Indel PDB: a database of structural insertions and deletions derived from sequence alignments of closely related proteins.
Indel PDB: a database of structural insertions and deletions derived from sequence alignments of closely related proteins.
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Indel PDB：一个从密切相关蛋白质的序列比对得出的结构插入和缺失数据库。
DOI：
10.1186/1471-2105-9-293
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发表时间：
2008-06-25
影响因子：
3
通讯作者：
Cherkasov, Artem
中科院分区：
文献类型：
--
作者：
Hsing, Michael;Cherkasov, Artem
插入和缺失（indels）是一种常见的序列变异类型，研究较少，并提出了许多重要的生物学问题。最近的研究表明，在蛋白质序列中存在相当大的indel可能表明蛋白质的必要性及其在蛋白质相互作用网络中的作用。最近还展示了利用插入缺失进行基于结构的药物设计的实例。然而，许多结构和功能特征的indel仍然较少研究或未知。我们已经创建了一个基于网络的资源，Indel PDB，代表从蛋白质数据库（PDB）中发现的高度相似的蛋白质的序列比对中鉴定的插入/缺失的结构数据库。Indel PDB利用大量可用的结构信息来表征indel位点的1-、2-和3-维特征。Indel PDB含有从11，294个含indel的蛋白质中提取的117，266个非冗余indel位点。与环数据库不同，Indel PDB具有更多的具有二级结构的indel序列，除了环之外，二级结构还包括α-螺旋和β-折叠。插入片段的特征在于它们的序列、长度、位置、二级结构组成、溶剂可及性、蛋白质结构域缔合和三维结构。利用Indel PDB中的数据，我们研究并展示了indel的一些序列和结构特征。我们预计，插入缺失PDB不仅将使未来的功能研究的插入缺失，但也将有助于蛋白质建模的努力和鉴定的插入缺失导向的药物结合位点。
Insertions and deletions (indels) represent a common type of sequence variations, which are less studied and pose many important biological questions. Recent research has shown that the presence of sizable indels in protein sequences may be indicative of protein essentiality and their role in protein interaction networks. Examples of utilization of indels for structure-based drug design have also been recently demonstrated. Nonetheless many structural and functional characteristics of indels remain less researched or unknown. We have created a web-based resource, Indel PDB, representing a structural database of insertions/deletions identified from the sequence alignments of highly similar proteins found in the Protein Data Bank (PDB). Indel PDB utilized large amounts of available structural information to characterize 1-, 2- and 3-dimensional features of indel sites. Indel PDB contains 117,266 non-redundant indel sites extracted from 11,294 indel-containing proteins. Unlike loop databases, Indel PDB features more indel sequences with secondary structures including alpha-helices and beta-sheets in addition to loops. The insertion fragments have been characterized by their sequences, lengths, locations, secondary structure composition, solvent accessibility, protein domain association and three dimensional structures. By utilizing the data available in Indel PDB, we have studied and presented here several sequence and structural features of indels. We anticipate that Indel PDB will not only enable future functional studies of indels, but will also assist protein modeling efforts and identification of indel-directed drug binding sites.
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Pfam：氏族、网络工具和服务。
影响因子：
14.9
作者：
Finn, Robert D.;Mistry, Jaina;Schuster-Bockler, Benjamin;Griffiths-Jones, Sam;Hollich, Volker;Lassmann, Timo;Moxon, Simon;Marshall, Mhairi;Khanna, Ajay;Durbin, Richard;Eddy, Sean R.;Sonnhammer, Erik L. L.;Bateman, Alex
通讯作者：
Bateman, Alex
影响因子：
3.9
作者：
GU, X;LI, WH
通讯作者：
LI, WH
影响因子：
4
作者：
Thorne, JL
通讯作者：
Thorne, JL
影响因子：
5.6
作者：
PASCARELLA, S;ARGOS, P
通讯作者：
ARGOS, P
影响因子：
14.9
作者：
Espadaler, J;Fernandez-Fuentes, N;Oliva, B
通讯作者：
Oliva, B