publication . Conference object . Article . 2005

Generation of 3D templates of active sites of proteins with rigid prosthetic groups

Nebel, Jean-Christophe;
  • Published: 01 Jan 2005
  • Country: United Kingdom
Abstract
Motivation: With the increasing availability of protein structures, the generation of biologically meaningful 3D patterns from the simultaneous alignment of several protein structures is an exciting prospect: active sites could be better understood, protein functions and protein 3D structures could be predicted more accurately. Although patterns can already be generated at the fold and topological levels, no system produces high-resolution 3D patterns including atom and cavity positions. To address this challenge, our research focuses on generating patterns from proteins with rigid prosthetic groups. Since these groups are key elements of protein active sites, t...
Subjects
free text keywords: Template, Cytochrome P450 Superfamily, Human cytochrome, Protein model, Bioinformatics, Hydrogen bond, Cofactor, biology.protein, biology, Protein structure, Active site, Computer science, biological, computer
Related Organizations
35 references, page 1 of 3

Ahmed,S. (2004) The use of the novel substrate-heme complex approach in the derivation of a representation of the active site of the enzyme complex 17alpha-hydroxylase and 17,20-lyase. Biochem. Biophys. Res. Commun., 316, 595-598.

Berman,H.M. et al. (2000) The Protein Data Bank. Nucleic Acids Res., 28, 235-242.

Bertini,I. et al. (2004) NMR-validated structural model for oxidized Rhodopseudomonas palustris cytochrome c(556). J. Biol. Inorg. Chem., 9, 224-230.

Brady,G.P. and Stouten,P.F.W. (2000) Fast prediction and visualization of protein binding pockets with PASS. J. Computer-Aided Mol. Design, 14, 383-401. [OpenAIRE]

Campbell,S.J. et al. (2003) Ligand binding: functional site location, similarity and docking. Curr. Opin. Struct. Biol., 13, 389-395.

Cicek,M.S. et al. (2004) Association of prostate cancer risk and aggressiveness to androgen pathway genes: SRD5A2, CYP17, and the AR. Prostate, 59, 69-76.

Douglas,J.A. et al. (2005) Identifying susceptibility genes for prostate cancer-a family-based association study of polymorphisms in CYP17, CYP19, CYP11A1, and LH-beta. Cancer Epidemiol. Biomarkers Prev., 14, 2035-2039.

Eyal,E. et al. (2005) The limit of accuracy of protein modeling: influence of crystal packing on protein structure. J. Mol. Biol., 351, 431-442.

Falquet,L. et al. (2002) The PROSITE database, its status in 2002. Nucleic Acids Res., 30, 235-238. [OpenAIRE]

Gibrat,J.F. et al. (1996) Surprising similarities in structure comparison. Curr. Opin. Struct. Biol., 6, 377-385. [OpenAIRE]

Gilbert,D. et al. (2001) A computer system to perform structure comparison using TOPS representations of protein structure. Comput. Chem., 26, 23-30.

Gotoh,O. (1992) Substrate recognition sites in cytochrome P450 family 2 (CYP2) proteins inferred from comparative analyses of amino acid and coding nucleotide sequences. J. Biol. Chem., 267, 83-90.

Guda,C. et al. (2004) CE-MC: a multiple protein structure alignment server. Nucleic Acids Res., 32 (Web Server issue), W100-W103. [OpenAIRE]

Hefler,L.A. et al. (2004) Estrogen-metabolizing gene polymorphisms in the assessment of breast carcinoma risk and fibroadenoma risk in Caucasian women. Cancer, 101, 264-269. [OpenAIRE]

Hishiki,T. et al. (2000) X-ray crystal structure and catalytic properties of Thr252Ile mutant of cytochrome P450cam: roles of Thr252 and water in the active center. J. Biochem., 128, 965-974.

35 references, page 1 of 3
Abstract
Motivation: With the increasing availability of protein structures, the generation of biologically meaningful 3D patterns from the simultaneous alignment of several protein structures is an exciting prospect: active sites could be better understood, protein functions and protein 3D structures could be predicted more accurately. Although patterns can already be generated at the fold and topological levels, no system produces high-resolution 3D patterns including atom and cavity positions. To address this challenge, our research focuses on generating patterns from proteins with rigid prosthetic groups. Since these groups are key elements of protein active sites, t...
Subjects
free text keywords: Template, Cytochrome P450 Superfamily, Human cytochrome, Protein model, Bioinformatics, Hydrogen bond, Cofactor, biology.protein, biology, Protein structure, Active site, Computer science, biological, computer
Related Organizations
35 references, page 1 of 3

Ahmed,S. (2004) The use of the novel substrate-heme complex approach in the derivation of a representation of the active site of the enzyme complex 17alpha-hydroxylase and 17,20-lyase. Biochem. Biophys. Res. Commun., 316, 595-598.

Berman,H.M. et al. (2000) The Protein Data Bank. Nucleic Acids Res., 28, 235-242.

Bertini,I. et al. (2004) NMR-validated structural model for oxidized Rhodopseudomonas palustris cytochrome c(556). J. Biol. Inorg. Chem., 9, 224-230.

Brady,G.P. and Stouten,P.F.W. (2000) Fast prediction and visualization of protein binding pockets with PASS. J. Computer-Aided Mol. Design, 14, 383-401. [OpenAIRE]

Campbell,S.J. et al. (2003) Ligand binding: functional site location, similarity and docking. Curr. Opin. Struct. Biol., 13, 389-395.

Cicek,M.S. et al. (2004) Association of prostate cancer risk and aggressiveness to androgen pathway genes: SRD5A2, CYP17, and the AR. Prostate, 59, 69-76.

Douglas,J.A. et al. (2005) Identifying susceptibility genes for prostate cancer-a family-based association study of polymorphisms in CYP17, CYP19, CYP11A1, and LH-beta. Cancer Epidemiol. Biomarkers Prev., 14, 2035-2039.

Eyal,E. et al. (2005) The limit of accuracy of protein modeling: influence of crystal packing on protein structure. J. Mol. Biol., 351, 431-442.

Falquet,L. et al. (2002) The PROSITE database, its status in 2002. Nucleic Acids Res., 30, 235-238. [OpenAIRE]

Gibrat,J.F. et al. (1996) Surprising similarities in structure comparison. Curr. Opin. Struct. Biol., 6, 377-385. [OpenAIRE]

Gilbert,D. et al. (2001) A computer system to perform structure comparison using TOPS representations of protein structure. Comput. Chem., 26, 23-30.

Gotoh,O. (1992) Substrate recognition sites in cytochrome P450 family 2 (CYP2) proteins inferred from comparative analyses of amino acid and coding nucleotide sequences. J. Biol. Chem., 267, 83-90.

Guda,C. et al. (2004) CE-MC: a multiple protein structure alignment server. Nucleic Acids Res., 32 (Web Server issue), W100-W103. [OpenAIRE]

Hefler,L.A. et al. (2004) Estrogen-metabolizing gene polymorphisms in the assessment of breast carcinoma risk and fibroadenoma risk in Caucasian women. Cancer, 101, 264-269. [OpenAIRE]

Hishiki,T. et al. (2000) X-ray crystal structure and catalytic properties of Thr252Ile mutant of cytochrome P450cam: roles of Thr252 and water in the active center. J. Biochem., 128, 965-974.

35 references, page 1 of 3
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