ArticleBMC bioinformatics2008
Indel PDB: a database of structural insertions and deletions derived from sequence alignments of closely related proteins.
Article in BMC bioinformatics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Insertion-Deletion Events Are Depleted in Protein Regions with Predicted Secondary Structure.Genome biology and evolution · 2024Article
- Structural Dynamics Predominantly Determine the Adaptability of Proteins to Amino Acid Deletions.International journal of molecular sciences · 2023Article
- Elucidating the Structural Impacts of Protein InDels.Biomolecules · 2022Article
- An integrated package for bisulfite DNA methylation data analysis with Indel-sensitive mapping.BMC bioinformatics · 2019Article
- Extensive libraries of gene truncation variants generated by in vitro transposition.Nucleic acids research · 2017Article
- Solving the master equation for Indels.BMC bioinformatics · 2017Article
- Characterization of parasite-specific indels and their proposed relevance for selective anthelminthic drug targeting.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2016Article
- Discriminating between deleterious and neutral non-frameshifting indels based on protein interaction networks and hybrid properties.Molecular genetics and genomics : MGG · 2015Article
- Nucleotide insertions and deletions complement point mutations to massively expand the diversity created by somatic hypermutation of antibodies.The Journal of biological chemistry · 2014Article
- LenVarDB: database of length-variant protein domains.Nucleic acids research · 2014Article
- Evolution of protein indels in plants, animals and fungi.BMC evolutionary biology · 2013Article
- SeqFIRE: a web application for automated extraction of indel regions and conserved blocks from protein multiple sequence alignments.Nucleic acids research · 2012Article
- Exploring the implications of INDELs in neuropsychiatric genetics: challenges and perspectives.Journal of molecular neuroscience : MN · 2012Article
- IndelFR: a database of indels in protein structures and their flanking regions.Nucleic acids research · 2012Article
- Systematic analysis of short internal indels and their impact on protein folding.BMC structural biology · 2010Article
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Authors and funding
2 authors.
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Abstract
backgroundInsertions 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. DESCRIPTION: 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.
conclusionBy 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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