Improving the representation of peptide-like inhibitor and antibiotic molecules in the Protein Data Bank.
Improving the representation of peptide-like inhibitor and antibiotic molecules in the Protein Data Bank.
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DOI：
10.1002/bip.22434
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发表时间：
2014-06
期刊：
影响因子：
2.9
通讯作者：
Berman, Helen M.
中科院分区：
文献类型：
--
作者：
Dutta, Shuchismita;Dimitropoulos, Dimitris;Feng, Zukang;Persikova, Irina;Sen, Sanchayita;Shao, Chenghua;Westbrook, John;Young, Jasmine;Zhuravleva, Marina A.;Kleywegt, Gerard J.;Berman, Helen M.
随着蛋白质数据库（PDB）中分子的数量和种类的积累，有时需要对其表示进行审查和改进。Worldwide PDB （wwPDB）合作伙伴定期更新结构化数据表示的各个方面，以改进归档的完整性和一致性。本文描述的修复工作主要集中在改善肽样抑制剂和抗生素分子的表征，以便它们可以容易地识别和分析。在超过1000个PDB条目中鉴定出肽样抑制剂或抗生素，系统地审查并表示为具有聚合物序列的肽或单个组分。对于大多数单组分分子，它们的肽样组成以一种新的表示形式被捕获，称为亚组分序列。一个被称为“群”的新概念被开发出来，用于表示由多种聚合物和非聚合物组分组成的复杂肽样抗生素和抑制剂。此外，还编写了一个参考词典，详细介绍了这些肽样分子的信息，以帮助它们的注释、鉴定和分析。基于在此修复中获得的经验，开发了指南、程序和工具，以准确和一致地注释含有肽样抑制剂和抗生素的新沉积。©2013 Wiley期刊公司生物工程学报（自然科学版），2014。
With the accumulation of a large number and variety of molecules in the Protein Data Bank (PDB) comes the need on occasion to review and improve their representation. The Worldwide PDB (wwPDB) partners have periodically updated various aspects of structural data representation to improve the integrity and consistency of the archive. The remediation effort described here was focused on improving the representation of peptide-like inhibitor and antibiotic molecules so that they can be easily identified and analyzed. Peptide-like inhibitors or antibiotics were identified in over 1000 PDB entries, systematically reviewed and represented either as peptides with polymer sequence or as single components. For the majority of the single-component molecules, their peptide-like composition was captured in a new representation, called the subcomponent sequence. A novel concept called “group” was developed for representing complex peptide-like antibiotics and inhibitors that are composed of multiple polymer and nonpolymer components. In addition, a reference dictionary was developed with detailed information about these peptide-like molecules to aid in their annotation, identification and analysis. Based on the experience gained in this remediation, guidelines, procedures, and tools were developed to annotate new depositions containing peptide-like inhibitors and antibiotics accurately and consistently. © 2013 Wiley Periodicals, Inc. Biopolymers 101: 659–668, 2014.
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影响因子：
14.9
作者：
UniProt Consortium
通讯作者：
UniProt Consortium
影响因子：
14.9
作者：
Henrick K;Feng Z;Bluhm WF;Dimitropoulos D;Doreleijers JF;Dutta S;Flippen-Anderson JL;Ionides J;Kamada C;Krissinel E;Lawson CL;Markley JL;Nakamura H;Newman R;Shimizu Y;Swaminathan J;Velankar S;Ory J;Ulrich EL;Vranken W;Westbrook J;Yamashita R;Yang H;Young J;Yousufuddin M;Berman HM
通讯作者：
Berman HM
DOI：
10.1107/s0907444912050469
发表时间：
2013-04-01
影响因子：
2.2
作者：
Economou, Nicoleta J.;Zentner, Isaac J.;Loll, Patrick J.
通讯作者：
Loll, Patrick J.
DOI：
10.1038/nsb0194-55
发表时间：
1994-01-01
期刊：
NATURE STRUCTURAL BIOLOGY
影响因子：
--
作者：
MATTOS, C;RASMUSSEN, B;RINGE, D
通讯作者：
RINGE, D
DOI：
10.1107/s0907444901003134
发表时间：
2001-05-01
影响因子：
2.2
作者：
Bond, CS;Shaw, MP;Hunter, WN
通讯作者：
Hunter, WN