RosettaHoles2: A volumetric packing measure for protein structure refinement and validation

被引:30
作者
Sheffler, William [1 ]
Baker, David [1 ]
机构
[1] Univ Washington, Dept Biochem, Seattle, WA 98195 USA
关键词
protein folding; protein design; protein core packing; protein structure validation; crystallography; COMPLEX;
D O I
10.1002/pro.458
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
We present an improved version of RosettaHoles, a methodology for quantitative and visual characterization of protein core packing. RosettaHoles2 features a packing measure more rapidly computable, accurate and physically transparent, as well as a new validation score intended for structures submitted to the Protein Data Bank. The differential packing measure is parameterized to maximize the gap between computationally generated and experimentally determined X-ray structures, and can be used in refinement of protein structure models. The parameters of the model provide insight into components missing in current force fields, and the validation score gives an upper bound on the X-ray resolution of Protein Data Bank structures; a crystal structure should have a validation score as good as or better than its resolution.
引用
收藏
页码:1991 / 1995
页数:5
相关论文
共 15 条
[1]   The Protein Data Bank [J].
Berman, HM ;
Westbrook, J ;
Feng, Z ;
Gilliland, G ;
Bhat, TN ;
Weissig, H ;
Shindyalov, IN ;
Bourne, PE .
NUCLEIC ACIDS RESEARCH, 2000, 28 (01) :235-242
[2]   High-resolution structures of retinol-binding protein in complex with retinol: pH-induced protein structural changes in the crystal state [J].
Calderone, V ;
Berni, R ;
Zanotti, G .
JOURNAL OF MOLECULAR BIOLOGY, 2003, 329 (04) :841-850
[3]   STAPHYLOCOCCAL NUCLEASE - PROPOSED MECHANISM OF ACTION BASED ON STRUCTURE OF ENZYME-THYMIDINE 3',5'-BISPHOSPHATE-CALCIUM ION COMPLEX AT 1.5-A RESOLUTION [J].
COTTON, FA ;
HAZEN, EE ;
LEGG, MJ .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1979, 76 (06) :2551-2555
[4]   Macromolecular modeling with Rosetta [J].
Das, Rhiju ;
Baker, David .
ANNUAL REVIEW OF BIOCHEMISTRY, 2008, 77 :363-382
[5]   MolProbity: all-atom contacts and structure validation for proteins and nucleic acids [J].
Davis, Ian W. ;
Leaver-Fay, Andrew ;
Chen, Vincent B. ;
Block, Jeremy N. ;
Kapral, Gary J. ;
Wang, Xueyi ;
Murray, Laura W. ;
Arendall, W. Bryan, III ;
Snoeyink, Jack ;
Richardson, Jane S. ;
Richardson, David C. .
NUCLEIC ACIDS RESEARCH, 2007, 35 :W375-W383
[6]  
DRUCKER B, SUPPORT VECTOR REGRE, P155
[7]  
EDELSBRUNNER E, COMBINATORIAL COMPUT, V52, P243
[8]   Errors in protein structures [J].
Hooft, RWW ;
Vriend, G ;
Sander, C ;
Abola, EE .
NATURE, 1996, 381 (6580) :272-272
[9]  
Lazaridis T, 1999, PROTEINS, V35, P133, DOI 10.1002/(SICI)1097-0134(19990501)35:2<133::AID-PROT1>3.0.CO
[10]  
2-N