Literature DB >> 17977883

NPIDB: a database of nucleic acids-protein interactions.

Sergei Spirin1, Mikhail Titov, Anna Karyagina, Andrei Alexeevski.   

Abstract

UNLABELLED: The database NPIDB (Nucleic Acids-Protein Interaction DataBase) contains information derived from structures of DNA-protein and RNA-protein complexes extracted from PDB (1834 complexes in July 2007). It is organized as a collection of files in PDB format and is equipped with a web-interface and a set of tools for extracting biologically meaningful characteristics of complexes. The content of the database is weekly updated. AVAILABILITY: http://monkey.belozersky.msu.ru/NPIDB/

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Year:  2007        PMID： 17977883     DOI： 10.1093/bioinformatics/btm519

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  10 in total

Review 1.  DNA-protein interaction: identification, prediction and data analysis.

Authors:  Abbasali Emamjomeh; Darush Choobineh; Behzad Hajieghrari; Nafiseh MahdiNezhad; Amir Khodavirdipour
Journal:  Mol Biol Rep       Date:  2019-03-26       Impact factor: 2.316

2.  Statistics and physical origins of pK and ionization state changes upon protein-ligand binding.

Authors:  Boris Aguilar; Ramu Anandakrishnan; Jory Z Ruscio; Alexey V Onufriev
Journal:  Biophys J       Date:  2010-03-03       Impact factor: 4.033

3.  A coarse-grained potential for fold recognition and molecular dynamics simulations of proteins.

Authors:  Peter Májek; Ron Elber
Journal:  Proteins       Date:  2009-09

4.  The Protein-DNA Interface database.

Authors:  Tomás Norambuena; Francisco Melo
Journal:  BMC Bioinformatics       Date:  2010-05-18       Impact factor: 3.169

5.  PRIDB: a Protein-RNA interface database.

Authors:  Benjamin A Lewis; Rasna R Walia; Michael Terribilini; Jeff Ferguson; Charles Zheng; Vasant Honavar; Drena Dobbs
Journal:  Nucleic Acids Res       Date:  2010-11-11       Impact factor: 16.971

6.  Small cofactors may assist protein emergence from RNA world: clues from RNA-protein complexes.

Authors:  Liang Shen; Hong-Fang Ji
Journal:  PLoS One       Date:  2011-07-18       Impact factor: 3.240

7.  Optimizing scoring function of protein-nucleic acid interactions with both affinity and specificity.

Authors:  Zhiqiang Yan; Jin Wang
Journal:  PLoS One       Date:  2013-09-30       Impact factor: 3.240

8.  3D-footprint: a database for the structural analysis of protein-DNA complexes.

Authors:  Bruno Contreras-Moreira
Journal:  Nucleic Acids Res       Date:  2009-09-18       Impact factor: 16.971

9.  TFinDit: transcription factor-DNA interaction data depository.

Authors:  Daniel Turner; RyangGuk Kim; Jun-tao Guo
Journal:  BMC Bioinformatics       Date:  2012-09-03       Impact factor: 3.169

10.  NPIDB: Nucleic acid-Protein Interaction DataBase.

Authors:  Dmitry D Kirsanov; Olga N Zanegina; Evgeniy A Aksianov; Sergei A Spirin; Anna S Karyagina; Andrei V Alexeevski
Journal:  Nucleic Acids Res       Date:  2012-11-27       Impact factor: 16.971
  10 in total

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