Comparison of multiple Amber force fields and development of improved protein backbone parameters.
作者： Viktor Hornak , Robert Abel , Asim Okur , Bentley Strockbine , Adrian Roitberg
DOI: 10.1002/PROT.21123
关键词:
摘要: … another variant of Amber force field but strives to improve the existing ff94 and ff99 force fields, as … Thus rather than contributing to the diverging set of Amber force fields, we extend the …
sci-hub.se 参考文章(70)
Steven W. Rick, Steven J. Stuart, Potentials and Algorithms for Incorporating Polarizability in Computer Simulations Reviews in Computational Chemistry, Volume 18. pp. 89- 146 ,(2003) , 10.1002/0471433519.CH3
Eric J. Sorin, Vijay S. Pande, Empirical force-field assessment: The interplay between backbone torsions and noncovalent term scaling. Journal of Computational Chemistry. ,vol. 26, pp. 682- 690 ,(2005) , 10.1002/JCC.20208
Fatma Eker, Xiaolin Cao, Laurence Nafie, Reinhard Schweitzer-Stenner, Tripeptides adopt stable structures in water. A combined polarized visible Raman, FTIR, and VCD spectroscopy study. Journal of the American Chemical Society. ,vol. 124, pp. 14330- 14341 ,(2002) , 10.1021/JA027381W
Z. Shi, K. Chen, Z. Liu, A. Ng, W. C. Bracken, N. R. Kallenbach, Polyproline II propensities from GGXGG peptides reveal an anticorrelation with β-sheet scales Proceedings of the National Academy of Sciences of the United States of America. ,vol. 102, pp. 17964- 17968 ,(2005) , 10.1073/PNAS.0507124102
Alexander D. MacKerell, Michael Feig, Charles L. Brooks, Improved treatment of the protein backbone in empirical force fields. Journal of the American Chemical Society. ,vol. 126, pp. 698- 699 ,(2004) , 10.1021/JA036959E
William L. Jorgensen, Jayaraman Chandrasekhar, Jeffry D. Madura, Roger W. Impey, Michael L. Klein, Comparison of simple potential functions for simulating liquid water The Journal of Chemical Physics. ,vol. 79, pp. 926- 935 ,(1983) , 10.1063/1.445869
Lu Wang, Yong Duan, Rebecca Shortle, Barbara Imperiali, Peter A. Kollman, Study of the stability and unfolding mechanism of BBA1 by molecular dynamics simulations at different temperatures Protein Science. ,vol. 8, pp. 1292- 1304 ,(1999) , 10.1110/PS.8.6.1292
S. Vijay-Kumar, C. E. Bugg, K. D. Wilkinson, W. J. Cook, Three-dimensional structure of ubiquitin at 2.8 A resolution. Proceedings of the National Academy of Sciences of the United States of America. ,vol. 82, pp. 3582- 3585 ,(1985) , 10.1073/PNAS.82.11.3582
Sander Woutersen, Rolf Pfister, Peter Hamm, Yuguang Mu, Daniel S. Kosov, Gerhard Stock, Peptide conformational heterogeneity revealed from nonlinear vibrational spectroscopy and molecular dynamics simulations Journal of Chemical Physics. ,vol. 117, pp. 6833- 6840 ,(2002) , 10.1063/1.1506151
Urs Stocker, Wilfred F. van Gunsteren, Molecular dynamics simulation of hen egg white lysozyme: A test of the GROMOS96 force field against nuclear magnetic resonance data Proteins. ,vol. 40, pp. 145- 153 ,(2000) , 10.1002/(SICI)1097-0134(20000701)40:1<145::AID-PROT160>3.0.CO;2-Y