DPA-Site version 0.1a

Los Alamos Laboratory O# (O5169)

Use the code in this repository to perform Fast Dynamics Perturbation Analysis (Fast DPA) for prediction of functional sites in proteins.

From the abstract of the 2008 paper:

The original DPA algorithm finds regions in proteins where interactions cause a large change in the protein conformational distribution, as measured using the relative entropy D_x. Such regions are associated with functional sites. The Fast DPA algorithm, which accelerates DPA calculations, is motivated by an empirical observation that Dx in a normal-modes model is highly correlated with an entropic term that only depends on the eigenvalues of the normal modes. The eigenvalues are accurately estimated using first-order perturbation theory, resulting in a N-fold reduction in the overall computational requirements of the algorithm, where N is the number of residues in the protein.

Main publications:

• Ming D, Wall ME. Quantifying allosteric effects in proteins. Proteins. 2005 Jun 1;59(4):697-707. doi: 10.1002/prot.20440. PMID: 15822100.

• Ming D, Wall ME. Interactions in native binding sites cause a large change in protein dynamics. J Mol Biol. 2006 Apr 21;358(1):213-23. doi: 10.1016/j.jmb.2006.01.097. Epub 2006 Feb 14. PMID: 16513135.

• Ming D, Cohn JD, Wall ME. Fast dynamics perturbation analysis for prediction of protein functional sites. BMC Struct Biol. 2008 Jan 30;8:5. doi: 10.1186/1472-6807-8-5. PMID: 18234095; PMCID: PMC2276503.

Related publications:

• Ming D, Wall ME. Allostery in a coarse-grained model of protein dynamics. Phys Rev Lett. 2005 Nov 4;95(19):198103. doi: https://doi.org/10.1103/PhysRevLett.95.198103. Epub 2005 Nov 2. PMID: 16384030.

• Wall ME. Ligand Binding, Protein Fluctuations, and Allosteric Free Energy. arXiv:q-bio/0603027. doi: https://doi.org/10.48550/arXiv.q-bio/0603027

• Verspoor KM, Cohn JD, Ravikumar KE, Wall ME. Text mining improves prediction of protein functional sites. PLoS One. 2012;7(2):e32171. doi: https://doi.org/10.1371/journal.pone.0032171. Epub 2012 Feb 29. PMID: 22393388; PMCID: PMC3290545.

Usage

See QUICK_REFERENCE.txt for some information about how to get started

License

This software is made freely available under an MIT license (see LICENSE file)

Authors

• Dengming Ming
• Michael Wall