Mean-field minimization methods for biological macromolecules - PubMed (original) (raw)
Review
Mean-field minimization methods for biological macromolecules
P Koehl et al. Curr Opin Struct Biol. 1996 Apr.
Abstract
Simulations of macromolecular structures involve the minimization of a potential-energy function that presents many local minima. Mean-field theory provides a tool that enables us to escape these minima, by enhancing sampling in conformational space. The number of applications of this technique has increased significantly over the past year, enabling problems with protein-homology modelling and inverted protein structure prediction to be solved.
Similar articles
- A novel approach to decoy set generation: designing a physical energy function having local minima with native structure characteristics.
Keasar C, Levitt M. Keasar C, et al. J Mol Biol. 2003 May 23;329(1):159-74. doi: 10.1016/s0022-2836(03)00323-1. J Mol Biol. 2003. PMID: 12742025 Free PMC article. - Optimal protocol and trajectory visualization for conformational searches of peptides and proteins.
Abagyan R, Argos P. Abagyan R, et al. J Mol Biol. 1992 May 20;225(2):519-32. doi: 10.1016/0022-2836(92)90936-e. J Mol Biol. 1992. PMID: 1593634 - Sculpting proteins interactively: continual energy minimization embedded in a graphical modeling system.
Surles MC, Richardson JS, Richardson DC, Brooks FP Jr. Surles MC, et al. Protein Sci. 1994 Feb;3(2):198-210. doi: 10.1002/pro.5560030205. Protein Sci. 1994. PMID: 8003957 Free PMC article. Review. - RNA and protein 3D structure modeling: similarities and differences.
Rother K, Rother M, Boniecki M, Puton T, Bujnicki JM. Rother K, et al. J Mol Model. 2011 Sep;17(9):2325-36. doi: 10.1007/s00894-010-0951-x. Epub 2011 Jan 22. J Mol Model. 2011. PMID: 21258831 Free PMC article. Review.
Cited by
- Protein-small molecule docking with receptor flexibility in iMOLSDOCK.
Sam Paul D, Gautham N. Sam Paul D, et al. J Comput Aided Mol Des. 2018 Sep;32(9):889-900. doi: 10.1007/s10822-018-0152-8. Epub 2018 Aug 20. J Comput Aided Mol Des. 2018. PMID: 30128925 - MOLS sampling and its applications in structural biophysics.
Ramya L, Nehru Viji S, Arun Prasad P, Kanagasabai V, Gautham N. Ramya L, et al. Biophys Rev. 2010 Dec;2(4):169-179. doi: 10.1007/s12551-010-0039-y. Epub 2010 Nov 16. Biophys Rev. 2010. PMID: 28510038 Free PMC article. Review. - MOLS 2.0: software package for peptide modeling and protein-ligand docking.
Paul DS, Gautham N. Paul DS, et al. J Mol Model. 2016 Oct;22(10):239. doi: 10.1007/s00894-016-3106-x. Epub 2016 Sep 16. J Mol Model. 2016. PMID: 27638416 - Amino acid signature enables proteins to recognize modified tRNA.
Spears JL, Xiao X, Hall CK, Agris PF. Spears JL, et al. Biochemistry. 2014 Feb 25;53(7):1125-33. doi: 10.1021/bi401174h. Epub 2014 Feb 14. Biochemistry. 2014. PMID: 24483944 Free PMC article. - Adapting Poisson-Boltzmann to the self-consistent mean field theory: application to protein side-chain modeling.
Koehl P, Orland H, Delarue M. Koehl P, et al. J Chem Phys. 2011 Aug 7;135(5):055104. doi: 10.1063/1.3621831. J Chem Phys. 2011. PMID: 21823735 Free PMC article.
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Other Literature Sources
Miscellaneous