BioShell - a package of tools for structural biology computations

被引:44
作者
Gront, D [1 ]
Kolinski, A [1 ]
机构
[1] Warsaw Univ, Fac Chem, PL-02093 Warsaw, Poland
关键词
D O I
10.1093/bioinformatics/btk037
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
BioShell is a suite of programs performing common tasks accompanying protein structure modeling. BioShell design is based on UNIX shell flexibility and should be used as its extension. Using BioShell various molecular modeling procedures can be integrated in a single pipeline. Availability: BioShell package can be downloaded from its website http://biocomp.chem.uw.edu.pl/BioShell and these pages provide many examples and a detailed documentation for the newest version. Contact: dgront@chem.uw.edu.pl.
引用
收藏
页码:621 / 622
页数:2
相关论文
共 12 条
[1]   CHARMM - A PROGRAM FOR MACROMOLECULAR ENERGY, MINIMIZATION, AND DYNAMICS CALCULATIONS [J].
BROOKS, BR ;
BRUCCOLERI, RE ;
OLAFSON, BD ;
STATES, DJ ;
SWAMINATHAN, S ;
KARPLUS, M .
JOURNAL OF COMPUTATIONAL CHEMISTRY, 1983, 4 (02) :187-217
[2]   MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology [J].
Feig, M ;
Karanicolas, J ;
Brooks, CL .
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 2004, 22 (05) :377-395
[3]   HCPM - program for hierarchical clustering of protein models [J].
Gront, D ;
Kolinski, A .
BIOINFORMATICS, 2005, 21 (14) :3179-3180
[4]   PDB file parser and structure class implemented in Python']Python [J].
Hamelryck, T ;
Manderick, B .
BIOINFORMATICS, 2003, 19 (17) :2308-2310
[5]  
Kolinski A, 2004, ACTA BIOCHIM POL, V51, P349
[6]   Analysis and application of potential energy smoothing and search methods for global optimization [J].
Pappu, RV ;
Hart, RK ;
Ponder, JW .
JOURNAL OF PHYSICAL CHEMISTRY B, 1998, 102 (48) :9725-9742
[7]   AMBER, A PACKAGE OF COMPUTER-PROGRAMS FOR APPLYING MOLECULAR MECHANICS, NORMAL-MODE ANALYSIS, MOLECULAR-DYNAMICS AND FREE-ENERGY CALCULATIONS TO SIMULATE THE STRUCTURAL AND ENERGETIC PROPERTIES OF MOLECULES [J].
PEARLMAN, DA ;
CASE, DA ;
CALDWELL, JW ;
ROSS, WS ;
CHEATHAM, TE ;
DEBOLT, S ;
FERGUSON, D ;
SEIBEL, G ;
KOLLMAN, P .
COMPUTER PHYSICS COMMUNICATIONS, 1995, 91 (1-3) :1-41
[8]   EMBOSS: The European molecular biology open software suite [J].
Rice, P ;
Longden, I ;
Bleasby, A .
TRENDS IN GENETICS, 2000, 16 (06) :276-277
[9]   Large-scale protein structure modeling of the Saccharomyces cerevisiae genome [J].
Sánchez, R ;
Sali, A .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1998, 95 (23) :13597-13602
[10]   SWISS-MODEL: an automated protein homology-modeling server [J].
Schwede, T ;
Kopp, J ;
Guex, N ;
Peitsch, MC .
NUCLEIC ACIDS RESEARCH, 2003, 31 (13) :3381-3385