Minimally complex system problem set for Ab initio protein structure prediction study

被引:1
作者
Kim, R
Choi, CY [1 ]
机构
[1] Seoul Natl Univ, Coll Engn, Interdisciplinary Program Biochem Engn & Biotechn, Seoul 151742, South Korea
[2] Seoul Natl Univ, Coll Engn, Sch Chem Engn, Seoul 151742, South Korea
关键词
ab initio protein structure prediction; crystal-packing effect; protein databank; dataset;
D O I
10.1007/BF02933067
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
摘要
A "minimally complex problem set" for ab initio protein structure prediction has been proposed. As well as consisting of non-redundant and crystallographically determined high-resolution protein structures, without disulphicle bonds, modified residues, unusual connectivities and heteromolecules, it is more importantly a collection of protein structures, with a high probability of being the same in the crystal form as in solution. To our knowledge, this is the first attempt at this kind of dataset. Considering the lattice constraint in crystals, and the possible flexibility in solution of crystallographically determined protein structures, our dataset is thought to be the safest starting points for an ab initio protein structure prediction study.
引用
收藏
页码:414 / 418
页数:5
相关论文
共 18 条
[1]  
ANFINSEN CB, 1954, J BIOL CHEM, V207, P201
[2]   PRINCIPLES THAT GOVERN FOLDING OF PROTEIN CHAINS [J].
ANFINSEN, CB .
SCIENCE, 1973, 181 (4096) :223-230
[3]   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
[4]   Trigger Factor and DnaK possess overlapping substrate pools and binding specificities [J].
Deuerling, E ;
Patzelt, H ;
Vorderwülbecke, S ;
Rauch, T ;
Kramer, G ;
Schaffitzel, E ;
Mogk, A ;
Schulze-Specking, A ;
Langen, H ;
Bukau, B .
MOLECULAR MICROBIOLOGY, 2003, 47 (05) :1317-1328
[5]  
Ghetu AF, 2000, NAT STRUCT BIOL, V7, P565
[6]   What is the role of thermodynamics on protein stability? [J].
Gummadi, SN .
BIOTECHNOLOGY AND BIOPROCESS ENGINEERING, 2003, 8 (01) :9-18
[7]   On the role of the crystal environment in determining protein side-chain conformations [J].
Jacobson, MP ;
Friesner, RA ;
Xiang, ZX ;
Honig, B .
JOURNAL OF MOLECULAR BIOLOGY, 2002, 320 (03) :597-608
[8]   Predicting protein three-dimensional structure [J].
Moult, J .
CURRENT OPINION IN BIOTECHNOLOGY, 1999, 10 (06) :583-588
[9]  
MURZIN AG, 1995, J MOL BIOL, V247, P536, DOI 10.1016/S0022-2836(05)80134-2
[10]   IMPROVED TOOLS FOR BIOLOGICAL SEQUENCE COMPARISON [J].
PEARSON, WR ;
LIPMAN, DJ .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1988, 85 (08) :2444-2448