Software

Molecular Docking

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

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

3. 1-Click-Docking (Autodock Vina) - https://mcule.com/apps/1-click-docking/ 

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

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

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

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

Protein Modeling

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

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

3. 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

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. PDB

2. GPCR - 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 

Other tools

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

2.