Intermolecular Binding Affinity Calculators: A Comprehensive List with PubMed References

Intermolecular Binding Affinity Calculators: A Comprehensive List

This page provides a list of currently available intermolecular binding affinity calculators. These tools are essential for researchers in drug discovery, structural biology, and related fields to understand the strength of interactions between molecules. Each calculator is accompanied by its respective reference from PubMed for further exploration.

1. AutoDock Vina

• Trott O, Olson AJ. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem. 2010 Jan 30;31(2):455-61. doi: 10.1002/jcc.21334. PMID: 19499576.

2. SwissDock

• Gfeller D, Michielin O, Zoete V. SwissDock, a protein-small molecule docking web service based on EADock DSS. Nucleic Acids Res. 2014 Jul;42(Web Server issue):W545-9. doi: 10.1093/nar/gku380. Epub 2014 May 6. PMID: 24803546; PMCID: PMC4086077.

3. PatchDock

• Schneidman-Duhovny D, Inbar Y, Nussinov R, Wolfson HJ. PatchDock and SymmDock: servers for rigid and symmetric docking. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W363-7. doi: 10.1093/nar/gki481. PMID: 15980498; PMCID: PMC1160235.

4. HADDOCK

• Dominguez C, Boelens R, Bonvin AM. HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. J Am Chem Soc. 2003 Mar 26;125(12):1731-7. doi: 10.1021/ja026939x. PMID: 12643608.

5. PLANTS

• Korb O, Sttzle T, Exner TE. PLANTS: application of ant colony optimization to structure-based drug design. Ant Colony Optimization and Swarm Intelligence. Lecture Notes in Computer Science, vol 3172. Springer, Berlin, Heidelberg. 2004. doi: 10.1007/978-3-540-28643-1_22.

Please note: The availability and features of these calculators might change over time. Always refer to the official sources and publications for the most up-to-date information.