PRIMO/PRIMONA: A coarse-grained model for proteins and nucleic acids that preserves near-atomistic accuracy

被引：90

作者：

Gopal, Srinivasa M. ^{[1
]}

Mukherjee, Shayantani ^{[1
]}

Cheng, Yi-Ming ^{[1
]}

Feig, Michael ^{[1
]}

机构：

[1] Michigan State Univ, Dept Chem, Dept Biochem & Mol Biol, E Lansing, MI 48824 USA

来源：

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS | 2010年 / 78卷 / 05期

关键词：

coarse-graining; all-atom reconstruction; proteins; nucleic acids; multiscale modeling; FORCE-FIELD; ALL-ATOM; STRUCTURE PREDICTION; MOLECULAR-DYNAMICS; SIMULATION; BACKBONE; REPRESENTATIONS; RECONSTRUCTION; NUCLEOSOME; CAPSIDS;

D O I：

10.1002/prot.22645

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

The new coarse graining model PRIMO/PRIMONA for proteins and nucleic acids is proposed. This model combines one to several heavy atoms into coarse-grained sites that are chosen to allow an analytical, high-resolution reconstruction of all-atom models based on molecular bonding geometry constraints. The accuracy of proposed reconstruction method in terms of structure and energetics is tested and compared with other popular reconstruction methods for a variety of protein and nucleic acid test sets.

引用

页码：1266 / 1281

页数：16

共 45 条

[1] Stability and dynamics of virus capsids described by coarse-grained modeling [J].

Arkhipov, Anton ;

Freddolino, Peter L. ;

Schulten, Klaus .

STRUCTURE, 2006, 14 (12) :1767-1777

[2] A coarse-grained protein-protein potential derived from an all-atom force field [J].

Basdevant, Nathalie ;

Borgis, Daniel ;

Ha-Duong, Tap .

JOURNAL OF PHYSICAL CHEMISTRY B, 2007, 111 (31) :9390-9399

[3] A 1.8 A RESOLUTION POTENTIAL FUNCTION FOR PROTEIN FOLDING [J].

CRIPPEN, GM ;

SNOW, ME .

BIOPOLYMERS, 1990, 29 (10-11) :1479-1489

[4] Ab initio RNA folding by discrete molecular dynamics: From structure prediction to folding mechanisms [J].

Ding, Feng ;

Sharma, Shantanu ;

Chalasani, Poornima ;

Demidov, Vadim V. ;

Broude, Natalia E. ;

Dokholyan, Nikolay V. .

RNA, 2008, 14 (06) :1164-1173

[5] Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution [J].

Duan, Y ;

Kollman, PA .

SCIENCE, 1998, 282 (5389) :740-744

[6] BACKBONE-DEPENDENT ROTAMER LIBRARY FOR PROTEINS - APPLICATION TO SIDE-CHAIN PREDICTION [J].

DUNBRACK, RL ;

KARPLUS, M .

JOURNAL OF MOLECULAR BIOLOGY, 1993, 230 (02) :543-574

[7] Rotamer libraries in the 21st century [J].

Dunbrack, RL .

CURRENT OPINION IN STRUCTURAL BIOLOGY, 2002, 12 (04) :431-440

[8]

ENRICO OP, 1984, BIOPOLYMERS, V23, P1207

[9]

Feig M, 2000, PROTEINS, V41, P86, DOI 10.1002/1097-0134(20001001)41:1<86::AID-PROT110>3.3.CO

[10]

2-P

← 1 2 3 4 5 →