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Volumn 25, Issue 23, 2009, Pages 3099-3107

LIBRUS: Combined machine learning and homology information for sequence-based ligand-binding residue prediction

Author keywords

[No Author keywords available]

Indexed keywords

LIGAND; PROTEIN;

EID: 75949116562     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btp561     Document Type: Article
Times cited : (23)

References (24)
  • 1
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
    • Altschul, S. et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 3389-3402
    • Altschul, S.1
  • 2
    • 0033954256 scopus 로고    scopus 로고
    • The Protein Data Bank
    • Berman, H.M. et al. (2000) The Protein Data Bank. Nucleic Acids Res., 28, 235-242.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 235-242
    • Berman, H.M.1
  • 3
    • 0038387389 scopus 로고    scopus 로고
    • Hit and lead generation: beyond high-throughput screening
    • Bleicher, K.H. et al. (2003) Hit and lead generation: beyond high-throughput screening. Nat. Rev. Drug Discov., 2, 369-378.
    • (2003) Nat. Rev. Drug Discov. , vol.2 , pp. 369-378
    • Bleicher, K.H.1
  • 4
    • 26944463088 scopus 로고    scopus 로고
    • Virtuals creen for ligands of orphan g protein-coupled receptors
    • Bock, J.R. and Gough, D.A. (2005)Virtuals creen for ligands of orphan g protein-coupled receptors. J. Chem. Inf. Model., 45, 1402-1414.
    • (2005) J. Chem. Inf. Model. , vol.45 , pp. 1402-1414
    • Bock, J.R.1    Gough, D.A.2
  • 5
    • 38349100452 scopus 로고    scopus 로고
    • A threading-based method (findsite) for ligand-binding site prediction and functional annotation
    • Brylinski, M. and Skolnick, J. (2008) A threading-based method (findsite) for ligand-binding site prediction and functional annotation. Proc. Natl Acad. Sci. USA, 105, 129-134.
    • (2008) Proc. Natl Acad. Sci. USA , vol.105 , pp. 129-134
    • Brylinski, M.1    Skolnick, J.2
  • 6
    • 0036089049 scopus 로고    scopus 로고
    • Astral compendium enhancements
    • Chandonia, J.-M. et al. (2002) Astral compendium enhancements. Nucleic Acids Res., 30, 260-263.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 260-263
    • Chandonia, J.-M.1
  • 7
    • 36448960843 scopus 로고    scopus 로고
    • Pfres: protein fold classification by using evolutionary information and predicted secondary structure
    • Chen, K. and Kurgan, L. (2007) Pfres: protein fold classification by using evolutionary information and predicted secondary structure. Bioinformatics, 23, 2843-2850.
    • (2007) Bioinformatics , vol.23 , pp. 2843-2850
    • Chen, K.1    Kurgan, L.2
  • 8
    • 33646023117 scopus 로고    scopus 로고
    • An introduction to ROC analysis
    • Fawcett, T. (2006)An introduction to ROC analysis. Pattern Recogn. Lett., 27, 861-874.
    • (2006) Pattern Recogn. Lett. , vol.27 , pp. 861-874
    • Fawcett, T.1
  • 9
    • 40049091146 scopus 로고    scopus 로고
    • Prediction of protein functional residues from sequence by probability density estimation
    • Fischer, J.D. et al. (2008) Prediction of protein functional residues from sequence by probability density estimation. Bioinformatics, 24, 613-620.
    • (2008) Bioinformatics , vol.24 , pp. 613-620
    • Fischer, J.D.1
  • 10
    • 0042121000 scopus 로고    scopus 로고
    • ORFeus: detection of distant homology using sequence profiles and predicted secondary structure
    • Ginalski, K. et al. (2003) ORFeus: detection of distant homology using sequence profiles and predicted secondary structure. Nucleic Acids Res., 31, 3804-3807.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3804-3807
    • Ginalski, K.1
  • 11
    • 0035070578 scopus 로고    scopus 로고
    • Picasso: generating a covering set of protein family profiles
    • Heger, A. and Holm, L. (2001) Picasso: generating a covering set of protein family profiles. Bioinformatics, 17, 272-279.
    • (2001) Bioinformatics , vol.17 , pp. 272-279
    • Heger, A.1    Holm, L.2
  • 13
    • 33746267388 scopus 로고    scopus 로고
    • YASSPP: better kernels and coding schemes lead to improvements in SVM-based secondary structure prediction
    • Karypis, G. (2006) YASSPP: better kernels and coding schemes lead to improvements in SVM-based secondary structure prediction. Proteins Struct. Funct. Bioinform., 64, 575-586.
    • (2006) Proteins Struct. Funct. Bioinform. , vol.64 , pp. 575-586
    • Karypis, G.1
  • 14
    • 85086810601 scopus 로고    scopus 로고
    • Improving homology models for protein-ligand binding sites
    • San Francisco, CA. Available at, (last accessed date October 12, 2009)
    • Kauffman, C. et al. (2008) Improving homology models for protein-ligand binding sites. In LSS Comput Syst Bioinformatics Conference, San Francisco, CA. Available at www.cs.umn.edu/~karypis (last accessed date October 12, 2009).
    • (2008) LSS Comput Syst Bioinformatics Conference
    • Kauffman, C.1
  • 15
    • 34547575992 scopus 로고    scopus 로고
    • firestar-prediction of functionally important residues using structural templates and alignment reliability
    • López, G. et al. (2007) firestar-prediction of functionally important residues using structural templates and alignment reliability. Nucleic Acids Res., 35, W573-W577.
    • (2007) Nucleic Acids Res. , vol.35
    • López, G.1
  • 16
    • 0041886960 scopus 로고    scopus 로고
    • Probabilistic scoring measures for profile-profile comparison yield more accurate short seed alignments
    • Mittelman, D. et al. (2003) Probabilistic scoring measures for profile-profile comparison yield more accurate short seed alignments. Bioinformatics, 19, 1531-1539.
    • (2003) Bioinformatics , vol.19 , pp. 1531-1539
    • Mittelman, D.1
  • 17
    • 40349087133 scopus 로고    scopus 로고
    • Towards the development of universal, fast and highly accurate docking//scoring methods: a long way to go
    • Moitessier, N. et al. (2007) Towards the development of universal, fast and highly accurate docking//scoring methods: a long way to go. Br. J. Pharmacol., 153, S7-S26.
    • (2007) Br. J. Pharmacol. , vol.153
    • Moitessier, N.1
  • 18
    • 33746950964 scopus 로고    scopus 로고
    • Prediction of catalytic residues using support vector machine with selected protein sequence and structural properties
    • Petrova, N.V. and Wu, C.H. (2006) Prediction of catalytic residues using support vector machine with selected protein sequence and structural properties. BMC Bioinformatics, 7, 312.
    • (2006) BMC Bioinformatics , vol.7 , pp. 312
    • Petrova, N.V.1    Wu, C.H.2
  • 19
    • 38449083927 scopus 로고    scopus 로고
    • frmsdpred: predicting local RMSD between structural fragments using sequence information
    • Rangwala, H. and Karypis, G. (2007) frmsdpred: predicting local RMSD between structural fragments using sequence information. Comput. Syst. Bioinform. Conf., 6, 311-322.
    • (2007) Comput. Syst. Bioinform. Conf. , vol.6 , pp. 311-322
    • Rangwala, H.1    Karypis, G.2
  • 21
    • 13044272912 scopus 로고    scopus 로고
    • Automated analysis of interatomic contacts in proteins
    • Sobolev, V. et al. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332.
    • (1999) Bioinformatics , vol.15 , pp. 327-332
    • Sobolev, V.1
  • 23
    • 0035993847 scopus 로고    scopus 로고
    • Systematic optimization of a lead-structure identities for a selective short peptide agonist for the human orphan receptor BRS-3
    • Weber, D. et al. (2002) Systematic optimization of a lead-structure identities for a selective short peptide agonist for the human orphan receptor BRS-3. J. Pept. Sci., 8, 461-475.
    • (2002) J. Pept. Sci. , vol.8 , pp. 461-475
    • Weber, D.1
  • 24
    • 33846554792 scopus 로고    scopus 로고
    • Evaluation of features for catalytic residue prediction in novel folds
    • Youn, E. et al. (2007) Evaluation of features for catalytic residue prediction in novel folds. Protein Sci., 16, 216-226.
    • (2007) Protein Sci. , vol.16 , pp. 216-226
    • Youn, E.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.