Ligand–protein inverse docking and its potential use in the computer search of protein targets of a small molecule

By Yu Zong Chen, Degui Zhi. Proteins: Structure, Function, and Bioinformatics, 2001

327 citations recorded by the source corpus.

Subfields: Computational Theory and Mathematics, Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/132cf7d323308a0fc139782d9301305a0d584390

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Computational Theory and Mathematics

1. Sean Ekins
2. Jordi Mestres
3. Bernard Testa
4. Tommi S. Jaakkola
5. Hannes Stärk
6. Le Zhang
7. Giulio Rastelli
8. Jiyu Fan

In Materials Chemistry

1. Sean Ekins
2. Hannes Stärk
3. Le Zhang
4. Giulio Rastelli
5. Jiyu Fan
6. Tommi S. Jaakkola
7. Luca Pinzi
8. Ailing Fu

In Molecular Biology

1. Sean Ekins
2. Jordi Mestres
3. Bernard Testa
4. Hannes Stärk
5. Tommi S. Jaakkola
6. Le Zhang
7. Giulio Rastelli
8. Jiyu Fan

Citations in the corpus

• In silico pharmacology for drug discovery: methods for virtual ligand screening and profiling (2007, background): “Application of an inverse docking approach involving multiple-conformer shape-matching alignment of a molecule to a protein cavity on two therapeutic agents showed that 50% of the computer-identified potential protein targets were implicated or confirmed by experiments (Chen and Zhi, 2001b).”
• Progress in molecular docking (2019, methodology): “Here, we employed Figure 6 to describe the reverse docking technique [2].”
• Molecular Docking: Shifting Paradigms in Drug Discovery (2019, methodology): “In particular, INVDOCK [145] is a software based on docking, which has been devised for the identification of potential targets for drugs, candidates under clinical trials and ligands, and to facilitate the study of their potential side effects.”
• TarFisDock: a web server for identifying drug targets with docking approach (2006, background): “So far, 10 proteins have been identified as interaction targets for 4H-tamoxifen or for its metabolite, tamoxifen (16) (Supplementary Table S1).”
• Benchmarking AlphaFold‐enabled molecular docking predictions for antibiotic discovery (2022, background): “Although versatile, reverse docking requires a priori knowledge of the protein structures of interest, and its application to drug-target identification has been limited by the number and quality of target protein structures (Chen & Zhi, 2001; Kharkar et al , 2014; Lee et al , 2016).”