메뉴 건너뛰기




Volumn 76, Issue 4, 2009, Pages 930-945

Building and assessing atomic models of proteins from structural templates: Learning and benchmarks

Author keywords

Feature selection; Homology modeling; Mathematical programming; Structure determination

Indexed keywords

ALGORITHM; ARTICLE; INFORMATION SERVICE; LEARNING; MATHEMATICAL MODEL; ONLINE SYSTEM; PRIORITY JOURNAL; PROTEIN DATA BANK; PROTEIN STRUCTURE; QUALITY CONTROL; STRUCTURAL HOMOLOGY; STRUCTURE ANALYSIS; SYSTEM ANALYSIS; TRAINING;

EID: 68149132088     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22401     Document Type: Article
Times cited : (22)

References (25)
  • 2
    • 47349110113 scopus 로고    scopus 로고
    • A template-finding algorithm and a comprehensive benchmark for homology modeling of proteins
    • DOI 10.1002/prot.21976
    • Vallat BK, Pillardy J, Elber R. A template-finding algorithm and a comprehensive benchmark for homology modeling of proteins. Proteins 2008;72:910-928. (Pubitemid 352000869)
    • (2008) Proteins: Structure, Function and Genetics , vol.72 , Issue.3 , pp. 910-928
    • Vallat, B.K.1    Pillardy, J.2    Elber, R.3
  • 4
    • 33644837197 scopus 로고    scopus 로고
    • SSALN: An alignment algorithm using structure-dependent substitution matrices and gap penalties learned from structurally aligned protein pairs
    • DOI 10.1002/prot.20854
    • Qiu J, Elber R. SSALN: An alignment algorithm using structuredependent substitution matrices and gap penalties learned from structurally aligned protein pairs. Proteins 2006;62:881-891. (Pubitemid 43364153)
    • (2006) Proteins: Structure, Function and Genetics , vol.62 , Issue.4 , pp. 881-891
    • Qiu, J.1    Elber, R.2
  • 5
    • 0028961335 scopus 로고
    • SCOP - A structural classification of proteins database for the investigation of sequences and structures
    • Murzin AG, Brenner SE, Hubbard T, Chothia C. SCOP - a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 1995;247:536-540.
    • (1995) J Mol Biol , vol.247 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 7
    • 17644392830 scopus 로고    scopus 로고
    • TM-align: A protein structure alignment algorithm based on the TM-score
    • DOI 10.1093/nar/gki524
    • Zhang Y, Skolnick J. TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res 2005;33:2302-2309. (Pubitemid 41439897)
    • (2005) Nucleic Acids Research , vol.33 , Issue.7 , pp. 2302-2309
    • Zhang, Y.1    Skolnick, J.2
  • 8
    • 20444484434 scopus 로고    scopus 로고
    • A decade of CASP: Progress, bottlenecks and prognosis in protein structure prediction
    • DOI 10.1016/j.sbi.2005.05.011, PII S0959440X05000953
    • Moult J. A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction. Curr Opin Struct Biol 2005;15:285-289. (Pubitemid 40826447)
    • (2005) Current Opinion in Structural Biology , vol.15 , Issue.3 SPEC. ISS , pp. 285-289
    • Moult, J.1
  • 10
    • 4043052866 scopus 로고    scopus 로고
    • Accurate prediction of solvent accessibility using neural networks-based regression
    • DOI 10.1002/prot.20176
    • Adamczak R, Porollo A, Meller J. Accurate prediction of solvent accessibility using neural networks-based regression. Proteins 2004;56:753-767. (Pubitemid 39063318)
    • (2004) Proteins: Structure, Function and Genetics , vol.56 , Issue.4 , pp. 753-767
    • Adamczak, R.1    Porollo, A.2    Meller, J.3
  • 11
    • 17844392864 scopus 로고    scopus 로고
    • Combining prediction of secondary structure and solvent accessibility in proteins
    • DOI 10.1002/prot.20441
    • Adamczak R, Porollo A, Meller J. Combining prediction of secondary structure and solvent accessibility in proteins. Proteins 2005;59:467-475. (Pubitemid 40594291)
    • (2005) Proteins: Structure, Function and Genetics , vol.59 , Issue.3 , pp. 467-475
    • Adamczak, R.1    Porollo, A.2    Meller, J.3
  • 12
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure- Pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch W, Sander C. Dictionary of protein secondary structure- pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983;22:2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 13
    • 0035889689 scopus 로고    scopus 로고
    • Linear programming optimization and a double statistical filter for protein threading protocols
    • DOI 10.1002/prot.1145
    • Meller J, Elber R. Linear programming optimization and a double statistical filter for protein threading protocols. Proteins: Struct Funct Genet 2001;45:241-261. (Pubitemid 32988586)
    • (2001) Proteins: Structure, Function and Genetics , vol.45 , Issue.3 , pp. 241-261
    • Meller, J.1    Elber, R.2
  • 14
    • 23044531267 scopus 로고    scopus 로고
    • Protein recognition by sequence-to-structure fitness: Bridging efficiency and capacity of threading models
    • Friesner RA, editor. New York: Wiley
    • Meller J, Elber R. Protein recognition by sequence-to-structure fitness: bridging efficiency and capacity of threading models. In: Friesner RA, editor. Computational methods for protein folding: a special volume of advances in chemical physics, Vol.20. New York: Wiley; 2002. pp 77-130.
    • (2002) Computational Methods for Protein Folding: A Special Volume of Advances in Chemical Physics , vol.20 , pp. 77-130
    • Meller, J.1    Elber, R.2
  • 15
    • 25644439091 scopus 로고    scopus 로고
    • Calibrating E-values for hidden Markov models using reverse-sequence null models
    • DOI 10.1093/bioinformatics/bti629
    • Karplus K, Karchin R, Shackelford G, Hughey R. Calibrating E-values for hidden Markov models using reverse-sequence null models. Bioinformatics 2005;21:4107-4115. (Pubitemid 41672100)
    • (2005) Bioinformatics , vol.21 , Issue.22 , pp. 4107-4115
    • Karplus, K.1    Karchin, R.2    Shackelford, G.3    Hughey, R.4
  • 17
    • 24344479166 scopus 로고    scopus 로고
    • Atomically detailed potentials to recognize native and approximate protein structures
    • Jian Qiu, Ron Elber. Atomically detailed potentials to recognize native and approximate protein structures. Proteins 2005;61:44-55.
    • (2005) Proteins , vol.61 , pp. 44-55
    • Qiu, J.1    Elber, R.2
  • 18
    • 0034308163 scopus 로고    scopus 로고
    • Distance-dependent, pair potential for protein folding: Results from linear optimization
    • DOI 10.1002/1097-0134(20001001)41:1<40::AID-PROT70>3.0.CO;2-U
    • Tobi D, Elber R. Distance dependent, pair potential for protein folding: Results from linear optimization. Proteins 2000;41:40-116 (Pubitemid 30666911)
    • (2000) Proteins: Structure, Function and Genetics , vol.41 , Issue.1 , pp. 40-46
    • Tobi, D.1    Elber, R.2
  • 19
    • 84860160829 scopus 로고    scopus 로고
    • A coarse grained potential for fold recognition and molecular dynamics simulations of proteins
    • in press
    • Májek P, Elber R. A coarse grained potential for fold recognition and molecular dynamics simulations of proteins. Proteins, in press.
    • Proteins
    • Májek, P.1    Elber, R.2
  • 20
    • 4744376072 scopus 로고    scopus 로고
    • On the transferability of folding and threading potentials and sequence-independent filters for protein folding simulations
    • Adamczak R, Meller J. On the transferability of folding and threading potentials and sequence-independent filters for protein folding simulations. Mol Phys 2004;102:1291-1305.
    • (2004) Mol Phys , vol.102 , pp. 1291-1305
    • Adamczak, R.1    Meller, J.2
  • 22
    • 1842857770 scopus 로고    scopus 로고
    • Large-scale linear programming techniques for the design of protein folding potentials
    • Wagner M, Meller J, Elber R. Large-scale linear programming techniques for the design of protein folding potentials. Math Program 2004;101:301-318.
    • (2004) Math Program , vol.101 , pp. 301-318
    • Wagner, M.1    Meller, J.2    Elber, R.3
  • 23
    • 0037079580 scopus 로고    scopus 로고
    • Maximum feasibility guideline in the design and analysis of protein folding potentials
    • DOI 10.1002/jcc.10014
    • Meller J, Wagner M, Elber R. Maximum feasibility guideline in the design and analysis of protein folding potentials. J Comput Chem 2002;23:111-118. (Pubitemid 34063135)
    • (2002) Journal of Computational Chemistry , vol.23 , Issue.1 , pp. 111-118
    • Meller, J.1    Wagner, M.2    Elber, R.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.