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Volumn , Issue , 2012, Pages 662-669

Improving accuracy in binding site comparison with homology modeling

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; BINDING SITES; BIOINFORMATICS; PROTEINS;

EID: 84875621364     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/BIBMW.2012.6470291     Document Type: Conference Paper
Times cited : (7)

References (47)
  • 1
    • 0029785147 scopus 로고    scopus 로고
    • Mapping the protein universe
    • Aug
    • L. Holm and C. Sander' "Mapping the protein universe." Science' vol. 273' no. 5275' pp. 595-603' Aug. 1996.
    • (1996) Science , vol.273 , Issue.5275 , pp. 595-603
    • Holm, L.1    Sander, C.2
  • 2
    • 0346122798 scopus 로고    scopus 로고
    • GRASP2: Visualization' surface properties' and electrostatics of macromolecular structures and sequences
    • Jan
    • D. Petrey and B. Honig' "GRASP2: visualization' surface properties' and electrostatics of macromolecular structures and sequences." Method Enzymol' vol. 374' no. 1991' pp. 492-509' Jan. 2003.
    • (2003) Method Enzymol , vol.374 , Issue.1991 , pp. 492-509
    • Petrey, D.1    Honig, B.2
  • 3
    • 44449139387 scopus 로고    scopus 로고
    • Detecting evolutionary relationships across existing fold space' using sequence order-independent profile-profile alignments
    • Apr
    • L. Xie and P. E. Bourne' "Detecting evolutionary relationships across existing fold space' using sequence order-independent profile-profile alignments." Proc Natl Acad Sci USA' vol. 105' no. 14' pp. 5441-6' Apr. 2008.
    • (2008) Proc Natl Acad Sci USA , vol.105 , Issue.14 , pp. 5441-5446
    • Xie, L.1    Bourne, P.E.2
  • 4
    • 0025719208 scopus 로고
    • Efficient detection of threedimensional structural motifs in biological macromolecules by computer vision techniques
    • Dec
    • R. Nussinov and H. 1. Wolfson' "Efficient detection of threedimensional structural motifs in biological macromolecules by computer vision techniques." Proc Natl Acad Sci USA' vol. 88' no. 23' pp. 10495-9' Dec. 1991.
    • (1991) Proc Natl Acad Sci USA , vol.88 , Issue.23 , pp. 10495-10499
    • Nussinov, R.1    Wolfson, H.J.2
  • 5
    • 0029948001 scopus 로고    scopus 로고
    • SSAP: Sequential structure alignment program for protein structure comparison
    • C. A. Orengo and W. R. Taylor' "SSAP: Sequential Structure Alignment Program for Protein Structure Comparison'" Method Enzymol' vol. 266' pp. 617-635' 1996.
    • (1996) Method Enzymol , vol.266 , pp. 617-635
    • Orengo, C.A.1    Taylor, W.R.2
  • 6
    • 0031715982 scopus 로고    scopus 로고
    • Protein structure alignment by incremental combinatorial extension (CE) of the optimal path
    • Sep
    • I. N. Shindyalov and P. E. Bourne' "Protein structure alignment by incremental combinatorial extension (CE) of the optimal path." Protein Eng' vol. 11' no. 9' pp. 739-47' Sep. 1998.
    • (1998) Protein Eng , vol.11 , Issue.9 , pp. 739-747
    • Shindyalov, I.N.1    Bourne, P.E.2
  • 8
    • 0141850386 scopus 로고    scopus 로고
    • An algorithm for constraintbased structural template matching: Application to 3D templates with statistical analysis
    • J. A. Barker and 1. M. Thornton' "An algorithm for constraintbased structural template matching: application to 3D templates with statistical analysis'" Bioinformatics' vol. 19' no. 13' pp. 1644-1649' 2003.
    • (2003) Bioinformatics , vol.19 , Issue.13 , pp. 1644-1649
    • Barker, J.A.1    Thornton, J.M.2
  • 9
    • 0032568859 scopus 로고    scopus 로고
    • Detection of protein three-dimensional sidechain patterns: New examples of convergent evolution
    • Jun
    • R. B. Russell' "Detection of protein three-dimensional sidechain patterns: new examples of convergent evolution." J Mol BioI' vol. 279' no. 5' pp. 1211-27' Jun. 1998.
    • (1998) J Mol BioI , vol.279 , Issue.5 , pp. 1211-1227
    • Russell, R.B.1
  • 11
    • 0037424601 scopus 로고    scopus 로고
    • A model for statistical significance of local similarities in structure
    • A. Stark' S. Sunyaev' and R. B. Russell' "A Model for Statistical Significance of Local Similarities in Structure'" J Mol BioI' vol. 326' pp. 1307-1316' 2003.
    • (2003) J Mol BioI , vol.326 , pp. 1307-1316
    • Stark, A.1    Sunyaev, S.2    Russell, R.B.3
  • 13
    • 78049444594 scopus 로고    scopus 로고
    • VASP: A volumetric analysis of surface properties yields insights into protein-ligand binding specificity
    • B. Y. Chen and B. Honig' "VASP: A Volumetric Analysis of Surface Properties Yields Insights into Protein-Ligand Binding Specificity'" PLoS Comput Biol' vol. 6' no. 8' p. 11' 2010.
    • (2010) PLoS Comput Biol , vol.6 , Issue.8 , pp. 11
    • Chen, B.Y.1    Honig, B.2
  • 16
    • 0032905858 scopus 로고    scopus 로고
    • A brighter future for protein structure prediction
    • P. Koehl' M. Levitt et aI.' "A brighter future for protein structure prediction'" nature structural biology' vol. 6' pp. 108Ill' 1999.
    • (1999) Nature Structural Biology , vol.6 , pp. 108
    • Koehl, P.1    Levitt, M.2    Ai, E.3
  • 17
    • 0035812694 scopus 로고    scopus 로고
    • Protein structure prediction and structural genomics
    • D. Baker and A. Sali' "Protein structure prediction and structural genomics'" Science's STKE' vol. 294' no. 5540' p. 93' 2001.
    • (2001) Science's STKE , vol.294 , Issue.5540 , pp. 93
    • Baker, D.1    Sali, A.2
  • 19
    • 0035838974 scopus 로고    scopus 로고
    • Extending the accuracy limits of prediction for side-chain conformations1
    • Z. Xiang and B. Honig' "Extending the accuracy limits of prediction for side-chain conformations1'" Journal of molecular biology' vol. 311' no. 2' pp. 421-430' 2001.
    • (2001) Journal of Molecular Biology , vol.311 , Issue.2 , pp. 421-430
    • Xiang, Z.1    Honig, B.2
  • 20
    • 0034682881 scopus 로고    scopus 로고
    • An integrated approach to the analysis and modeling of protein sequences and structures. I. Protein structural alignment and a quantitative measure for protein structural distance
    • Aug
    • A.-S. Yang and B. Honig' "An integrated approach to the analysis and modeling of protein sequences and structures. I. Protein structural alignment and a quantitative measure for protein structural distance." J Mol BioI' vol. 301' no. 3' pp. 665-78' Aug. 2000.
    • (2000) J Mol BioI , vol.301 , Issue.3 , pp. 665-678
    • Yang, A.-S.1    Honig, B.2
  • 21
    • 0029936121 scopus 로고    scopus 로고
    • Surprising similarities in structure comparison
    • Jun
    • J. F. Gibrat' T. Madej' and S. H. Bryant' "Surprising similarities in structure comparison." Curr Opin Struct Biol' vol. 6' no. 3' pp. 377-85' Jun. 1996.
    • (1996) Curr Opin Struct Biol , vol.6 , Issue.3 , pp. 377-385
    • Gibrat, J.F.1    Madej, T.2    Bryant, S.H.3
  • 22
    • 78149332085 scopus 로고    scopus 로고
    • The LabelHash algorithm for substructure matching
    • Jan
    • M. Moll' D. H. Bryant' and L. E. Kavraki' "The LabelHash algorithm for substructure matching." BMC Bioinformatics' vol. 11' no. 1' p. 555' Jan. 2010.
    • (2010) BMC Bioinformatics , vol.11 , Issue.1 , pp. 555
    • Moll, M.1    Bryant, D.H.2    Kavraki, L.E.3
  • 24
    • 26444502671 scopus 로고    scopus 로고
    • Recognition of binding patterns common to a set of protein structures
    • M. Shatsky' A. Shulman-peleg' R. Nussinov' and H. J' "Recognition of Binding Patterns Common to a Set of Protein Structures'" Lect Notes Comput Sc' vol. 3500' pp. 440-455' 2005.
    • (2005) Lect Notes Comput Sc , vol.3500 , pp. 440-455
    • Shatsky, M.1    Shulman-Peleg, A.2    Nussinov, R.3    Ja, H.4
  • 25
    • 0036406643 scopus 로고    scopus 로고
    • A new method to detect related function among proteins independent of sequence and fold homology
    • Oct
    • S. Schmitt' D. Kuhn' and G. Klebe' "A New Method to Detect Related Function Among Proteins Independent of Sequence and Fold Homology'" J Mol BioI' vol. 323' no. 2' pp. 387406' Oct. 2002.
    • (2002) J Mol BioI , vol.323 , Issue.2 , pp. 387406
    • Schmitt, S.1    Kuhn, D.2    Klebe, G.3
  • 26
    • 12944249776 scopus 로고
    • A discussion of the solution for the best rotation to relate two sets of vectors
    • W. Kabsch' "A discussion of the solution for the best rotation to relate two sets of vectors'" Acta Crystallographica A' vol. 34' pp. 827-828' 1978.
    • (1978) Acta Crystallographica A , vol.34 , pp. 827-828
    • Kabsch, W.1
  • 27
    • 0026137964 scopus 로고
    • Least-squares estimation of transformation parameters between two point patterns
    • S. Umeyama' "Least-squares estimation of transformation parameters between two point patterns'" IEEE Transactions on Pattern Analysis and Machine Intelligence' vol. 13' no. 4' pp. 376-380' 1991.
    • (1991) IEEE Transactions on Pattern Analysis and Machine Intelligence , vol.13 , Issue.4 , pp. 376-380
    • Umeyama, S.1
  • 29
    • 1842450688 scopus 로고    scopus 로고
    • FlexProt: Alignment of flexible protein structures without a predefinition of hinge regions
    • Jan
    • M. Shatsky' R. Nussinov' and H. 1. Wolfson' "FlexProt: alignment of flexible protein structures without a predefinition of hinge regions." J Comput BioI' vol. 11' no. 1' pp. 83-106' Jan. 2004.
    • (2004) J Comput BioI , vol.11 , Issue.1 , pp. 83-106
    • Shatsky, M.1    Nussinov, R.2    Wolfson, H.J.3
  • 30
    • 77951197269 scopus 로고    scopus 로고
    • Flexsnap: Flexible nonsequential protein structure alignment
    • S. Salem' M. Zaki' and C. Bystroff' "Flexsnap: Flexible nonsequential protein structure alignment'" Algorithms for Molecular Biology' vol. 5' p. 12' 2010.
    • (2010) Algorithms for Molecular Biology , vol.5 , pp. 12
    • Salem, S.1    Zaki, M.2    Bystroff, C.3
  • 31
    • 19544388989 scopus 로고    scopus 로고
    • Multiple flexible structure alignment using partial order graphs
    • May
    • Y Ye and A. Godzik' "Multiple flexible structure alignment using partial order graphs." Bioinformatics' vol. 21' no. 10' pp. 2362-9' May 2005.
    • (2005) Bioinformatics , vol.21 , Issue.10 , pp. 2362-2369
    • Ye, Y.1    Godzik, A.2
  • 32
    • 0021107965 scopus 로고
    • Solvent-accessible surfaces of proteins and nucleic acids
    • Aug
    • M. Connolly' "Solvent-accessible surfaces of proteins and nucleic acids'" Science' vol. 221' no. 4612' pp. 709-713' Aug. 1983.
    • (1983) Science , vol.221 , Issue.4612 , pp. 709-713
    • Connolly, M.1
  • 33
    • 33646757492 scopus 로고    scopus 로고
    • On the nature of cavities on protein surfaces : Application to the identification of drug-binding sites
    • M. Nayal and B. Honig' "On the Nature of Cavities on Protein Surfaces : Application to the Identification of Drug-Binding Sites'" Proteins: Struct. Funct. Genet.' vol. 63' pp. 892-906' 2006.
    • (2006) Proteins: Struct. Funct. Genet , vol.63 , pp. 892-906
    • Nayal, M.1    Honig, B.2
  • 34
    • 84875610086 scopus 로고    scopus 로고
    • Modeling regionalized volumetric differences in protein-ligand binding cavities
    • B. Y. Chen and S. Bandyopadhyay' "Modeling regionalized volumetric differences in protein-ligand binding cavities'" Proteome Science' vol. 10' no. Suppl 1' p. S6' 2012.
    • (2012) Proteome Science , vol.10 SUPPL. 1
    • Chen, B.Y.1    Bandyopadhyay, S.2
  • 35
    • 84862505221 scopus 로고    scopus 로고
    • A regionalizable statistical model of intersecting regions in protein ligand binding cavities
    • A regionalizable statistical model of intersecting regions in protein ligand binding cavities'" Journal of Bioinformatics and Computational Biology' vol. 10' no. 3' p. 1242004' 2012.
    • (2012) Journal of Bioinformatics and Computational Biology , vol.10 , Issue.3 , pp. 1242004
  • 40
    • 0035955548 scopus 로고    scopus 로고
    • Crystal structure ofthe Escherichia coli RNA degradosome component enolase
    • Oct
    • K. Kuhnel and B. F. Luisi' "Crystal structure ofthe Escherichia coli RNA degradosome component enolase." J Mol BioI' vol. 313' no. 3' pp. 583-92' Oct. 2001.
    • (2001) J Mol BioI , vol.313 , Issue.3 , pp. 583-592
    • Kuhnel, K.1    Luisi, B.F.2
  • 43
    • 22044442973 scopus 로고    scopus 로고
    • Tyrosine kinases as targets for cancer therapy
    • D. Krause and R. Van Etten' "Tyrosine kinases as targets for cancer therapy'" New England Journal ofMedicine' vol. 353' no. 2' pp. 172-187' 2005.
    • (2005) New England Journal OfMedicine , vol.353 , Issue.2 , pp. 172-187
    • Krause, D.1    Van Etten, R.2
  • 44
    • 15944404601 scopus 로고    scopus 로고
    • The development of imatinib as a therapeutic agent for chronic myeloid leukemia
    • M. Deininger' E. Buchdunger' and B. Druker' "The development of imatinib as a therapeutic agent for chronic myeloid leukemia'" Blood' vol. 105' no. 7' pp. 2640-2653' 2005.
    • (2005) Blood , vol.105 , Issue.7 , pp. 2640-2653
    • Deininger, M.1    Buchdunger, E.2    Druker, B.3
  • 45
    • 0031709073 scopus 로고    scopus 로고
    • A molecular gate which controls unnatural ATP analogue recognition by the tyrosine kinase v-Src
    • Aug
    • Y. Liu' K. Shah' F. Yang' L. Witucki' and K. M. Shokat' "A molecular gate which controls unnatural ATP analogue recognition by the tyrosine kinase v-Src." Bioorganic & medicinal chemistry' vol. 6' no. 8' pp. 1219-26' Aug. 1998.
    • (1998) Bioorganic & Medicinal Chemistry , vol.6 , Issue.8 , pp. 1219-1226
    • Liu, Y.1    Shah, K.2    Yang, F.3    Witucki, L.4    Shokat, K.M.5
  • 46
    • 15244350902 scopus 로고    scopus 로고
    • Targeting the gatekeeper residue in phosphoinositide 3-kinases
    • Apr
    • P. 1. Alaimo' Z. a. Knight' and K. M. Shokat' "Targeting the gatekeeper residue in phosphoinositide 3-kinases." Bioorganic & medicinal chemistry' vol. 13' no. 8' pp. 2825-36' Apr. 2005.
    • (2005) Bioorganic & Medicinal Chemistry , vol.13 , Issue.8 , pp. 2825-2836
    • Alaimo, P.J.1    Knight, Z.A.2    Shokat, K.M.3


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