Author, as appears in the article.: Magyar, C; Gromiha, MM; Pujadas, G; Tusnady, GE; Simon, I;

Department: Bioquímica i Biotecnologia

e-ISSN: 1362-4962

URV's Author/s: Pujadas Anguiano, Gerard

Keywords: Long-range interactions Identification Folded proteins Centers

Abstract: Residues expected to play key roles in the stabilization of proteins [stabilizing residues (SRs)] are selected by combining several methods based mainly on the interactions of a given residue with its spatial, rather than its sequential neighborhood and by considering the evolutionary conservation of the residues. A residue is selected as a stabilizing residue if it has high surrounding hydrophobicity, high long-range order, high conservation score and if it belongs to a stabilization center. The definition of all these parameters and the thresholds used to identify the SRs are discussed in detail. The algorithm for identifying SRs was originally developed for TIM-barrel proteins [M. M. Gromiha, G. Pujadas, C. Magyar, S. Selvaraj, and I. Simon (2004), Proteins, 55, 316-329] and is now generalized for all proteins of known 3D structure. SRs could be applied in protein engineering and homology modeling and could also help to explain certain folds with significant stability. The SRide server is located at http://sride.enzim.hu.

Thematic Areas: Zootecnia / recursos pesqueiros Saúde coletiva Química Nutrição Medicina ii Medicina i Matemática / probabilidade e estatística Interdisciplinar Genetics Farmacia Engenharias ii Ciências biológicas iii Ciências biológicas ii Ciências biológicas i Ciências agrárias i Ciência da computação Biotecnología Biodiversidade Biochemistry & molecular biology Astronomia / física

licence for use: https://creativecommons.org/licenses/by/3.0/es/

ISSN: 0305-1048

Author's mail: gerard.pujadas@urv.cat

Author identifier: 0000-0003-2598-8089

Last page: W305

Record's date: 2023-02-18

Journal volume: 33

Papper version: info:eu-repo/semantics/publishedVersion

Link to the original source: https://academic.oup.com/nar/article/33/suppl_2/W303/2505549

Licence document URL: http://repositori.urv.cat/ca/proteccio-de-dades/

Papper original source: Nucleic Acids Research. 33 (Supl 2): W303-W305

APA: Magyar, C; Gromiha, MM; Pujadas, G; Tusnady, GE; Simon, I; (2005). SRide: a server for identifying stabilizing residues in proteins. Nucleic Acids Research, 33(Supl 2), W303-W305. DOI: 10.1093/nar/gki409

Article's DOI: 10.1093/nar/gki409

Entity: Universitat Rovira i Virgili

Journal publication year: 2005

First page: W303

Publication Type: Journal Publications