Small molecule annotation for the Protein Data Bank.
Small molecule annotation for the Protein Data Bank.
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DOI：
10.1093/database/bau116
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发表时间：
2014
期刊：
影响因子：
--
通讯作者：
Zhuravleva MA
中科院分区：
文献类型：
--
作者：
Sen S;Young J;Berrisford JM;Chen M;Conroy MJ;Dutta S;Di Costanzo L;Gao G;Ghosh S;Hudson BP;Igarashi R;Kengaku Y;Liang Y;Peisach E;Persikova I;Mukhopadhyay A;Narayanan BC;Sahni G;Sato J;Sekharan M;Shao C;Tan L;Zhuravleva MA
蛋白质数据库（PDB）是生物大分子及其复合物的三维结构的唯一全球存储库，其10万多个结构包含2万多个与蛋白质和核酸结合的不同配体或小分子。关于这些小分子及其与蛋白质和核酸相互作用的信息对于我们理解生物化学过程至关重要，对于基于结构的药物设计至关重要。存在于沉积结构中的小分子可以连接到聚合物上，或者可以作为单独的非共价连接的配体出现。在wwPDB注释人员对新沉积结构的管理过程中，每个分子都与PDB化学成分词典（CCD）交叉引用。如果该分子是PDB中的新分子，则为其创建字典描述。PDB中发现的所有小分子组分的信息通过ftp存档作为外部参考文件分发。PDB中的小分子注释还包括关于配体结合位点以及配体和大分子之间的共价键和其他键的信息。在2011年PDB档案中存在的肽类抗生素和抑制剂的补救过程中，很明显需要额外的注释来一致地表示这些分子，这些分子通常由几个连续的子组分组成，包括修饰的氨基酸和其他化学基团。修饰的氨基酸的连接性信息对于正确表示这些生物学上有趣的分子是必要的。通过一个名为生物学有趣分子参考词典的新资源提供综合信息，该资源是CCD的补充，现在通常用于肽类抗生素和抑制剂的注释。
The Protein Data Bank (PDB) is the single global repository for three-dimensional structures of biological macromolecules and their complexes, and its more than 100 000 structures contain more than 20 000 distinct ligands or small molecules bound to proteins and nucleic acids. Information about these small molecules and their interactions with proteins and nucleic acids is crucial for our understanding of biochemical processes and vital for structure-based drug design. Small molecules present in a deposited structure may be attached to a polymer or may occur as a separate, non-covalently linked ligand. During curation of a newly deposited structure by wwPDB annotation staff, each molecule is cross-referenced to the PDB Chemical Component Dictionary (CCD). If the molecule is new to the PDB, a dictionary description is created for it. The information about all small molecule components found in the PDB is distributed via the ftp archive as an external reference file. Small molecule annotation in the PDB also includes information about ligand-binding sites and about covalent and other linkages between ligands and macromolecules. During the remediation of the peptide-like antibiotics and inhibitors present in the PDB archive in 2011, it became clear that additional annotation was required for consistent representation of these molecules, which are quite often composed of several sequential subcomponents including modified amino acids and other chemical groups. The connectivity information of the modified amino acids is necessary for correct representation of these biologically interesting molecules. The combined information is made available via a new resource called the Biologically Interesting molecules Reference Dictionary, which is complementary to the CCD and is now routinely used for annotation of peptide-like antibiotics and inhibitors.
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影响因子：
14.9
作者：
Gutmanas A;Alhroub Y;Battle GM;Berrisford JM;Bochet E;Conroy MJ;Dana JM;Fernandez Montecelo MA;van Ginkel G;Gore SP;Haslam P;Hatherley R;Hendrickx PM;Hirshberg M;Lagerstedt I;Mir S;Mukhopadhyay A;Oldfield TJ;Patwardhan A;Rinaldi L;Sahni G;Sanz-García E;Sen S;Slowley RA;Velankar S;Wainwright ME;Kleywegt GJ
通讯作者：
Kleywegt GJ
影响因子：
14.9
作者：
Kinjo AR;Suzuki H;Yamashita R;Ikegawa Y;Kudou T;Igarashi R;Kengaku Y;Cho H;Standley DM;Nakagawa A;Nakamura H
通讯作者：
Nakamura H
影响因子：
14.9
作者：
Ulrich EL;Akutsu H;Doreleijers JF;Harano Y;Ioannidis YE;Lin J;Livny M;Mading S;Maziuk D;Miller Z;Nakatani E;Schulte CF;Tolmie DE;Kent Wenger R;Yao H;Markley JL
通讯作者：
Markley JL
DOI：
10.1107/s0907444911050359
发表时间：
2012-04
期刊：
Acta crystallographica. Section D, Biological crystallography
影响因子：
--
作者：
Gore S;Velankar S;Kleywegt GJ
通讯作者：
Kleywegt GJ
影响因子：
14.9
作者：
UniProt Consortium
通讯作者：
UniProt Consortium