Software

Molecular Docking

1. MolModa - https://durrantlab.pitt.edu/molmoda/ 

2. Autodock Vina - https://vina.scripps.edu/

3. AMDock (Autodock Vina) https://github.com/Valdes-Tresanco-MS/AMDock

4. 1-Click-Docking (Autodock Vina) - https://mcule.com/apps/1-click-docking/ 

5. PyRx - https://pyrx.sourceforge.io/ 

6. CBDock - http://cao.labshare.cn/cb-dock/ 

7. SwissDock - https://www.swissdock.ch/

8. SeamDock (Vina, QVina, SMina - https://bioserv.rpbs.univ-paris-diderot.fr/services/SeamDock/ 

Protein-Protein Docking

1. HawkDock - http://cadd.zju.edu.cn/hawkdock/ 

2. ZDock - https://zdock.wenglab.org/ 

Protein Modeling

1. AlphaFold - https://alphafold.ebi.ac.uk/ 

2. Swiss-Model - https://swissmodel.expasy.org/

3. Modeller - https://salilab.org/modeller/

4. I-Tasser - https://zhanggroup.org/I-TASSER/

Binding Pocket Prediction

1. DogSiteScore - https://proteins.plus/#dogsite Predict Druggable Pockets

Structure and Interactions Analysis

1. Molprobity - http://molprobity.biochem.duke.edu/ |Free

2. PoseView - https://www.zbh.uni-hamburg.de/en/forschung/amd/server/poseview.html | Free - Visualize residue-ligand interactions

3. Biovia Discovery Studio- https://discover.3ds.com/discovery-studio-visualizer-download

Sequence Analysis

1. Uniprot Align - https://www.uniprot.org/align/ 

2. Clustal Omega - https://www.ebi.ac.uk/Tools/msa/clustalo/ |Multiple Sequence Alignment

3. BLAST NCBI+ - https://www.ebi.ac.uk/Tools/sss/ncbiblast/ 

4. HMMER - https://www.ebi.ac.uk/Tools/hmmer/ | Protein homology search

Database

1. Protein Databank (PDB)

2. GPCR Structure Database - https://gpcrdb.org/ 

3. Membrane Protein Database - https://opm.phar.umich.edu/ 

4. Uniprot - https://www.uniprot.org/ 

5. PubChem - https://pubchem.ncbi.nlm.nih.gov/

6. ChEMBL - 

7. DrugBank - 

8. ZINC https://zinc.docking.org/ 

Molecular Dynamics Simulation

1. Gromacs - https://www.gromacs.org/ 

2. Amber - https://ambermd.org/ 

3. NAMD http://www.ks.uiuc.edu/Research/namd/ 

Lipids and Force Fields

1. Oxford Lipidbook - https://www.lipidbook.org/ 

2. Automated Topology Builder - https://atb.uq.edu.au/

3. CHARMM-GUI - https://www.charmm-gui.org/

4. Slipids - http://www.fos.su.se/~sasha/SLipids/Downloads.html

5. Martini FF for Coarse-Grained MD - https://cgmartini.nl/ 

Other Tools

1. PDB2PQR - https://server.poissonboltzmann.org/pdb2pqr - to protonate a protein

2. Computational Alanine Scanning - https://cpclab.uni-duesseldorf.de/dsppi/ 

Training & Tutorials

1. AlphaFold - https://www.ebi.ac.uk/training/online/courses/alphafold/ 

2. Gromacs - http://www.mdtutorials.com/gmx/ 

3. Gromacs - https://pubs.acs.org/doi/10.1021/acs.jpcb.4c04901 

4. CGMD - https://cgmartini.nl/docs/tutorials/