Molecular recognition and docking algorithms
- PMID: 12574069
- DOI: 10.1146/annurev.biophys.32.110601.142532
Molecular recognition and docking algorithms
Abstract
Molecular docking is an invaluable tool in modern drug discovery. This review focuses on methodological developments relevant to the field of molecular docking. The forces important in molecular recognition are reviewed and followed by a discussion of how different scoring functions account for these forces. More recent applications of computational chemistry tools involve library design and database screening. Last, we summarize several critical methodological issues that must be addressed in future developments.
Similar articles
-
Principles of docking: An overview of search algorithms and a guide to scoring functions.Proteins. 2002 Jun 1;47(4):409-43. doi: 10.1002/prot.10115. Proteins. 2002. PMID: 12001221 Review.
-
Latest developments in molecular docking: 2010-2011 in review.J Mol Recognit. 2013 May;26(5):215-39. doi: 10.1002/jmr.2266. J Mol Recognit. 2013. PMID: 23526775 Review.
-
A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance.Proteins. 2004 Aug 1;56(2):235-49. doi: 10.1002/prot.20088. Proteins. 2004. PMID: 15211508
-
Importance of molecular computer modeling in anticancer drug development.J BUON. 2007 Sep;12 Suppl 1:S101-18. J BUON. 2007. PMID: 17935268 Review.
-
Assessing protein-ligand docking for the binding of organometallic compounds to proteins.J Comput Chem. 2014 Jan 30;35(3):192-8. doi: 10.1002/jcc.23472. Epub 2013 Oct 28. J Comput Chem. 2014. PMID: 24375319
Cited by
-
Docking pose selection by interaction pattern graph similarity: application to the D3R grand challenge 2015.J Comput Aided Mol Des. 2016 Sep;30(9):669-683. doi: 10.1007/s10822-016-9930-3. Epub 2016 Aug 1. J Comput Aided Mol Des. 2016. PMID: 27480696
-
Binding mechanism of naringenin with monoamine oxidase - B enzyme: QM/MM and molecular dynamics perspective.Heliyon. 2021 Apr 8;7(4):e06684. doi: 10.1016/j.heliyon.2021.e06684. eCollection 2021 Apr. Heliyon. 2021. PMID: 33898820 Free PMC article.
-
Relating the shape of protein binding sites to binding affinity profiles: is there an association?BMC Struct Biol. 2010 Oct 5;10:32. doi: 10.1186/1472-6807-10-32. BMC Struct Biol. 2010. PMID: 20923553 Free PMC article.
-
The measured and calculated affinity of methyl- and methoxy-substituted benzoquinones for the Q(A) site of bacterial reaction centers.Proteins. 2010 Sep;78(12):2638-54. doi: 10.1002/prot.22779. Proteins. 2010. PMID: 20607696 Free PMC article.
-
Key Topics in Molecular Docking for Drug Design.Int J Mol Sci. 2019 Sep 15;20(18):4574. doi: 10.3390/ijms20184574. Int J Mol Sci. 2019. PMID: 31540192 Free PMC article. Review.
Publication types
MeSH terms
Substances
LinkOut - more resources
Other Literature Sources