OPUS-Ca: a Knowledge-based Potential Function Requiring Only Calpha Positions

Overview

Journal Protein Sci

Specialty Biochemistry

Date 2007 Jun 26

PMID 17586777

Citations 38

Authors

Yinghao Wu

Mingyang Lu

Mingzhi Chen

Jialin Li

Jianpeng Ma

Affiliations

Soon will be listed here.

Abstract

In this paper, we report a knowledge-based potential function, named the OPUS-Ca potential, that requires only Calpha positions as input. The contributions from other atomic positions were established from pseudo-positions artificially built from a Calpha trace for auxiliary purposes. The potential function is formed based on seven major representative molecular interactions in proteins: distance-dependent pairwise energy with orientational preference, hydrogen bonding energy, short-range energy, packing energy, tri-peptide packing energy, three-body energy, and solvation energy. From the testing of decoy recognition on a number of commonly used decoy sets, it is shown that the new potential function outperforms all known Calpha-based potentials and most other coarse-grained ones that require more information than Calpha positions. We hope that this potential function adds a new tool for protein structural modeling.

Citing Articles

MUfoldQA_G: High-accuracy protein model QA via retraining and transformation.

Wang W, Wang J, Li Z, Xu D, Shang Y Comput Struct Biotechnol J. 2021; 19:6282-6290.

PMID: 34900138 PMC: 8636996. DOI: 10.1016/j.csbj.2021.11.021.

PSICA: a fast and accurate web service for protein model quality analysis.

Wang W, Li Z, Wang J, Xu D, Shang Y Nucleic Acids Res. 2019; 47(W1):W443-W450.

PMID: 31127307 PMC: 6602450. DOI: 10.1093/nar/gkz402.

OPUS-SSF: A side-chain-inclusive scoring function for ranking protein structural models.

Xu G, Ma T, Wang Q, Ma J Protein Sci. 2019; 28(6):1157-1162.

PMID: 30919509 PMC: 6511834. DOI: 10.1002/pro.3608.

Two New Heuristic Methods for Protein Model Quality Assessment.

Wang W, Wang J, Xu D, Shang Y IEEE/ACM Trans Comput Biol Bioinform. 2018; 17(4):1430-1439.

PMID: 30418914 PMC: 8988942. DOI: 10.1109/TCBB.2018.2880202.

Binding site matching in rational drug design: algorithms and applications.

Naderi M, Lemoine J, Govindaraj R, Kana O, Feinstein W, Brylinski M Brief Bioinform. 2018; 20(6):2167-2184.

PMID: 30169563 PMC: 6954434. DOI: 10.1093/bib/bby078.

References

McConkey B, Sobolev V, Edelman M . Discrimination of native protein structures using atom-atom contact scoring. Proc Natl Acad Sci U S A. 2003; 100(6):3215-20. PMC: 152272. DOI: 10.1073/pnas.0535768100. View

Zhang J, Chen R, Liang J . Empirical potential function for simplified protein models: combining contact and local sequence-structure descriptors. Proteins. 2006; 63(4):949-60. DOI: 10.1002/prot.20809. View

Stapley B, Doig A . Hydrogen bonding interactions between glutamine and asparagine in alpha-helical peptides. J Mol Biol. 1997; 272(3):465-73. DOI: 10.1006/jmbi.1997.1262. View

Bystroff C . MASKER: improved solvent-excluded molecular surface area estimations using Boolean masks. Protein Eng. 2003; 15(12):959-65. DOI: 10.1093/protein/15.12.959. View

Buchete N, Straub J, Thirumalai D . Development of novel statistical potentials for protein fold recognition. Curr Opin Struct Biol. 2004; 14(2):225-32. DOI: 10.1016/j.sbi.2004.03.002. View

Fidelis K, Stern P, Bacon D, Moult J . Comparison of systematic search and database methods for constructing segments of protein structure. Protein Eng. 1994; 7(8):953-60. DOI: 10.1093/protein/7.8.953. View

Thomas P, Dill K . Statistical potentials extracted from protein structures: how accurate are they?. J Mol Biol. 1996; 257(2):457-69. DOI: 10.1006/jmbi.1996.0175. View

Steward R, Thornton J . Prediction of strand pairing in antiparallel and parallel beta-sheets using information theory. Proteins. 2002; 48(2):178-91. DOI: 10.1002/prot.10152. View

Wu Y, Tian X, Lu M, Chen M, Wang Q, Ma J . Folding of small helical proteins assisted by small-angle X-ray scattering profiles. Structure. 2005; 13(11):1587-97. DOI: 10.1016/j.str.2005.07.023. View

10.

Gohlke H, Klebe G . Statistical potentials and scoring functions applied to protein-ligand binding. Curr Opin Struct Biol. 2001; 11(2):231-5. DOI: 10.1016/s0959-440x(00)00195-0. View

11.

Lu H, Skolnick J . A distance-dependent atomic knowledge-based potential for improved protein structure selection. Proteins. 2001; 44(3):223-32. DOI: 10.1002/prot.1087. View

12.

Hutchinson E, Sessions R, Thornton J, Woolfson D . Determinants of strand register in antiparallel beta-sheets of proteins. Protein Sci. 1998; 7(11):2287-300. PMC: 2143855. DOI: 10.1002/pro.5560071106. View

13.

Xia Y, Huang E, Levitt M, Samudrala R . Ab initio construction of protein tertiary structures using a hierarchical approach. J Mol Biol. 2000; 300(1):171-85. DOI: 10.1006/jmbi.2000.3835. View

14.

Zhang Y, Kolinski A, Skolnick J . TOUCHSTONE II: a new approach to ab initio protein structure prediction. Biophys J. 2003; 85(2):1145-64. PMC: 1303233. DOI: 10.1016/S0006-3495(03)74551-2. View

15.

Dong Q, Wang X, Lin L . Novel knowledge-based mean force potential at the profile level. BMC Bioinformatics. 2006; 7:324. PMC: 1534065. DOI: 10.1186/1471-2105-7-324. View

16.

Hinds D, Levitt M . A lattice model for protein structure prediction at low resolution. Proc Natl Acad Sci U S A. 1992; 89(7):2536-40. PMC: 48696. DOI: 10.1073/pnas.89.7.2536. View

17.

Shi Z, Olson C, Kallenbach N . Cation-pi interaction in model alpha-helical peptides. J Am Chem Soc. 2002; 124(13):3284-91. DOI: 10.1021/ja0174938. View

18.

Loose C, Klepeis J, Floudas C . A new pairwise folding potential based on improved decoy generation and side-chain packing. Proteins. 2003; 54(2):303-14. DOI: 10.1002/prot.10521. View

19.

Colubri A, Jha A, Shen M, Sali A, Berry R, Sosnick T . Minimalist representations and the importance of nearest neighbor effects in protein folding simulations. J Mol Biol. 2006; 363(4):835-57. DOI: 10.1016/j.jmb.2006.08.035. View

20.

Keasar C, Levitt M . A novel approach to decoy set generation: designing a physical energy function having local minima with native structure characteristics. J Mol Biol. 2003; 329(1):159-74. PMC: 2693481. DOI: 10.1016/s0022-2836(03)00323-1. View