Literature DB >> 11752320

ProTherm, Thermodynamic Database for Proteins and Mutants: developments in version 3.0.

M Michael Gromiha1, Hatsuho Uedaira, Jianghong An, Samuel Selvaraj, Ponraj Prabakaran, Akinori Sarai.   

Abstract

The current release of ProTherm, Thermodynamic Database for Proteins and Mutants, contains more than 10 000 numerical data (300% of the first version) of several thermodynamic parameters, experimental methods and conditions, reversibility of folding, details about the surrounding residues in space for all mutants, structural, functional and literature information. In the current version, we have added information about the source of each protein, identification codes for SWISS-PROT and Protein Information Resource and unique Protein Data Bank (PDB) code for proteins with relevant source. We have also provided additional options to search for data based on PDB code, number of states and reversibility. ProTherm is cross-linked with other sequence, structural, functional and literature databases, and the mutant sites and surrounding residues are automatically mapped on the structure. The ProTherm database is freely available at http://www.rtc.riken.go.jp/jouhou/protherm/protherm.html.

Entities:  

Mesh:

Substances:

Year:  2002        PMID: 11752320      PMCID: PMC99068          DOI: 10.1093/nar/30.1.301

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN: 0305-1048            Impact factor:   16.971


  6 in total

1.  ProTherm, version 2.0: thermodynamic database for proteins and mutants.

Authors:  M M Gromiha; J An; H Kono; M Oobatake; H Uedaira; P Prabakaran; A Sarai
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

2.  The Protein Data Bank.

Authors:  H M Berman; J Westbrook; Z Feng; G Gilliland; T N Bhat; H Weissig; I N Shindyalov; P E Bourne
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

3.  The protein information resource (PIR).

Authors:  W C Barker; J S Garavelli; H Huang; P B McGarvey; B C Orcutt; G Y Srinivasarao; C Xiao; L S Yeh; R S Ledley; J F Janda; F Pfeiffer; H W Mewes; A Tsugita; C Wu
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

4.  The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000.

Authors:  A Bairoch; R Apweiler
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

5.  ProTherm: Thermodynamic Database for Proteins and Mutants.

Authors:  M M Gromiha; J An; H Kono; M Oobatake; H Uedaira; A Sarai
Journal:  Nucleic Acids Res       Date:  1999-01-01       Impact factor: 16.971

6.  3DinSight: an integrated relational database and search tool for the structure, function and properties of biomolecules.

Authors:  J An; T Nakama; Y Kubota; A Sarai
Journal:  Bioinformatics       Date:  1998       Impact factor: 6.937

  6 in total
  13 in total

1.  A simple physical model for binding energy hot spots in protein-protein complexes.

Authors:  Tanja Kortemme; David Baker
Journal:  Proc Natl Acad Sci U S A       Date:  2002-10-15       Impact factor: 11.205

2.  ProTherm, version 4.0: thermodynamic database for proteins and mutants.

Authors:  K Abdulla Bava; M Michael Gromiha; Hatsuho Uedaira; Koji Kitajima; Akinori Sarai
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

3.  Calculation of mutational free energy changes in transition states for protein folding.

Authors:  Kresten Lindorff-Larsen; Emanuele Paci; Luis Serrano; Christopher M Dobson; Michele Vendruscolo
Journal:  Biophys J       Date:  2003-08       Impact factor: 4.033

Review 4.  Computational approaches to study the effects of small genomic variations.

Authors:  Kamil Khafizov; Maxim V Ivanov; Olga V Glazova; Sergei P Kovalenko
Journal:  J Mol Model       Date:  2015-09-08       Impact factor: 1.810

5.  ProThermDB: thermodynamic database for proteins and mutants revisited after 15 years.

Authors:  Rahul Nikam; A Kulandaisamy; K Harini; Divya Sharma; M Michael Gromiha
Journal:  Nucleic Acids Res       Date:  2021-01-08       Impact factor: 16.971

6.  Capturing, sharing and analysing biophysical data from protein engineering and protein characterization studies.

Authors:  Damien Farrell; Fergal O'Meara; Michael Johnston; John Bradley; Chresten R Søndergaard; Nikolaj Georgi; Helen Webb; Barbara Mary Tynan-Connolly; Una Bjarnadottir; Tommy Carstensen; Jens Erik Nielsen
Journal:  Nucleic Acids Res       Date:  2010-08-19       Impact factor: 16.971

7.  Molecular modeling of retinoschisin with functional analysis of pathogenic mutations from human X-linked retinoschisis.

Authors:  Y V Sergeev; R C Caruso; M R Meltzer; N Smaoui; I M MacDonald; P A Sieving
Journal:  Hum Mol Genet       Date:  2010-01-08       Impact factor: 6.150

8.  Stability of domain structures in multi-domain proteins.

Authors:  Ramachandra M Bhaskara; Narayanaswamy Srinivasan
Journal:  Sci Rep       Date:  2011-07-18       Impact factor: 4.379

9.  ProTherm and ProNIT: thermodynamic databases for proteins and protein-nucleic acid interactions.

Authors:  M D Shaji Kumar; K Abdulla Bava; M Michael Gromiha; Ponraj Prabakaran; Koji Kitajima; Hatsuho Uedaira; Akinori Sarai
Journal:  Nucleic Acids Res       Date:  2006-01-01       Impact factor: 16.971

10.  Structure Based Thermostability Prediction Models for Protein Single Point Mutations with Machine Learning Tools.

Authors:  Lei Jia; Ramya Yarlagadda; Charles C Reed
Journal:  PLoS One       Date:  2015-09-11       Impact factor: 3.240

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.