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Volumn , Issue , 2005, Pages 97-135

Structural Aspects Of Binding Site Similarity: A 3D Upgrade for Chemogenomics

Author keywords

Application of binding site analyses; Chemogenomics; Detecting binding site similarity; Similar shape and property searches; Structural aspects of binding site similarity; Structural biology of binding sites

Indexed keywords

CHEMOGENOMICS; DETECTING BINDING SITE SIMILARITY; SIMILAR SHAPE AND PROPERTY SEARCHES; STRUCTURAL ASPECTS; STRUCTURAL BIOLOGY;

EID: 32544437125     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/3527603948.ch4     Document Type: Chapter
Times cited : (5)

References (147)
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    • (This outstanding website by Novo Nordisk provides a comprehensive resource for classification and amino acid sequence analysis of protein tyrosine phosphatases.)
    • http://www.science.novonordisk.com/ PTP/ (This outstanding website by Novo Nordisk provides a comprehensive resource for classification and amino acid sequence analysis of protein tyrosine phosphatases.).
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    • It is worth mentioning recent investigations on the phosphate binding sites of protein-mononucleotide complexes (Kinoshita et al., Protein Eng. 1999, 11-14) and pyridoxal phosphate binding proteins
    • Both studies highlight the presence of distinctively different phosphate recognition motifs, which are conserved within the protein families they belong to.
    • It is worth mentioning recent investigations on the phosphate binding sites of protein-mononucleotide complexes (Kinoshita et al., Protein Eng. 1999, 11-14) and pyridoxal phosphate binding proteins (Denesyuk et al., J. Mol. Biol. 2002, 155-172). Both studies highlight the presence of distinctively different phosphate recognition motifs, which are conserved within the protein families they belong to.
    • (2002) J. Mol. Biol. , pp. 155-172
    • Denesyuk1
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    • It should be mentioned that the significance of structural differences can be assessed by means of X-ray crystallography by using local density correlation maps
    • This can help to avoid problems linked to structure elucidation methods, prior to drawing conclusions regarding the biological significance of structural variations.
    • It should be mentioned that the significance of structural differences can be assessed by means of X-ray crystallography by using local density correlation maps (G.J. Kleywegt, Acta Crystallogr. D Biol. Crystallogr. 1999, 1878-1884). This can help to avoid problems linked to structure elucidation methods, prior to drawing conclusions regarding the biological significance of structural variations.
    • (1999) Acta Crystallogr. D Biol. Crystallogr. , pp. 1878-1884
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    • Docking calculations using GOLD
    • suggest that the 4PP ligand could fit into the binding site in a more extended conformation, filling up the S4 pocket and forming an H-bond with the Glu97.O oxygen atom; (B. Wegscheid, A. Bergner, unpublished results)
    • Docking calculations using GOLD (G. Jones, P. Willett, R.C. Glen, A.R. Leach, R. Taylor, J. Mol. Biol. 1997, 727-48) suggest that the 4PP ligand could fit into the binding site in a more extended conformation, filling up the S4 pocket and forming an H-bond with the Glu97.O oxygen atom; (B. Wegscheid, A. Bergner, unpublished results).
    • (1997) J. Mol. Biol. , pp. 727-48
    • Jones, G.1    Willett, P.2    Glen, R.C.3    Leach, A.R.4    Taylor, R.5
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* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.