Bioinformatics

Tools:

Sequence analysis:

1. VEP- Variant effect predictor
2. AlphaMissense along with alpha fold
3. scvi tools
4. Scanpy
5. Bioconductor
6. ANNData
7. Seurat

Protein structure prediction:

1. Alpha-fold
2. ESM-Fold

Molecular docking:

1. DiffDock
2. Smina
3. gnina

Uniprot Tools:

1. BLAST
2. Align
3. Expression Atlas
4. PDBe knowledge based protein-ligand iteraction

QuickGO is a web-based browser for viewing and exploring the Gene Ontology (GO), the Evidence and Conclusion Ontology (ECO), and GO annotations

Arctic3D: ARCTIC-3D is a software for data-mining and clustering of protein interface information (https://wenmr.science.uu.nl/arctic3d/)

SPMWeb: SPMweb is the online webserver of the Shortest Path Map (SPM) tool for identifying the key conformationally- relevant positions of a given enzyme structure and dynamics. (https://spmosuna.com/)

GlycoSHIELD is a simple MD pipeline to generate glycoprotein models. "Glycan shields" refers to the protective structures formed by complex sugars attached to proteins through glycosylation. These shields are dynamic and cover a significant portion of the protein surface, impacting protein conformation and surface accessibility. Computational methods like GlycoSHIELD can model these glycan structures efficiently, providing insights into their morphology and impact on protein structure.