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Literature DB >> 10592247

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

M M Gromiha¹, J An, H Kono, M Oobatake, H Uedaira, P Prabakaran, A Sarai.

Abstract

ProTherm 2.0 is the second release of the Thermo-dynamic Database for Proteins and Mutants that includes numerical data for several thermodynamic parameters, structural information, experimental methods and conditions, functional and literature information. The present release contains >5500 entries, an approximately 67% increase over the previous version. In addition, we have included information about reversibility of data, details about buffer and ion concentrations and the surrounding residues in space for all mutants. A WWW interface enables users to search data based on various conditions with different sorting options for outputs. Further, ProTherm has links with other structural and literature databases, and the mutation sites and surrounding residues are automatically mapped on the structures and can be directly viewed through 3DinSight developed in our laboratory. The ProTherm database is freely available through the WWW at http://www.rtc.riken.go.jp/protherm.html

Mesh：

Substances：
Proteins

Year: 2000 PMID： 10592247 PMCID： PMC102403 DOI： 10.1093/nar/28.1.283

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

6 in total

1. Role of structural and sequence information in the prediction of protein stability changes: comparison between buried and partially buried mutations.

Authors: M M Gromiha; M Oobatake; H Kono; H Uedaira; A Sarai
Journal: Protein Eng Date: 1999-07

2. 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

3. The Protein Mutant Database.

Authors: T Kawabata; M Ota; K Nishikawa
Journal: Nucleic Acids Res Date: 1999-01-01 Impact factor: 16.971

4. 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

5. The Protein Data Bank: a computer-based archival file for macromolecular structures.

Authors: F C Bernstein; T F Koetzle; G J Williams; E F Meyer; M D Brice; J R Rodgers; O Kennard; T Shimanouchi; M Tasumi
Journal: J Mol Biol Date: 1977-05-25 Impact factor: 5.469

6. RASMOL: biomolecular graphics for all.

Authors: R A Sayle; E J Milner-White
Journal: Trends Biochem Sci Date: 1995-09 Impact factor: 13.807

6 in total

20 in total

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

1. Role of structural and sequence information in the prediction of protein stability changes: comparison between buried and partially buried mutations.

2. ProTherm: Thermodynamic Database for Proteins and Mutants.

3. The Protein Mutant Database.

4. 3DinSight: an integrated relational database and search tool for the structure, function and properties of biomolecules.

5. The Protein Data Bank: a computer-based archival file for macromolecular structures.

6. RASMOL: biomolecular graphics for all.

1. NTDB: Thermodynamic Database for Nucleic Acids.

2. On the thermal unfolding character of globular proteins.

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

4. Role of hydrophobic clusters and long-range contact networks in the folding of (alpha/beta)8 barrel proteins.

5. Prediction of protein thermostability with a direction- and distance-dependent knowledge-based potential.

6. Assessment of protein side-chain conformation prediction methods in different residue environments.

7. Disease risk of missense mutations using structural inference from predicted function.

Review 8. Towards precision medicine: advances in computational approaches for the analysis of human variants.

9. Prediction of the responsiveness to pharmacological chaperones: lysosomal human alpha-galactosidase, a case of study.

10. Machine learning integration for predicting the effect of single amino acid substitutions on protein stability.