Table 2.
Resources used in the screening workflow for TRPV1.
| Stage | Resource | Description |
|---|---|---|
| Target structure | RCSB Protein Data Bank (PDB) | PDB is the data center for the global Protein Data Bank (PDB) of 3D structure data for large biological molecules. https://www.rcsb.org; accessed 2 September 2022. |
| Ligand structures | ChEMBL | ChEMBL is a database of bioactive molecules with drug-like properties. https://www.ebi.ac.uk/chembl/; accessed 2 September 2022. |
| Decoys from DUD-E | DUD-E is designed to help benchmark molecular docking programs by providing challenging decoys. http://dude.docking.org; accessed 2 September 2022. | |
| Target preparation | YASARA 22.5.22 | YASARA is a molecular modeling and simulation program for structure validation and prediction tools. It is used to rebuild missing side chains and loops. http://www.yasara.org; accessed 1 September 2022. |
| Ligand preparation | Openbabel 2.4.1 | Openbabel. Addition of MMFF94 partial charges, salts removing, protonation at pH 7.4, conversion 2D-3D. https://openbabel.org/docs/dev/Command-line_tools/babel.html; accessed 3 October 2022. |
| RDKit 2020.09.1.0 | RDKit (Chem package from RDKit). http://www.rdkit.org; accessed 3 October 2022. | |
| Marvin 6.0 | Marvin (molconvert). https://chemaxon.com/marvin; accessed 3 October 2022. | |
| Ligand optimization | RDKit | RDKit (package AllChem). http://www.rdkit.org; accessed 3 October 2022. |
| YASARA | YASARA (NOVA force field and energy minimization steps). | |
| ADMET descriptors | Marvin 6 | Marvin. ChemAxon’s calculator (cxcalc) is a command line program that performs chemical calculations using calculator plugins. https://chemaxon.com/marvin; accessed 3 October 2022. |
| XLOGP3 | XLOGP3 is an optimized atom-additive method for the fast calculation of logP. http://www.sioc-ccbg.ac.cn/skins/ccbgwebsite/software/xlogp3/; accessed 6 September 2022. | |
| RDKit | RDKit is used to obtain molecular descriptors. http://www.rdkit.org; accessed 3 October 2022. | |
| FILTER-IT | FILTER-IT obtains some molecular descriptors and filters out molecules with unwanted properties. https://github.com/silicos-it/filter-it; accessed 6 September 2022. | |
| UCSF Chimera 1.15 | UCSF Chimera is used for calculations of some molecular descriptors such as SASA and SESA (surf tool). https://www.cgl.ucsf.edu/chimera/; accessed 6 September 2022. | |
| AMSOL 7.1 | AMSOL is used for calculating the free energies of solvation of molecules and ions in solution and partial atomic charges. https://comp.chem.umn.edu/amsol/; accessed 6 September 2022. | |
| Docking | UCSF DOCK6.7 | UCSF DOCK6 identifies potential binding geometries and interactions of a molecule to a target using the anchor-and-grow search algorithm. https://dock.compbio.ucsf.edu/DOCK_6/index.htm; accessed 1 September 2022. |
| AutoDock4 | AutoDock4 performs the docking of the ligands to a set of grids describing the target protein and pre-calculates these grids. https://autodock.scripps.edu; accessed 1 September 2022. | |
| YASARA | YASARA is used to run macro executing VINA docking algorithms. | |
| PLANTS | PLANTS is based on ant colony optimization employed to find a minimum energy conformation of the ligand in the protein’s binding site. https://github.com/discoverdata/parallel-PLANTS; accessed 1 September 2022. | |
| RxDock | RxDock is designed for high-throughput virtual screening campaigns and binding mode prediction studies. https://rxdock.gitlab.io; accessed 1 September 2022. | |
| XScore | XScore is an empirical scoring function which computes the binding affinities of the given ligand molecules to their target protein. https://www.ics.uci.edu/~dock/manuals/xscore1.1_manual/intro.html; accessed 1 September 2022. | |
| DSX | DSX is a knowledge-based scoring function that consists of distance-dependent pair potentials, novel torsion angel potentials, and newly defined solvent accessible surface-dependent potentials. | |
| Hits identification (Score-based consensus strategies) | NSR | NSR: Normalized score ratio |
| ECR | ECR: Exponential Consensus Ranking | |
| RBR | RBR: Rank-by-rank | |
| RBV | RBV: Rank-by-vote | |
| RBN | RBN: Rank-by-number | |
| AASS | AASS: Average of auto-scaled score | |
| Z-Score | Z-Score |