A short description of other selected ab initio methods for protein structure prediction
作者： I. Roterman-Konieczna
DOI: 10.1533/9781908818256.165
关键词:
摘要: Abstract: This chapter discusses three models representing the ab initio approach: UNRES, lattice model, and model implemented by ROSETTA package. Given fact that some sources treat tertiary conformation corresponds to protein’s global free-energy minimum as equivalent its native form, selected algorithms geared towards identifying such minima will also be discussed.
sci-hub.se 参考文章(38)
Harold A. Scheraga, Jaroslaw Kostrowicki, Some approaches to the multiple-minima problem in protein folding. Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding. pp. 123- 132 ,(1995)
Jaroslaw Kostrowicki, New Method for Calculation of the Exact End-to-end Distance Distributions for the Freely-rotating Chain Cornell University. ,(1994)
Harold A. Scheraga, Ming-Hong Hao, Jaroslaw Kostrowicki, Theoretical Studies of Protein Folding Springer, Boston, MA. pp. 457- 464 ,(1995) , 10.1007/978-1-4899-1031-8_41
Christopher Bystroff, Yu Shao, Modeling Protein Folding Pathways Springer, Berlin, Heidelberg. pp. 97- 122 ,(2008) , 10.1007/978-3-540-74268-5_5
Carol A Rohl, Charlie EM Strauss, Kira MS Misura, David Baker, None, Protein structure prediction using Rosetta. Methods in Enzymology. ,vol. 383, pp. 66- 93 ,(2004) , 10.1016/S0076-6879(04)83004-0
S. Oldziej, C. Czaplewski, A. Liwo, M. Chinchio, M. Nanias, J. A. Vila, M. Khalili, Y. A. Arnautova, A. Jagielska, M. Makowski, H. D. Schafroth, R. Kazmierkiewicz, D. R. Ripoll, J. Pillardy, J. A. Saunders, Y. K. Kang, K. D. Gibson, H. A. Scheraga, Physics-based protein-structure prediction using a hierarchical protocol based on the UNRES force field: assessment in two blind tests. Proceedings of the National Academy of Sciences of the United States of America. ,vol. 102, pp. 7547- 7552 ,(2005) , 10.1073/PNAS.0502655102
Kim T. Simons, Rich Bonneau, Ingo Ruczinski, David Baker, Ab initio protein structure prediction of CASP III targets using ROSETTA Proteins: Structure, Function, and Genetics. ,vol. 37, pp. 171- 176 ,(1999) , 10.1002/(SICI)1097-0134(1999)37:3+<171::AID-PROT21>3.0.CO;2-Z
Lucjan Piela, Jaroslaw Kostrowicki, Harold A. Scheraga, On the multiple-minima problem in the conformational analysis of molecules: deformation of the potential energy hypersurface by the diffusion equation method The Journal of Physical Chemistry. ,vol. 93, pp. 3339- 3346 ,(1989) , 10.1021/J100345A090
Christopher Bystroff, David Baker, Blind predictions of local protein structure in CASP2 targets using the I-sites library. Proteins. ,vol. 29, pp. 167- 171 ,(1997) , 10.1002/(SICI)1097-0134(1997)1+<167::AID-PROT21>3.0.CO;2-L
Katarzyna Prymula, Monika Piwowar, Marek Kochanczyk, Lukasz Flis, Maciej Malawski, Tomasz Szepieniec, Giovanni Evangelista, Giuseppe Minervini, Fabio Polticelli, ZdzisÅaw WisÌniowski, Kinga SaÅapa, Ewa MatczynÌska, Irena Roterman, In silico Structural Study of Random Amino Acid Sequence Proteins Not Present in Nature Chemistry & Biodiversity. ,vol. 6, pp. 2311- 2336 ,(2009) , 10.1002/CBDV.200800338