PyMod 2.0: improvements in protein sequence-structure analysis and homology modeling within PyMOL

被引：190

作者：

Janson, Giacomo ^{[1
]}

Zhang, Chengxin ^{[2
]}

Prado, Maria Giulia ^{[1
]}

Paiardini, Alessandro ^{[3
]}

机构：

[1] Sapienza Univ Roma, Dept Biochem Sci A Rossi Fanelli, I-00185 Rome, Italy

[2] Univ Michigan, Dept Computat Med & Bioinformat, Ann Arbor, MI 48109 USA

[3] Sapienza Univ Roma, Dept Biol & Biotechnol Charles Darwin, I-00185 Rome, Italy

来源：

BIOINFORMATICS | 2017年 / 33卷 / 03期

关键词：

UCSF CHIMERA; ALIGNMENT; GENERATION; PREDICTION; FEATURES; SYSTEM; BLAST;

D O I：

10.1093/bioinformatics/btw638

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Motivation: The recently released PyMod GUI integrates many of the individual steps required for protein sequence-structure analysis and homology modeling within the interactive visualization capabilities of PyMOL. Here we describe the improvements introduced into the version 2.0 of PyMod. Results: The original code of PyMod has been completely rewritten and improved in version 2.0 to extend PyMOL with packages such as Clustal Omega, PSIPRED and CAMPO. Integration with the popular web services ESPript and WebLogo is also provided. Finally, a number of new MODELLER functionalities have also been implemented, including SALIGN, modeling of quaternary structures, DOPE scores, disulfide bond modeling and choice of heteroatoms to be included in the final model.

引用

页码：444 / 446

页数：3

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