ArticleNucleic acids research2016
An updated version of NPIDB includes new classifications of DNA-protein complexes and their families.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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9 citing papers in PubMed.
- MeDBA: the Metalloenzyme Data Bank and Analysis platform.Nucleic acids research · 2023Article
- DNAproDB: an expanded database and web-based tool for structural analysis of DNA-protein complexes.Nucleic acids research · 2020Article
- The PhoPQ Two-Component System Is the Major Regulator of Cell Surface Properties, Stress Responses and Plant-Derived Substrate Utilisation During Development ofFrontiers in microbiology · 2020Article
- DNA-protein interaction: identification, prediction and data analysis.Molecular biology reports · 2019Review
- Individually double minimum-distance definition of protein-RNA binding residues and application to structure-based prediction.Journal of computer-aided molecular design · 2018Article
- dbAMEPNI: a database of alanine mutagenic effects for protein-nucleic acid interactions.Database : the journal of biological databases and curation · 2018Article
- Crystal structure of an engineered, HIV-specific recombinase for removal of integrated proviral DNA.Nucleic acids research · 2017Article
- Computational investigation of proton transfer, pKa shifts and pH-optimum of protein-DNA and protein-RNA complexes.Proteins · 2017Article
- Structures of an all-α protein running along the DNA major groove.Nucleic acids research · 2016Article
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6 authors.
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Abstract
The recent upgrade of nucleic acid-protein interaction database (NPIDB, http://npidb.belozersky.msu.ru/) includes a newly elaborated classification of complexes of protein domains with double-stranded DNA and a classification of families of related complexes. Our classifications are based on contacting structural elements of both DNA: the major groove, the minor groove and the backbone; and protein: helices, beta-strands and unstructured segments. We took into account both hydrogen bonds and hydrophobic interaction. The analyzed material contains 1942 structures of protein domains from 748 PDB entries. We have identified 97 interaction modes of individual protein domain-DNA complexes and 17 DNA-protein interaction classes of protein domain families. We analyzed the sources of diversity of DNA-protein interaction modes in different complexes of one protein domain family. The observed interaction mode is sometimes influenced by artifacts of crystallization or diversity in secondary structure assignment. The interaction classes of domain families are more stable and thus possess more biological sense than a classification of single complexes. Integration of the classification into NPIDB allows the user to browse the database according to the interacting structural elements of DNA and protein molecules. For each family, we present average DNA shape parameters in contact zones with domains of the family.
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