  title = {Dali server: conservation mapping in 3D},
  journal = {Nucleic Acids Research}
}

@article{dipaola2015,
  doi = {10.1016/j.sbi.2015.03.001},
  url = {https://doi.org/10.1016/j.sbi.2015.03.001},
  year = {2015},
  month = apr,
  publisher = {Elsevier {BV}},
  volume = {31},
  pages = {43--48},
  author = {Luisa Di Paola and Alessandro Giuliani},
  title = {Protein contact network topology: a natural language for allostery},
  journal = {Current Opinion in Structural Biology}
}

@article{docker,
  title={Docker: lightweight linux containers for consistent development and deployment},
  author={Merkel, Dirk},
  journal={Linux journal},
  volume={2014},
  number={239},
  pages={2},
  year={2014}
} 

@article{dodson1998,
  doi = {10.1016/s0968-0004(98)01254-7},
  url = {https://doi.org/10.1016/s0968-0004(98)01254-7},
  year = {1998},
  month = sep,
  publisher = {Elsevier {BV}},
  volume = {23},
  number = {9},
  pages = {347--352},
  author = {G Dodson},
  title = {Catalytic triads and their relatives},
  journal = {Trends in Biochemical Sciences}
}

@article{eichstaedt2019,
  title = {Self‐Assembly and Ordering of Peptide‐Based Cavitands in Water and DMSO: The Power of Hydrophobic Effects Combined with Neutral Hydrogen Bonds},
  volume = {25},
  ISSN = {1521-3765},
  url = {http://dx.doi.org/10.1002/chem.201805353},
  DOI = {10.1002/chem.201805353},
  number = {12},
  journal = {Chemistry -- A European Journal},
  publisher = {Wiley},
  author = {Eichstaedt,  Katarzyna and Szpotkowski,  Kamil and Grajda,  Marcin and Gilski,  Mirosław and Wosicki,  Stanisław and Jaskólski,  Mariusz and Szumna,  Agnieszka},
  year = {2019},
  month = jan,
  pages = {3091--3097}
}

@article{eisenberg1984,
  doi = {10.1073/pnas.81.1.140},
  url = {https://doi.org/10.1073/pnas.81.1.140},
  year = {1984},
  month = jan,
  publisher = {Proceedings of the National Academy of Sciences},
  volume = {81},
  number = {1},
  pages = {140--144},
  author = {D Eisenberg and R M Weiss and T C Terwilliger},
  title = {The hydrophobic moment detects periodicity in protein hydrophobicity.},
  journal = {Proceedings of the National Academy of Sciences}
}

@article{fehr2016,
  author = {Anthony R. Fehr and Rudragouda Channappanavar and Gytis Jankevicius and Craig Fett and Jincun Zhao and Jeremiah Athmer and David K. Meyerholz and Ivan Ahel and Stanley Perlman},
  title = {The Conserved Coronavirus Macrodomain Promotes Virulence and Suppresses the Innate Immune Response during Severe Acute Respiratory Syndrome Coronavirus Infection},
  journal = {mBio},
  volume = {7},
  number = {6},
  pages = {10.1128/mbio.01721-16},
  year = {2016},
  doi = {10.1128/mbio.01721-16},
  URL = {https://journals.asm.org/doi/abs/10.1128/mbio.01721-16},
  eprint = {https://journals.asm.org/doi/pdf/10.1128/mbio.01721-16},
  abstract = { ADP-ribosylation is a common posttranslational modification that may have antiviral properties and impact innate immunity. To regulate this activity, macrodomain proteins enzymatically remove covalently attached ADP-ribose from protein targets. All members of the Coronavirinae, a subfamily of positive-sense RNA viruses, contain a highly conserved macrodomain within nonstructural protein 3 (nsp3). However, its function or targets during infection remain unknown. We identified several macrodomain mutations that greatly reduced nsp3's de-ADP-ribosylation activity in vitro. Next, we created recombinant severe acute respiratory syndrome coronavirus (SARS-CoV) strains with these mutations. These mutations led to virus attenuation and a modest reduction of viral loads in infected mice, despite normal replication in cell culture. Further, macrodomain mutant virus elicited an early, enhanced interferon (IFN), interferon-stimulated gene (ISG), and proinflammatory cytokine response in mice and in a human bronchial epithelial cell line. Using a coinfection assay, we found that inclusion of mutant virus in the inoculum protected mice from an otherwise lethal SARS-CoV infection without reducing virus loads, indicating that the changes in innate immune response were physiologically significant. In conclusion, we have established a novel function for the SARS-CoV macrodomain that implicates ADP-ribose in the regulation of the innate immune response and helps to demonstrate why this domain is conserved in CoVs. IMPORTANCE The macrodomain is a ubiquitous structural domain that removes ADP-ribose from proteins, reversing the activity of ADP-ribosyltransferases. All coronaviruses contain a macrodomain, suggesting that ADP-ribosylation impacts coronavirus infection. However, its function during infection remains unknown. Here, we found that the macrodomain is an important virulence factor for a highly pathogenic human CoV, SARS-CoV. Viruses with macrodomain mutations that abrogate its ability to remove ADP-ribose from protein were unable to cause lethal disease in mice. Importantly, the SARS-CoV macrodomain suppressed the innate immune response during infection. Our data suggest that an early innate immune response can protect mice from lethal disease. Understanding the mechanism used by this enzyme to promote disease will open up novel avenues for coronavirus therapies and give further insight into the role of macrodomains in viral pathogenesis. The macrodomain is a ubiquitous structural domain that removes ADP-ribose from proteins, reversing the activity of ADP-ribosyltransferases. All coronaviruses contain a macrodomain, suggesting that ADP-ribosylation impacts coronavirus infection. However, its function during infection remains unknown. Here, we found that the macrodomain is an important virulence factor for a highly pathogenic human CoV, SARS-CoV. Viruses with macrodomain mutations that abrogate its ability to remove ADP-ribose from protein were unable to cause lethal disease in mice. Importantly, the SARS-CoV macrodomain suppressed the innate immune response during infection. Our data suggest that an early innate immune response can protect mice from lethal disease. Understanding the mechanism used by this enzyme to promote disease will open up novel avenues for coronavirus therapies and give further insight into the role of macrodomains in viral pathogenesis. }
}

@book{foulds1995,
  title     = "Graph Theory Applications",
  author    = "Foulds, L R",
  publisher = "Springer",
  series    = "Universitext",
  edition   =  1,
  month     =  jan,
  year      =  1995,
  address   = "New York, NY",
  language  = "en"
}

@book{foster1995,
  title={Designing and Building Parallel Programs: Concepts and Tools for Parallel Software Engineering},
  author={Foster, I. and Foster, J.},
  isbn={9780201575941},
  lccn={94003661},
  series={Literature and Philosophy},
  url={https://books.google.com.br/books?id=r5JsQgAACAAJ},
  year={1995},
  publisher={Addison-Wesley}
}

@article{fpocket,
  doi = {10.1186/1471-2105-10-168},
  url = {https://doi.org/10.1186/1471-2105-10-168},
  year = {2009},
  month = jun,
  publisher = {Springer Science and Business Media {LLC}},
  volume = {10},
  number = {1},
  author = {Vincent Le Guilloux and Peter Schmidtke and Pierre Tuffery},
  title = {Fpocket: An open source platform for ligand pocket detection},
  journal = {{BMC} Bioinformatics}
}

@article{fpocketweb,
  doi = {10.1186/s13321-022-00637-0},
  url = {https://doi.org/10.1186/s13321-022-00637-0},
  year = {2022},
  month = aug,
  publisher = {Springer Science and Business Media {LLC}},
  volume = {14},
  number = {1},
  author = {Yuri Kochnev and Jacob D. Durrant},
  title = {{FPocketWeb}: protein pocket hunting in a web browser},
  journal = {Journal of Cheminformatics}
}

@article{frodo,
  title={A very fast program for visualizing protein surfaces, channels and cavities},
  author={Voorintholt, Richard and Kosters, MT and Vegter, G and Vriend, Gerrit and Hol, WGJ},
  journal={Journal of Molecular Graphics},
  volume={7},
  number={4},
  pages={243--245},
  year={1989},
  publisher={Elsevier}
}

@article{fujita2016,
  title = {Self-assembly of tetravalent Goldberg polyhedra from 144 small components},
  volume = {540},
  ISSN = {1476-4687},
  url = {http://dx.doi.org/10.1038/nature20771},
  DOI = {10.1038/nature20771},
  number = {7634},
  journal = {Nature},
  publisher = {Springer Science and Business Media LLC},
  author = {Fujita,  Daishi and Ueda,  Yoshihiro and Sato,  Sota and Mizuno,  Nobuhiro and Kumasaka,  Takashi and Fujita,  Makoto},
  year = {2016},
  month = dec,
  pages = {563–566}
}

@article{ghecom,
  doi = {10.1002/prot.22639},
  url = {https://doi.org/10.1002/prot.22639},
  year = {2009},
  month = oct,
  publisher = {Wiley},
  volume = {78},
  number = {5},
  pages = {1195--1211},
  author = {Takeshi Kawabata},
  title = {Detection of multiscale pockets on protein surfaces using mathematical morphology},
  journal = {Proteins: Structure,  Function,  and Bioinformatics}
}

@article{glasser2024,
  title = {Accelerating the discovery of alkyl halide-derived natural products using halide depletion},
  ISSN = {1755-4349},
  url = {http://dx.doi.org/10.1038/s41557-023-01390-z},
  DOI = {10.1038/s41557-023-01390-z},
  journal = {Nature Chemistry},
  publisher = {Springer Science and Business Media LLC},
  author = {Glasser,  Nathaniel R. and Cui,  Dongtao and Risser,  Douglas D. and Okafor,  C. Denise and Balskus,  Emily P.},
  year = {2024},
  month = jan 
}

@book{grama2003,
  title={Introduction to Parallel Computing},
  author={Grama, A.},
  isbn={9780201648652},
  lccn={2002038351},
  series={Pearson Education},
  url={https://books.google.com.br/books?id=B3jR2EhdZaMC},
  year={2003},
  publisher={Addison-Wesley}
}

@article{gromacs,
  author = {Van Der Spoel, David and Lindahl, Erik and Hess, Berk and Groenhof, Gerrit and Mark, Alan E. and Berendsen, Herman J. C.},
  title = {GROMACS: Fast, flexible, and free},
  journal = {Journal of Computational Chemistry},
  volume = {26},
  number = {16},
  pages = {1701-1718},
  keywords = {GROMACS, molecular simulation software, molecular dynamics, free energy computation, parallel computation},
  doi = {https://doi.org/10.1002/jcc.20291},
  url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20291},
  eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/jcc.20291},
  abstract = {Abstract This article describes the software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s. The software, written in ANSI C, originates from a parallel hardware project, and is well suited for parallelization on processor clusters. By careful optimization of neighbor searching and of inner loop performance, GROMACS is a very fast program for molecular dynamics simulation. It does not have a force field of its own, but is compatible with GROMOS, OPLS, AMBER, and ENCAD force fields. In addition, it can handle polarizable shell models and flexible constraints. The program is versatile, as force routines can be added by the user, tabulated functions can be specified, and analyses can be easily customized. Nonequilibrium dynamics and free energy determinations are incorporated. Interfaces with popular quantum-chemical packages (MOPAC, GAMES-UK, GAUSSIAN) are provided to perform mixed MM/QM simulations. The package includes about 100 utility and analysis programs. GROMACS is in the public domain and distributed (with source code and documentation) under the GNU General Public License. It is maintained by a group of developers from the Universities of Groningen, Uppsala, and Stockholm, and the Max Planck Institute for Polymer Research in Mainz. Its Web site is http://www.gromacs.org. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1701--1718, 2005},
  year = {2005}
}

@mastersthesis{guerra2019,
  author = {Guerra,  João Victor},
  title = {Prospec\c{c}ão e caracteriza\c{c}ão de cavidades supramoleculares},
  school  = {Universidade Estadual de Campinas, Instituto de Biologia},
  year    = {2019},
  address = {Campinas, SP},
  month   = {jun},
  url = {https://hdl.handle.net/20.500.12733/1639705}
}

@article{guerra2020,
  doi = {10.1016/j.softx.2020.100606},
  url = {https://doi.org/10.1016/j.softx.2020.100606},
  year = {2020},
  month = jul,
  publisher = {Elsevier {BV}},
  volume = {12},
  pages = {100606},
  author = {Jo{\~{a}}o Victor da Silva Guerra and Helder Veras Ribeiro~Filho and Leandro Oliveira Bortot and Rodrigo Vargas Honorato and Jos{\'{e}} Geraldo de Carvalho Pereira and Paulo S{\'{e}}rgio Lopes-de-Oliveira},
  title = {{ParKVFinder}: A thread-level parallel approach in biomolecular cavity detection},
  journal = {{SoftwareX}}
}

@article{guerra2021,
  doi = {10.1186/s12859-021-04519-4},
  url = {https://doi.org/10.1186/s12859-021-04519-4},
  year = {2021},
  month = dec,
  publisher = {Springer Science and Business Media {LLC}},
  volume = {22},
  number = {1},
  author = {Jo{\~{a}}o Victor da Silva Guerra and Helder Veras Ribeiro-Filho and Gabriel Ernesto Jara and Leandro Oliveira Bortot and Jos{\'{e}} Geraldo de Carvalho Pereira and Paulo S{\'{e}}rgio Lopes-de-Oliveira},
  title = {{pyKVFinder}: an efficient and integrable Python package for biomolecular cavity detection and characterization in data science},
  journal = {{BMC} Bioinformatics}
}

@article{guerra2023A,
  doi = {10.1093/nar/gkad324},
  url = {https://doi.org/10.1093/nar/gkad324},
  year = {2023},
  month = may,
  publisher = {Oxford University Press ({OUP})},
  author = {Jo{\~{a}}o V S Guerra and Helder V Ribeiro-Filho and Jos{\'{e}} G C Pereira and Paulo~S Lopes-de-Oliveira},
  title = {{KVFinder}-web: a web-based application for detecting and characterizing biomolecular cavities},
  journal = {Nucleic Acids Research}
}

@article{guerra2023B,
  doi = {10.1021/acs.jcim.3c00328},
  url = {https://doi.org/10.1021/acs.jcim.3c00328},
  year = {2023},
  month = may,
  publisher = {American Chemical Society ({ACS})},
  author = {Jo{\~{a}}o V. S. Guerra and Luiz F. G. Alves and Didier Bourissou and Paulo S. Lopes-de-Oliveira and Gy\"{o}rgy Szal{\'{o}}ki},
  title = {Cavity Characterization in Supramolecular Cages},
  journal = {Journal of Chemical Information and Modeling}
}

@article{gustafson1988,
  doi = {10.1145/42411.42415},
  url = {https://doi.org/10.1145/42411.42415},
  year = {1988},
  month = may,
  publisher = {Association for Computing Machinery ({ACM})},
  volume = {31},
  number = {5},
  pages = {532--533},
  author = {John L. Gustafson},
  title = {Reevaluating Amdahl{\textquotesingle}s law},
  journal = {Communications of the {ACM}}
}

@article{heal2018,
  doi = {10.1093/bioinformatics/bty347},
  url = {https://doi.org/10.1093/bioinformatics/bty347},
  year = {2018},
  month = may,
  publisher = {Oxford University Press ({OUP})},
  volume = {34},
  number = {19},
  pages = {3316--3323},
  author = {Jack W Heal and Gail J Bartlett and Christopher W Wood and Andrew R Thomson and Derek N Woolfson},
  editor = {Alfonso Valencia},
  title = {Applying graph theory to protein structures: an Atlas of coiled coils},
  journal = {Bioinformatics}
}

@article{heiden1993,
  doi = {10.1007/bf00124359},
  url = {https://doi.org/10.1007/bf00124359},
  year = {1993},
  month = oct,
  publisher = {Springer Science and Business Media {LLC}},
  volume = {7},
  number = {5},
  pages = {503--514},
  author = {Wolfgang Heiden and Gerd Moeckel and J. Brickmann},
  title = {A new approach to analysis and display of local lipophilicity/hydrophilicity mapped on molecular surfaces},
  journal = {Journal of Computer-Aided Molecular Design}
}

@article{henrich2010,
  author = {Henrich, Stefan and Salo-Ahen, Outi M. H. and Huang, Bingding and Rippmann, Friedrich F. and Cruciani, Gabriele and Wade, Rebecca C.},
  title = {Computational approaches to identifying and characterizing protein binding sites for ligand design},
  journal = {Journal of Molecular Recognition},
  volume = {23},
  number = {2},
  pages = {209-219},
  keywords = {ligand binding site, protein pocket, drug design, drug target, druggability},
  doi = {https://doi.org/10.1002/jmr.984},
  url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/jmr.984},
  eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/jmr.984},
  abstract = {Given the three-dimensional structure of a protein, how can one find the sites where other molecules might bind to it? Do these sites have the properties necessary for high affinity binding? Is this protein a suitable target for drug design? Here, we discuss recent developments in computational methods to address these and related questions. Geometric methods to identify pockets on protein surfaces have been developed over many years but, with new algorithms, their performance is still improving. Simulation methods show promise in accounting for protein conformational variability to identify transient pockets but lack the ease of use of many of the (rigid) shape-based tools. Sequence and structure comparison approaches are benefiting from the constantly increasing size of sequence and structure databases. Energetic methods can aid identification and characterization of binding pockets, and have undergone recent improvements in the treatment of solvation and hydrophobicity. The “druggability” of a binding site is still difficult to predict with an automated procedure. The methodologies available for this purpose range from simple shape and hydrophobicity scores to computationally demanding free energy simulations. Copyright © 2009 John Wiley \& Sons, Ltd.},
  year = {2010}
}

@article{hessa2005,
  doi = {10.1038/nature03216},
  url = {https://doi.org/10.1038/nature03216},
  year = {2005},
  month = jan,
  publisher = {Springer Science and Business Media {LLC}},
  volume = {433},
  number = {7024},
  pages = {377--381},
  author = {Tara Hessa and Hyun Kim and Karl Bihlmaier and Carolina Lundin and Jorrit Boekel and Helena Andersson and IngMarie Nilsson and Stephen H. White and Gunnar von Heijne},
  title = {Recognition of transmembrane helices by the endoplasmic reticulum translocon},
  journal = {Nature}
}

@incollection{holyoak2013,
  doi = {10.1007/978-3-642-16712-6_468},
  url = {https://doi.org/10.1007/978-3-642-16712-6_468},
  year = {2013},
  publisher = {Springer Berlin Heidelberg},
  pages = {1584--1588},
  author = {Todd Holyoak},
  title = {Molecular Recognition: Lock-and-Key,  Induced Fit,  and Conformational Selection},
  booktitle = {Encyclopedia of Biophysics}
}

@article{honig1995,
  doi = {10.1126/science.7761829},
  url = {https://doi.org/10.1126/science.7761829},
  year = {1995},
  month = may,
  publisher = {American Association for the Advancement of Science ({AAAS})},
  volume = {268},
  number = {5214},
  pages = {1144--1149},
  author = {Barry Honig and Anthony Nicholls},
  title = {Classical Electrostatics in Biology and Chemistry},
  journal = {Science}
}

@article{hubbard1994,
  doi = {10.1002/pro.5560031205},
  url = {https://doi.org/10.1002/pro.5560031205},
  year = {1994},
  month = dec,
  publisher = {Wiley},
  volume = {3},
  number = {12},
  pages = {2194--2206},
  author = {Simon J. Hubbard and Patrick Argos},
  title = {Cavities and packing at protein interfaces},
  journal = {Protein Science}
}

@article{hummer2023,
	title = {Investigating the Volume and Diversity of Data Needed for Generalizable Antibody-Antigen $\Delta$$\Delta$G Prediction},
	author = {Alissa M. Hummer and Constantin Schneider and Lewis Chinery and Charlotte M. Deane},
	journal = {bioRxiv},
	doi = {10.1101/2023.05.17.541222},
	URL = {https://www.biorxiv.org/content/early/2023/05/19/2023.05.17.541222},
	year = {2023},
}

@article{jefferson2023,
  doi = {10.1038/s41467-023-38491-9},
  url = {https://doi.org/10.1038/s41467-023-38491-9},
  year = {2023},
  month = may,
  publisher = {Springer Science and Business Media {LLC}},
  volume = {14},
  number = {1},
  author = {Robert E. Jefferson and Aur{\'{e}}lien Oggier and Andreas F\"{u}glistaler and Nicolas Camviel and Mahdi Hijazi and Ana Rico Villarreal and Caroline Arber and Patrick Barth},
  title = {Computational design of dynamic receptor{\textemdash}peptide signaling complexes applied to chemotaxis},
  journal = {Nature Communications}
}

@article{johnson2002,
author = {Johnson, Darren W. and Hof, Fraser and Iovine, Peter M. and Nuckolls, Colin and Rebek, Jr., Julius},
title = {Solid-State and Solution Studies of a Tetrameric Capsule and Its Guests},
journal = {Angewandte Chemie},
volume = {114},
number = {20},
pages = {3947-3950},
keywords = {Molekulare Erkennung, Selbstorganisation, Supramolekulare Chemie, Wasserstoffbrücken, Wirt-Gast-Systeme},
doi = {https://doi.org/10.1002/1521-3757(20021018)114:20<3947::AID-ANGE3947>3.0.CO;2-X},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/1521-3757%2820021018%29114%3A20%3C3947%3A%3AAID-ANGE3947%3E3.0.CO%3B2-X},
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/1521-3757%2820021018%29114%3A20%3C3947%3A%3AAID-ANGE3947%3E3.0.CO%3B2-X},
abstract = {Festgehalten in der Höhle: Beim Einschluss von 2,6-Adamantandion in eine Kapsel entsteht ein kompliziertes Netzwerk von Wasserstoffbrücken, die das Gastmolekül in einer bestimmten Orientierung fixieren (siehe Bild). Die aus der Kristallstruktur gewonnenen Daten ergänzen solche über das Verhalten der Moleküle in Lösung und bieten Erklärungen für die Bindungsselektivitäten der Kapsel.},
year = {2002}
}

@article{jubb2012,
  title = {Structural biology and drug discovery for protein--protein interactions},
  volume = {33},
  ISSN = {0165-6147},
  url = {http://dx.doi.org/10.1016/j.tips.2012.03.006},
  DOI = {10.1016/j.tips.2012.03.006},
  number = {5},
  journal = {Trends in Pharmacological Sciences},
  publisher = {Elsevier BV},
  author = {Jubb,  Harry and Higueruelo,  Alicia P. and Winter,  Anja and Blundell,  Tom L.},
  year = {2012},
  month = may,
  pages = {241--248}
}

@article{jumper2021,
  doi = {10.1038/s41586-021-03819-2},
  url = {https://doi.org/10.1038/s41586-021-03819-2},
  year = {2021},
  month = jul,
  publisher = {Springer Science and Business Media {LLC}},
  volume = {596},
  number = {7873},
  pages = {583--589},
  author = {John Jumper and Richard Evans and Alexander Pritzel and Tim Green and Michael Figurnov and Olaf Ronneberger and Kathryn Tunyasuvunakool and Russ Bates and Augustin {\v{Z}}{\'{\i}}dek and Anna Potapenko and Alex Bridgland and Clemens Meyer and Simon A. A. Kohl and Andrew J. Ballard and Andrew Cowie and Bernardino Romera-Paredes and Stanislav Nikolov and Rishub Jain and Jonas Adler and Trevor Back and Stig Petersen and David Reiman and Ellen Clancy and Michal Zielinski and Martin Steinegger and Michalina Pacholska and Tamas Berghammer and Sebastian Bodenstein and David Silver and Oriol Vinyals and Andrew W. Senior and Koray Kavukcuoglu and Pushmeet Kohli and Demis Hassabis},
  title = {Highly accurate protein structure prediction with {AlphaFold}},
  journal = {Nature}
}

@article{juncker2009,
  doi = {10.1186/gb-2009-10-2-206},
  url = {https://doi.org/10.1186/gb-2009-10-2-206},
  year = {2009},
  publisher = {Springer Science and Business Media {LLC}},
  volume = {10},
  number = {2},
  pages = {206},
  author = {Agnieszka S Juncker and Lars J Jensen and Andrea Pierleoni and Andreas Bernsel and Michael L Tress and Peer Bork and Gunnar von Heijne and Alfonso Valencia and Christos A Ouzounis and Rita Casadio and S{\o}ren Brunak},
  title = {Sequence-based feature prediction and annotation of proteins},
  journal = {Genome Biology}
}

@article{kaynak2020,
  title = {Essential site scanning analysis: A new approach for detecting sites that modulate the dispersion of protein global motions},
  volume = {18},
  ISSN = {2001-0370},
  url = {http://dx.doi.org/10.1016/j.csbj.2020.06.020},
  DOI = {10.1016/j.csbj.2020.06.020},
  journal = {Computational and Structural Biotechnology Journal},
  publisher = {Elsevier BV},
  author = {Kaynak,  Burak T. and Bahar,  Ivet and Doruker,  Pemra},
  year = {2020},
  pages = {1577–1586}
}

@article{kantelis2022,
  doi = {10.1016/j.simpat.2022.102640},
  url = {https://doi.org/10.1016/j.simpat.2022.102640},
  year = {2022},
  month = dec,
  publisher = {Elsevier {BV}},
  volume = {121},
  pages = {102640},
  author = {Konstantinos F. Kantelis and Vassilios Asteriou and Aliki Papadimitriou-Tsantarliotou and Anthi Petrou and Lefteris Angelis and Petros Nicopolitidis and Georgios Papadimitriou and Ioannis S. Vizirianakis},
  title = {Graph theory-based simulation tools for protein structure networks},
  journal = {Simulation Modelling Practice and Theory}
}

@book{kaufman1990,
  title = {Finding Groups in Data: An Introduction to Cluster Analysis},
  ISBN = {9780470316801},
  ISSN = {1940-6347},
  url = {http://dx.doi.org/10.1002/9780470316801},
  DOI = {10.1002/9780470316801},
  journal = {Wiley Series in Probability and Statistics},
  publisher = {Wiley},
  author = {Kaufman,  Leonard and Rousseeuw,  Peter J.},
  year = {1990},
  month = mar 
}

@article{kawakami2019,
  title = {Silane catecholates: versatile tools for self-assembled dynamic covalent bond chemistry},
  volume = {55},
  ISSN = {1364-548X},
  url = {http://dx.doi.org/10.1039/C9CC02103E},
  DOI = {10.1039/c9cc02103e},
  number = {43},
  journal = {Chemical Communications},
  publisher = {Royal Society of Chemistry (RSC)},
  author = {Kawakami,  Yoshiteru and Ogishima,  Tsuyoshi and Kawara,  Tomoki and Yamauchi,  Shota and Okamoto,  Kazuhiko and Nikaido,  Singo and Souma,  Daiki and Jin,  Ren-Hua and Kabe,  Yoshio},
  year = {2019},
  pages = {6066–6069}
}

@article{kenzaki2011,
  author = {Kenzaki, Hiroo and Koga, Nobuyasu and Hori, Naoto and Kanada, Ryo and Li, Wenfei and Okazaki, Kei-ichi and Yao, Xin-Qiu and Takada, Shoji},
  title = {CafeMol: A Coarse-Grained Biomolecular Simulator for Simulating Proteins at Work},
  journal = {Journal of Chemical Theory and Computation},
  volume = {7},
  number = {6},
  pages = {1979-1989},
  year = {2011},
  doi = {10.1021/ct2001045},
  note ={PMID: 26596457},
  URL = {https://doi.org/10.1021/ct2001045},
  eprint = {https://doi.org/10.1021/ct2001045}
}

@article{kim2023,
  title = {Domain swapping of the C‐terminal helix promotes the dimerization of a novel ribonuclease protein from Mycobacterium tuberculosis},
  volume = {32},
  ISSN = {1469-896X},
  url = {http://dx.doi.org/10.1002/pro.4644},
  DOI = {10.1002/pro.4644},
  number = {6},
  journal = {Protein Science},
  publisher = {Wiley},
  author = {Kim,  Do‐Hee and Na,  Youngseo and Chang,  Heesun and Boo,  Jun‐Hyuk and Kang,  Sung‐Min and Jin,  Chenglong and Kang,  Su‐Jin and Lee,  Su Yeon and Lee,  Bong‐Jin},
  year = {2023},
  month = may 
}

@article{kozlikova2016,
  doi = {10.1111/cgf.13072},
  url = {https://doi.org/10.1111/cgf.13072},
  year = {2016},
  month = nov,
  publisher = {Wiley},
  volume = {36},
  number = {8},
  pages = {178--204},
  author = {B. Kozl{\'{\i}}kov{\'{a}} and M. Krone and M. Falk and N. Lindow and M. Baaden and D. Baum and I. Viola and J. Parulek and H.-C. Hege},
  title = {Visualization of Biomolecular Structures: State of the Art Revisited},
  journal = {Computer Graphics Forum}
}

@article{krone2016,
  author = {Krone, M. and Kozlíková, B. and Lindow, N. and Baaden, M. and Baum, D. and Parulek, J. and Hege, H.-C. and Viola, I.},
  title = {Visual Analysis of Biomolecular Cavities: State of the Art},
  journal = {Computer Graphics Forum},
  volume = {35},
  number = {3},
  pages = {527-551},
  keywords = {Categories and Subject Descriptors (according to ACM CCS), I.3.5 Computer Graphics: Computational Geometry and Object Modeling—Boundary representations, J.3 Computer Applications: Life and Medical Sciences—Biology and genetics},
  doi = {https://doi.org/10.1111/cgf.12928},
  url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/cgf.12928},
  eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1111/cgf.12928},
  abstract = {In this report we review and structure the branch of molecular visualization that is concerned with the visual analysis of cavities in macromolecular protein structures. First the necessary background, the domain terminology, and the goals of analytical reasoning are introduced. Based on a comprehensive collection of relevant research works, we present a novel classification for cavity detection approaches and structure them into four distinct classes: grid-based, Voronoi-based, surface-based, and probe-based methods. The subclasses are then formed by their combinations. We match these approaches with corresponding visualization technologies starting with direct 3D visualization, followed with non-spatial visualization techniques that for example abstract the interactions between structures into a relational graph, straighten the cavity of interest to see its profile in one view, or aggregate the time sequence into a single contour plot. We also discuss the current state of methods for the visual analysis of cavities in dynamic data such as molecular dynamics simulations. Finally, we give an overview of the most common tools that are actively developed and used in the structural biology and biochemistry research. Our report is concluded by an outlook on future challenges in the field.},
  year = {2016}
}

@article{kuntz1982,
  title={A geometric approach to macromolecule-ligand interactions},
  author={Kuntz, Irwin D and Blaney, Jeffrey M and Oatley, Stuart J and Langridge, Robert and Ferrin, Thomas E},
  journal={Journal of molecular biology},
  volume={161},
  number={2},
  pages={269--288},
  year={1982},
  publisher={Elsevier}
}

@article{kyte1982,
  doi = {10.1016/0022-2836(82)90515-0},
  url = {https://doi.org/10.1016/0022-2836(82)90515-0},
  year = {1982},
  month = may,
  publisher = {Elsevier {BV}},
  volume = {157},
  number = {1},
  pages = {105--132},
  author = {Jack Kyte and Russell F. Doolittle},
  title = {A simple method for displaying the hydropathic character of a protein},
  journal = {Journal of Molecular Biology}
}

@article{lam1994,
  doi = {10.1126/science.8278812},
  url = {https://doi.org/10.1126/science.8278812},
  year = {1994},
  month = jan,
  publisher = {American Association for the Advancement of Science ({AAAS})},
  volume = {263},
  number = {5145},
  pages = {380--384},
  author = {Patrick Y. S. Lam and Prabhakar K. Jadhav and Charles J. Eyermann and C. Nicholas Hodge and Yu Ru and Lee T. Bacheler and James L. Meek and Michael J. Otto and Marlene M. Rayner and Y. Nancy Wong and Chong-Hwan Chang and Patricia C. Weber and David A. Jackson and Thomas R. Sharpe and Susan Erickson-Viitanen},
  title = {Rational Design of Potent,  Bioavailable,  Nonpeptide Cyclic Ureas as {HIV} Protease Inhibitors},
  journal = {Science}
}

@article{laskowski1996,
	author = {Laskowski, R A and Luscombe, N M and Swindells, M B and Thornton, J M},
	doi = {10.1002/pro.5560051206},
	isbn = {0961-8368 (Print)$\backslash$r0961-8368 (Linking)},
	issn = {0961-8368},
	journal = {Protein science : a publication of the Protein Society},
	keywords = {Animals,Binding Sites,Humans,Protein Binding,Protein Conformation,Proteins,Proteins: chemistry,Proteins: metabolism},
	number = {12},
	pages = {2438--52},
	pmid = {8976552},
	title = {{Protein clefts in molecular recognition and function.}},
	url = {https://pubmed.ncbi.nlm.nih.gov/8976552/},
	volume = {5},
	year = {1996}
}

@book{lay2013,
  title={Convex Sets and Their Applications},
  author={Lay, S.R.},
  isbn={9780486788265},
  series={Dover Books on Mathematics Series},
  url={https://books.google.com.br/books?id=YU50swEACAAJ},
  year={2013},
  publisher={Dover Publications, Incorporated}
}

@article{li2024,
  title = {A rumen-derived bifunctional glucanase/mannanase uncanonically releases oligosaccharides with a high degree of polymerization preferentially from branched substrates},
  volume = {330},
  ISSN = {0144-8617},
  url = {http://dx.doi.org/10.1016/j.carbpol.2024.121828},
  DOI = {10.1016/j.carbpol.2024.121828},
  journal = {Carbohydrate Polymers},
  publisher = {Elsevier BV},
  author = {Li,  Nuo and Han,  Junyan and Zhou,  Yebo and Zhang,  Huien and Xu,  Xiaofeng and He,  Bo and Liu,  Mingqi and Wang,  Jiakun and Wang,  Qian},
  year = {2024},
  month = apr,
  pages = {121828}
}

@article{liang1998,
  doi = {10.1002/pro.5560070905},
  url = {https://doi.org/10.1002/pro.5560070905},
  year = {1998},
  month = sep,
  publisher = {Wiley},
  volume = {7},
  number = {9},
  pages = {1884--1897},
  author = {Jie Liang and Clare Woodward and Herbert Edelsbrunner},
  title = {Anatomy of protein pockets and cavities: Measurement of binding site geometry and implications for ligand design},
  journal = {Protein Science}
}

@article{liao2010,
  title = {Two-component control of guest binding in a self-assembled cage molecule},
  volume = {46},
  ISSN = {1364-548X},
  url = {http://dx.doi.org/10.1039/C0CC00234H},
  DOI = {10.1039/c0cc00234h},
  number = {27},
  journal = {Chemical Communications},
  publisher = {Royal Society of Chemistry (RSC)},
  author = {Liao,  Puhong and Langloss,  Brian W. and Johnson,  Amber M. and Knudsen,  Eric R. and Tham,  Fook S. and Julian,  Ryan R. and Hooley,  Richard J.},
  year = {2010},
  pages = {4932}
}

@article{ligsite,
  title={LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins},
  author={Hendlich, Manfred and Rippmann, Friedrich and Barnickel, Gerhard},
  journal={Journal of Molecular Graphics and Modelling},
  volume={15},
  number={6},
  pages={359--363},
  year={1997},
  publisher={Elsevier}
}

@article{lin2022,
  title={Language models of protein sequences at the scale of evolution enable accurate structure prediction},
  author={Lin, Zeming and Akin, Halil and Rao, Roshan and Hie, Brian and Zhu, Zhongkai and Lu, Wenting and Smetanin, Nikita and dos Santos Costa, Allan and Fazel-Zarandi, Maryam and Sercu, Tom and Candido, Sal and others},
  journal={bioRxiv},
  year={2022},
  publisher={Cold Spring Harbor Laboratory}
}

@article{macgillivray1997,
  title = {A chiral spherical molecular assembly held together by 60 hydrogen bonds},
  volume = {389},
  ISSN = {1476-4687},
  url = {http://dx.doi.org/10.1038/38985},
  DOI = {10.1038/38985},
  number = {6650},
  journal = {Nature},
  publisher = {Springer Science and Business Media LLC},
  author = {MacGillivray,  Leonard R. and Atwood,  Jerry L.},
  year = {1997},
  month = oct,
  pages = {469–472}
}

@article{majeed2020,
  AUTHOR = {Majeed, Abdul and Rauf, Ibtisam},
  TITLE = {Graph Theory: A Comprehensive Survey about Graph Theory Applications in Computer Science and Social Networks},
  JOURNAL = {Inventions},
  VOLUME = {5},
  YEAR = {2020},
  NUMBER = {1},
  ARTICLE-NUMBER = {10},
  URL = {https://www.mdpi.com/2411-5134/5/1/10},
  ISSN = {2411-5134},
  ABSTRACT = {Graph theory (GT) concepts are potentially applicable in the field of computer science (CS) for many purposes. The unique applications of GT in the CS field such as clustering of web documents, cryptography, and analyzing an algorithm&rsquo;s execution, among others, are promising applications. Furthermore, GT concepts can be employed to electronic circuit simplifications and analysis. Recently, graphs have been extensively used in social networks (SNs) for many purposes related to modelling and analysis of the SN structures, SN operation modelling, SN user analysis, and many other related aspects. Considering the widespread applications of GT in SNs, this article comprehensively summarizes GT use in the SNs. The goal of this survey paper is twofold. First, we briefly discuss the potential applications of GT in the CS field along with practical examples. Second, we explain the GT uses in the SNs with sufficient concepts and examples to demonstrate the significance of graphs in SN modeling and analysis.},
  DOI = {10.3390/inventions5010010}
}

@article{mannhold2009,
  doi = {10.1002/jps.21494},
  url = {https://doi.org/10.1002/jps.21494},
  year = {2009},
  month = mar,
  publisher = {Elsevier {BV}},
  volume = {98},
  number = {3},
  pages = {861--893},
  author = {Raimund Mannhold and Gennadiy I. Poda and Claude Ostermann and Igor V. Tetko},
  title = {Calculation of Molecular Lipophilicity: State-of-the-Art and Comparison of {LogP} Methods on more than 96, 000 Compounds},
  journal = {Journal of Pharmaceutical Sciences}
}

@article{mason2007,
  doi = {10.1049/iet-syb:20060038},
  url = {https://doi.org/10.1049/iet-syb:20060038},
  year = {2007},
  month = mar,
  publisher = {Institution of Engineering and Technology ({IET})},
  volume = {1},
  number = {2},
  pages = {89--119},
  author = {O. Mason and M. Verwoerd},
  title = {Graph theory and networks in Biology},
  journal = {{IET} Systems Biology}
}

@book{matheron1974,
  title={Random Sets and Integral Geometry},
  author={Matheron, G.},
  isbn={9780471576211},
  lccn={74013569},
  series={Probability and Statistics Series},
  url={https://books.google.com.br/books?id=bgzvAAAAMAAJ},
  year={1974},
  publisher={Wiley}
}

@book{matloff2012,
  title={Introduction to Parallel Computing},
  author={Matloff, N.},
  url={https://heather.cs.ucdavis.edu/~matloff/158/PLN/ParProcBook.pdf},
  year={2012},
  publisher={University of California }
}

@article{matplotlib,
  doi = {10.1109/mcse.2007.55},
  url = {https://doi.org/10.1109/mcse.2007.55},
  year = {2007},
  publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
  volume = {9},
  number = {3},
  pages = {90--95},
  author = {John D. Hunter},
  title = {Matplotlib: A 2D Graphics Environment},
  journal = {Computing in Science {\&}amp$\mathsemicolon$ Engineering}
}

@inproceedings{mdanalysis,
  doi = {10.25080/majora-629e541a-00e},
  url = {https://doi.org/10.25080/majora-629e541a-00e},
  year = {2016},
  publisher = {{SciPy}},
  author = {Richard Gowers and Max Linke and Jonathan Barnoud and Tyler Reddy and Manuel Melo and Sean Seyler and Jan Doma{\'{n}}ski and David Dotson and S{\'{e}}bastien Buchoux and Ian Kenney and Oliver Beckstein},
  title = {{MDAnalysis}: A Python Package for the Rapid Analysis of Molecular Dynamics Simulations},
  booktitle = {Proceedings of the Python in Science Conference}
}

@article{mecozzi1998,
  doi = {10.1002/(sici)1521-3765(19980615)4:6<1016::aid-chem1016>3.0.co;2-b},
  url = {https://doi.org/10.1002/(sici)1521-3765(19980615)4:6<1016::aid-chem1016>3.0.co;2-b},
  year = {1998},
  month = jun,
  publisher = {Wiley},
  volume = {4},
  number = {6},
  pages = {1016--1022},
  author = {Sandro Mecozzi and Julius Rebek,  Jr.},
  title = {The 55 {\%} Solution: A Formula for Molecular Recognition in the Liquid State},
  journal = {Chemistry - A European Journal}
}

@article{mendonca2021,
  title = {An atomic model for the human septin hexamer by cryo-EM},
  volume = {433},
  ISSN = {0022-2836},
  url = {http://dx.doi.org/10.1016/j.jmb.2021.167096},
  DOI = {10.1016/j.jmb.2021.167096},
  number = {15},
  journal = {Journal of Molecular Biology},
  publisher = {Elsevier BV},
  author = {Mendon\c{c}a,  Deborah C. and Guimarães,  Samuel L. and Pereira,  Humberto D’Muniz and Pinto,  Andressa A. and de Farias,  Marcelo A. and de Godoy,  Andre S. and Araujo,  Ana P.U. and van Heel,  Marin and Portugal,  Rodrigo V. and Garratt,  Richard C.},
  year = {2021},
  month = jul,
  pages = {167096}
}

@article{mercaldi2022,
  title = {Discovery and structural characterization of chicoric acid as a SARS-CoV-2 nucleocapsid protein ligand and RNA binding disruptor},
  volume = {12},
  ISSN = {2045-2322},
  url = {http://dx.doi.org/10.1038/s41598-022-22576-4},
  DOI = {10.1038/s41598-022-22576-4},
  number = {1},
  journal = {Scientific Reports},
  publisher = {Springer Science and Business Media LLC},
  author = {Mercaldi,  Gustavo Fernando and Bezerra,  Eduardo Henrique Salviano and Batista,  Fernanda Aparecida Heleno and Tonoli,  Celisa Caldana Costa and Soprano,  Adriana Santos and Shimizu,  Jacqueline Farinha and Nagai,  Alice and da Silva,  Jaqueline Cristina and Filho,  Helder Veras Ribeiro and do Nascimento Faria,  Jéssica and da Cunha,  Marcos Guilherme and Zeri,  Ana Carolina Mattos and Nascimento,  Andrey Fabricio Ziem and Proenca-Modena,  José Luiz and Bajgelman,  Marcio Chaim and Rocco,  Silvana Aparecida and Lopes-de-Oliveira,  Paulo Sérgio and Cordeiro,  Artur Torres and Bruder,  Marjorie and Marques,  Rafael Elias and Sfor\c{c}a,  Mauricio Luis and Franchini,  Kleber Gomes and Benedetti,  Celso Eduardo and Figueira,  Ana Carolina Migliorini and Trivella,  Daniela Barretto Barbosa},
  year = {2022},
  month = nov 
}

@article{michalska2020,
  author = "Michalska, Karolina and Kim, Youngchang and Jedrzejczak, Robert and Maltseva, Natalia I. and Stols, Lucy and Endres, Michael and Joachimiak, Andrzej",
  title = "{Crystal structures of SARS-CoV-2 ADP-ribose phosphatase: from the apo form to ligand complexes}",
  journal = "IUCrJ",
  year = "2020",
  volume = "7",
  number = "5",
  pages = "814--824",
  month = "Sep",
  doi = {10.1107/S2052252520009653},
  url = {https://doi.org/10.1107/S2052252520009653},
  abstract = {Among 15 nonstructural proteins (Nsps), the newly emerging Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) encodes a large, multidomain Nsp3. One of its units is the ADP-ribose phosphatase domain (ADRP; also known as the macrodomain, MacroD), which is believed to interfere with the host immune response. Such a function appears to be linked to the ability of the protein to remove ADP-ribose from ADP-ribosylated proteins and RNA, yet the precise role and molecular targets of the enzyme remain unknown. Here, five high-resolution (1.07{--}2.01{\AA}) crystal structures corresponding to the apo form of the protein and its complexes with 2-({\it N}-morpholino)ethanesulfonic acid (MES), AMP and ADP-ribose have been determined. The protein is shown to undergo conformational changes to adapt to the ligand in the manner previously observed in close homologues from other viruses. A conserved water molecule is also identified that may participate in hydrolysis. This work builds foundations for future structure-based research on ADRP, including the search for potential antiviral therapeutics.},
  keywords = {SARS-CoV-2, COVID-19, macrodomain, ADP-ribose phosphatase domain, ADRP, Nsp3, Mac1, crystal structure, ADP-ribosylation},
}

@article{molovol,
  doi = {10.1107/s1600576722004988},
  url = {https://doi.org/10.1107/s1600576722004988},
  year = {2022},
  month = jun,
  publisher = {International Union of Crystallography ({IUCr})},
  volume = {55},
  number = {4},
  pages = {1033--1044},
  author = {Jasmin B. Maglic and Roy Lavendomme},
  title = {$\less$i$\greater${MoloVol}$\less$/i$\greater$: an easy-to-use program for analyzing cavities,  volumes and surface areas of chemical structures},
  journal = {Journal of Applied Crystallography}
}

@article{moon2011,
  doi = {10.1073/pnas.1103979108},
  url = {https://doi.org/10.1073/pnas.1103979108},
  year = {2011},
  month = may,
  publisher = {Proceedings of the National Academy of Sciences},
  volume = {108},
  number = {25},
  pages = {10174--10177},
  author = {C. Preston Moon and Karen G. Fleming},
  title = {Side-chain hydrophobicity scale derived from transmembrane protein folding into lipid bilayers},
  journal = {Proceedings of the National Academy of Sciences}
}

@article{mspocket,
  author = {Zhu, Hongbo and Pisabarro, M. Teresa},
  title = "{MSPocket: an orientation-independent algorithm for the detection of ligand binding pockets}",
  journal = {Bioinformatics},
  volume = {27},
  number = {3},
  pages = {351-358},
  year = {2010},
  month = {12},
  abstract = {Motivation: Identification of ligand binding pockets on proteins is crucial for the characterization of protein functions. It provides valuable information for protein-ligand docking and rational engineering of small molecules that regulate protein functions. A major number of current prediction algorithms of ligand binding pockets are based on cubic grid representation of proteins and, thus, the results are often protein orientation dependent.Results: We present the MSPocket program for detecting pockets on the solvent excluded surface of proteins. The core algorithm of the MSPocket approach does not use any cubic grid system to represent proteins and is therefore independent of protein orientations. We demonstrate that MSPocket is able to achieve an accuracy of 75 \% in predicting ligand binding pockets on a test dataset used for evaluating several existing methods. The accuracy is 92\\% if the top three predictions are considered. Comparison to one of the recently published best performing methods shows that MSPocket reaches similar performance with the additional feature of being protein orientation independent. Interestingly, some of the predictions are different, meaning that the two methods can be considered complementary and combined to achieve better prediction accuracy. MSPocket also provides a graphical user interface for interactive investigation of the predicted ligand binding pockets. In addition, we show that overlap criterion is a better strategy for the evaluation of predicted ligand binding pockets than the single point distance criterion.Availability: The MSPocket source code can be downloaded from http://appserver.biotec.tu-dresden.de/MSPocket/. MSPocket is also available as a PyMOL plugin with a graphical user interface.Contact:  hongboz@biotec.tu-dresden.de; mayte@biotec.tu-dresden.deSupplementary information:  Supplementary data are available at Bioinformatics online.},
  issn = {1367-4803},
  doi = {10.1093/bioinformatics/btq672},
  url = {https://doi.org/10.1093/bioinformatics/btq672},
}

@article{mura2018,
  doi = {10.1016/j.sbi.2018.09.003},
  url = {https://doi.org/10.1016/j.sbi.2018.09.003},
  year = {2018},
  month = oct,
  publisher = {Elsevier {BV}},
  volume = {52},
  pages = {95--102},
  author = {Cameron Mura and Eli J Draizen and Philip E Bourne},
  title = {Structural biology meets data science: does anything change?},
  journal = {Current Opinion in Structural Biology}
}

@article{mustang,
  doi = {10.1002/prot.20921},
  url = {https://doi.org/10.1002/prot.20921},
  year = {2006},
  month = may,
  publisher = {Wiley},
  volume = {64},
  number = {3},
  pages = {559--574},
  author = {Arun S. Konagurthu and James C. Whisstock and Peter J. Stuckey and Arthur M. Lesk},
  title = {{MUSTANG}: A multiple structural alignment algorithm},
  journal = {Proteins: Structure,  Function,  and Bioinformatics}
}

@article{nakamura2013,
  title = {A C60-Templated Tetrameric Porphyrin Barrel Complex via Zinc-Mediated Self-Assembly Utilizing Labile Capping Ligands},
  volume = {135},
  ISSN = {1520-5126},
  url = {http://dx.doi.org/10.1021/ja4110446},
  DOI = {10.1021/ja4110446},
  number = {50},
  journal = {Journal of the American Chemical Society},
  publisher = {American Chemical Society (ACS)},
  author = {Nakamura,  Takashi and Ube,  Hitoshi and Miyake,  Ryosuke and Shionoya,  Mitsuhiko},
  year = {2013},
  month = dec,
  pages = {18790--18793}
}

@inproceedings{networkx,
	address = {Pasadena, CA USA},
	title = {Exploring {Network} {Structure}, {Dynamics}, and {Function} using {NetworkX}},
	booktitle = {Proceedings of the 7th {Python} in {Science} {Conference}},
	author = {Hagberg, Aric A. and Schult, Daniel A. and Swart, Pieter J.},
	editor = {Varoquaux, Gaël and Vaught, Travis and Millman, Jarrod},
	year = {2008},
	pages = {11 -- 15},
}

@article{nglview,
    author = {Nguyen, Hai and Case, David A and Rose, Alexander S},
    title = "{NGLview--interactive molecular graphics for Jupyter notebooks}",
    journal = {Bioinformatics},
    volume = {34},
    number = {7},
    pages = {1241-1242},
    year = {2017},
    month = {12},
    abstract = "{NGLview is a Jupyter/IPython widget to interactively view molecular structures as well as trajectories from molecular dynamics simulations. Fast and scalable molecular graphics are provided through the NGL Viewer. The widget supports showing data from the file-system, online data bases and from objects of many popular analysis libraries including mdanalysis, mdtraj, pytraj, rdkit and more.The source code is freely available under the MIT license at https://github.com/arose/nglview. Python packages are available from PyPI and bioconda. NGLview uses Python on the server-side and JavaScript on the client. The integration with Jupyter is done through the ipywidgets package. The NGL Viewer is embedded client-side to provide WebGL accelerated molecular graphics.}",
    issn = {1367-4803},
    doi = {10.1093/bioinformatics/btx789},
    url = {https://doi.org/10.1093/bioinformatics/btx789},
    eprint = {https://academic.oup.com/bioinformatics/article-pdf/34/7/1241/48914829/bioinformatics\_34\_7\_1241.pdf},
}

@article{nglviewer,
  doi = {10.1093/nar/gkv402},
  url = {https://doi.org/10.1093/nar/gkv402},
  year = {2015},
  month = apr,
  publisher = {Oxford University Press ({OUP})},
  volume = {43},
  number = {W1},
  pages = {W576--W579},
  author = {Alexander S. Rose and Peter W. Hildebrand},
  title = {{NGL} Viewer: a web application for molecular visualization},
  journal = {Nucleic Acids Research}
}

@Manual{nglviewerr,
  title = {NGLVieweR: Interactive 3D Visualization of Molecular Structures},
  author = {Niels {van der Velden}},
  year = {2023},
  note = {R package version 1.3.4},
  url = {https://github.com/nvelden/NGLVieweR},
}

@article{nsa,
  title = {A new approach to the automatic identification of candidates for ligand receptor sites in proteins: (I) Search for pocket regions},
  journal = {Journal of Molecular Graphics},
  volume = {11},
  number = {1},
  pages = {23-29},
  year = {1993},
  issn = {0263-7855},
  doi = {https://doi.org/10.1016/0263-7855(93)85003-9},
  url = {https://www.sciencedirect.com/science/article/pii/0263785593850039},
  author = {Carlos A. {Del Carpio} and Yoshimasa Takahashi and Shin-ichi Sasaki},
  keywords = {receptor site, receptor modeling, X-ray data, free surface point, solvent-accessible surface, protein surface depressions},
  abstract = {The work presented here is aimed at the topographical analysis of localized regions of receptor proteins leading to the identification of pocket areas (superficial depressions or internal cavities), which may play the role of receptor sites. An algorithm is described that yields complete information about the position of each cavity or superficial depression relative to any point of the protein molecules, as well as detailed information on the atoms constituting it. The applicability of this algorithm to the automatic identification of candidate receptor sites in a receptor protein is also discussed using the typical receptor structure dihydrofolate reductase-methotrexate complex.}
}

@article{numpy,
  title         = {Array programming with {NumPy}},
  author        = {Charles R. Harris and K. Jarrod Millman and St{\'{e}}fan J.
                  van der Walt and Ralf Gommers and Pauli Virtanen and David
                  Cournapeau and Eric Wieser and Julian Taylor and Sebastian
                  Berg and Nathaniel J. Smith and Robert Kern and Matti Picus
                  and Stephan Hoyer and Marten H. van Kerkwijk and Matthew
                  Brett and Allan Haldane and Jaime Fern{\'{a}}ndez del
                  R{\'{i}}o and Mark Wiebe and Pearu Peterson and Pierre
                  G{\'{e}}rard-Marchant and Kevin Sheppard and Tyler Reddy and
                  Warren Weckesser and Hameer Abbasi and Christoph Gohlke and
                  Travis E. Oliphant},
  year          = {2020},
  month         = sep,
  journal       = {Nature},
  volume        = {585},
  number        = {7825},
  pages         = {357--362},
  doi           = {10.1038/s41586-020-2649-2},
  publisher     = {Springer Science and Business Media {LLC}},
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@article{oliveira2014,
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  title = {{KVFinder}: steered identification of protein cavities as a {PyMOL} plugin},
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}

@article{pass,
  title={Fast prediction and visualization of protein binding pockets with PASS},
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@article{phecom,
  author = {Kawabata, Takeshi and Go, Nobuhiro},
  title = {Detection of pockets on protein surfaces using small and large probe spheres to find putative ligand binding sites},
  journal = {Proteins: Structure, Function, and Bioinformatics},
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  number = {2},
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  keywords = {binding site, pocket, protein surface, geometry, probe sphere},
  doi = {https://doi.org/10.1002/prot.21283},
  url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/prot.21283},
  eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/prot.21283},
  abstract = {Abstract One of the simplest ways to predict ligand binding sites is to identify pocket-shaped regions on the protein surface. Many programs have already been proposed to identify these pocket regions. Examination of their algorithms revealed that a pocket intrinsically has two arbitrary properties, “size” and “depth”. We proposed a new definition for pockets using two explicit adjustable parameters that correspond to these two arbitrary properties. A pocket region is defined as a space into which a small probe can enter, but a large probe cannot. The radii of small and large probe spheres are the two parameters that correspond to the “size” and “depth” of the pockets, respectively. These values can be adjusted individual putative ligand molecule. To determine the optimal value of the large probe spheres radius, we generated pockets for thousands of protein structures in the database, using several size of large probe spheres, examined the correspondence of these pockets with known binding site positions. A new measure of shallowness, a minimum inaccessible radius, Rinaccess, indicated that binding sites of coenzymes are very deep, while those for adenine/guanine mononucleotide have only medium shallowness and those for short peptides and oligosaccharides are shallow. The optimal radius of large probe spheres was 3--4 Å for the coenzymes, 4 Å for adenine/guanine mononucleotides, and 5 Å or more for peptides/oligosaccharides. Comparison of our program with two other popular pocket-finding programs showed that our program had a higher performance of detecting binding pockets, although it required more computational time. Proteins 2007. © 2007 Wiley-Liss, Inc.},
  year = {2007}
}

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