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Volumn 84, Issue S1, 2016, Pages 131-144

New encouraging developments in contact prediction: Assessment of the CASP11 results

Author keywords

CASP; co variation; contact prediction; correlated mutations; evolutionary coupling

Indexed keywords

ESCHERICHIA COLI PROTEIN; PROTEIN; YAAA PROTEIN, E COLI;

EID: 84947707636     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.24943     Document Type: Article
Times cited : (73)

References (47)
  • 1
    • 0031307080 scopus 로고    scopus 로고
    • CASP2: report on ab initio predictions
    • Lesk AM. CASP2: report on ab initio predictions. Proteins 1997;(Suppl 1):151–166.
    • (1997) Proteins , pp. 151-166
    • Lesk, A.M.1
  • 2
    • 0032828469 scopus 로고    scopus 로고
    • Analysis and assessment of ab initio three-dimensional prediction, secondary structure, and contacts prediction
    • Orengo CA, Bray JE, Hubbard T, LoConte L, Sillitoe I. Analysis and assessment of ab initio three-dimensional prediction, secondary structure, and contacts prediction. Proteins 1999;(Suppl 3):149–170.
    • (1999) Proteins , pp. 149-170
    • Orengo, C.A.1    Bray, J.E.2    Hubbard, T.3    LoConte, L.4    Sillitoe, I.5
  • 3
    • 0035703008 scopus 로고    scopus 로고
    • Assessment of novel fold targets in CASP4: predictions of three-dimensional structures, secondary structures, and interresidue contacts
    • Lesk AM, Lo Conte L, Hubbard TJ. Assessment of novel fold targets in CASP4: predictions of three-dimensional structures, secondary structures, and interresidue contacts. Proteins 2001;(Suppl 5):98–118.
    • (2001) Proteins , pp. 98-118
    • Lesk, A.M.1    Lo Conte, L.2    Hubbard, T.J.3
  • 4
    • 0242299187 scopus 로고    scopus 로고
    • Predictions without templates: new folds, secondary structure, and contacts in CASP5
    • Aloy P, Stark A, Hadley C, Russell RB. Predictions without templates: new folds, secondary structure, and contacts in CASP5. Proteins 2003;53:436–456.
    • (2003) Proteins , vol.53 , pp. 436-456
    • Aloy, P.1    Stark, A.2    Hadley, C.3    Russell, R.B.4
  • 7
    • 74249108517 scopus 로고    scopus 로고
    • Assessment of domain boundary predictions and the prediction of intramolecular contacts in CASP8
    • Ezkurdia I, Grana O, Izarzugaza JM, Tress ML. Assessment of domain boundary predictions and the prediction of intramolecular contacts in CASP8. Proteins 2009;77:196–209.
    • (2009) Proteins , vol.77 , pp. 196-209
    • Ezkurdia, I.1    Grana, O.2    Izarzugaza, J.M.3    Tress, M.L.4
  • 10
    • 0028084754 scopus 로고
    • Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations?
    • Shindyalov IN, Kolchanov NA, Sander C. Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations? Protein Eng 1994;7:349–358.
    • (1994) Protein Eng , vol.7 , pp. 349-358
    • Shindyalov, I.N.1    Kolchanov, N.A.2    Sander, C.3
  • 11
    • 0028295169 scopus 로고
    • Correlated mutations and residue contacts in proteins
    • Gobel U, Sander C, Schneider R, Valencia A. Correlated mutations and residue contacts in proteins. Proteins 1994;18:309–317.
    • (1994) Proteins , vol.18 , pp. 309-317
    • Gobel, U.1    Sander, C.2    Schneider, R.3    Valencia, A.4
  • 12
    • 76749112068 scopus 로고    scopus 로고
    • Disentangling direct from indirect co-evolution of residues in protein alignments
    • Burger L, van Nimwegen E. Disentangling direct from indirect co-evolution of residues in protein alignments. PLoS Comput Biol 2010;6:e1000633.
    • (2010) PLoS Comput Biol , vol.6
    • Burger, L.1    van Nimwegen, E.2
  • 13
    • 58549114185 scopus 로고    scopus 로고
    • Identification of direct residue contacts in protein-protein interaction by message passing
    • Weigt M, White RA, Szurmant H, Hoch JA, Hwa T. Identification of direct residue contacts in protein-protein interaction by message passing. Proc Natl Acad Sci USA 2009;106:67–72.
    • (2009) Proc Natl Acad Sci USA , vol.106 , pp. 67-72
    • Weigt, M.1    White, R.A.2    Szurmant, H.3    Hoch, J.A.4    Hwa, T.5
  • 15
    • 84869447010 scopus 로고    scopus 로고
    • Protein structure prediction from sequence variation
    • Marks DS, Hopf TA, Sander C. Protein structure prediction from sequence variation. Nat Biotechnol 2012;30:1072–1080.
    • (2012) Nat Biotechnol , vol.30 , pp. 1072-1080
    • Marks, D.S.1    Hopf, T.A.2    Sander, C.3
  • 19
    • 84856090271 scopus 로고    scopus 로고
    • PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments
    • Jones DT, Buchan DW, Cozzetto D, Pontil M. PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments. Bioinformatics 2012;28:184–190.
    • (2012) Bioinformatics , vol.28 , pp. 184-190
    • Jones, D.T.1    Buchan, D.W.2    Cozzetto, D.3    Pontil, M.4
  • 20
    • 84929144039 scopus 로고    scopus 로고
    • MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins
    • Jones DT, Singh T, Kosciolek T, Tetchner S. MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins. Bioinformatics 2015;31:999–1006.
    • (2015) Bioinformatics , vol.31 , pp. 999-1006
    • Jones, D.T.1    Singh, T.2    Kosciolek, T.3    Tetchner, S.4
  • 21
    • 84884603324 scopus 로고    scopus 로고
    • Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era
    • Kamisetty H, Ovchinnikov S, Baker D. Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era. Proc Natl Acad Sci USA 2013;110:15674–15679.
    • (2013) Proc Natl Acad Sci USA , vol.110 , pp. 15674-15679
    • Kamisetty, H.1    Ovchinnikov, S.2    Baker, D.3
  • 22
    • 84899847547 scopus 로고    scopus 로고
    • Robust and accurate prediction of residue-residue interactions across protein interfaces using evolutionary information
    • Ovchinnikov S, Kamisetty H, Baker D. Robust and accurate prediction of residue-residue interactions across protein interfaces using evolutionary information. eLife 2014;3:e02030.
    • (2014) eLife , vol.3
    • Ovchinnikov, S.1    Kamisetty, H.2    Baker, D.3
  • 23
    • 84905637666 scopus 로고    scopus 로고
    • Fast pseudolikelihood maximization for direct-coupling analysis of protein structure from many homologous amino-acid sequences
    • Ekeberg M, Hartonen T, Aurell E. Fast pseudolikelihood maximization for direct-coupling analysis of protein structure from many homologous amino-acid sequences. J Comput Phys 2014;276:341–356.
    • (2014) J Comput Phys , vol.276 , pp. 341-356
    • Ekeberg, M.1    Hartonen, T.2    Aurell, E.3
  • 25
    • 84880209883 scopus 로고    scopus 로고
    • PconsC: combination of direct information methods and alignments improves contact prediction
    • Skwark MJ, Abdel-Rehim A, Elofsson A. PconsC: combination of direct information methods and alignments improves contact prediction. Bioinformatics 2013;29:1815–1816.
    • (2013) Bioinformatics , vol.29 , pp. 1815-1816
    • Skwark, M.J.1    Abdel-Rehim, A.2    Elofsson, A.3
  • 26
    • 84912100015 scopus 로고    scopus 로고
    • Improved contact predictions using the recognition of protein like contact patterns
    • Skwark MJ, Raimondi D, Michel M, Elofsson A. Improved contact predictions using the recognition of protein like contact patterns. PLoS Comput Biol 2014;10:e1003889.
    • (2014) PLoS Comput Biol , vol.10
    • Skwark, M.J.1    Raimondi, D.2    Michel, M.3    Elofsson, A.4
  • 28
    • 84899072164 scopus 로고    scopus 로고
    • FreeContact: fast and free software for protein contact prediction from residue co-evolution
    • Kajan L, Hopf TA, Kalas M, Marks DS, Rost B. FreeContact: fast and free software for protein contact prediction from residue co-evolution. BMC Bioinformatics 2014;15:85.
    • (2014) BMC Bioinformatics , vol.15 , pp. 85.
    • Kajan, L.1    Hopf, T.A.2    Kalas, M.3    Marks, D.S.4    Rost, B.5
  • 31
    • 84893010856 scopus 로고    scopus 로고
    • CASP prediction center infrastructure and evaluation measures in CASP10 and CASP ROLL
    • Kryshtafovych A, Monastyrskyy B, Fidelis K. CASP prediction center infrastructure and evaluation measures in CASP10 and CASP ROLL. Proteins 2014;82(Suppl 2):7–13.
    • (2014) Proteins , vol.82 , pp. 7-13
    • Kryshtafovych, A.1    Monastyrskyy, B.2    Fidelis, K.3
  • 32
    • 84892968997 scopus 로고    scopus 로고
    • CASP10 results compared to those of previous CASP experiments
    • Kryshtafovych A, Fidelis K, Moult J. CASP10 results compared to those of previous CASP experiments. Proteins 2014;82:164–174.
    • (2014) Proteins , vol.82 , pp. 164-174
    • Kryshtafovych, A.1    Fidelis, K.2    Moult, J.3
  • 34
    • 0034657861 scopus 로고    scopus 로고
    • Bootstrap confidence intervals: when, which, what? A practical guide for medical statisticians
    • Carpenter J, Bithell J. Bootstrap confidence intervals: when, which, what? A practical guide for medical statisticians. Stat Med 2000;19:1141–1164.
    • (2000) Stat Med , vol.19 , pp. 1141-1164
    • Carpenter, J.1    Bithell, J.2
  • 35
    • 2942733491 scopus 로고    scopus 로고
    • Overlapping confidence intervals or standard error intervals: what do they mean in terms of statistical significance?
    • Payton ME, Greenstone MH, Schenker N. Overlapping confidence intervals or standard error intervals: what do they mean in terms of statistical significance? J Insect Sci 2003;3:34.
    • (2003) J Insect Sci , vol.3 , pp. 34.
    • Payton, M.E.1    Greenstone, M.H.2    Schenker, N.3
  • 36
    • 84870415234 scopus 로고    scopus 로고
    • Predicting protein residue-residue contacts using deep networks and boosting
    • Eickholt J, Cheng J. Predicting protein residue-residue contacts using deep networks and boosting. Bioinformatics 2012;28:3066–3072.
    • (2012) Bioinformatics , vol.28 , pp. 3066-3072
    • Eickholt, J.1    Cheng, J.2
  • 37
    • 67849110005 scopus 로고    scopus 로고
    • NNcon: improved protein contact map prediction using 2D-recursive neural networks
    • Tegge AN, Wang Z, Eickholt J, Cheng J. NNcon: improved protein contact map prediction using 2D-recursive neural networks. Nucleic Acids Res 2009;37:W515–W518.
    • (2009) Nucleic Acids Res , vol.37 , pp. W515-W518
    • Tegge, A.N.1    Wang, Z.2    Eickholt, J.3    Cheng, J.4
  • 38
    • 77955591777 scopus 로고    scopus 로고
    • Hidden Markov model speed heuristic and iterative HMM search procedure
    • Johnson LS, Eddy SR, Portugaly E. Hidden Markov model speed heuristic and iterative HMM search procedure. BMC Bioinformatics 2010;11:431.
    • (2010) BMC Bioinformatics , vol.11 , pp. 431.
    • Johnson, L.S.1    Eddy, S.R.2    Portugaly, E.3
  • 39
    • 84856489442 scopus 로고    scopus 로고
    • HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment
    • Remmert M, Biegert A, Hauser A, Soding J. HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nat Methods 2012;9:173–175.
    • (2012) Nat Methods , vol.9 , pp. 173-175
    • Remmert, M.1    Biegert, A.2    Hauser, A.3    Soding, J.4
  • 40
    • 84879976691 scopus 로고    scopus 로고
    • Predicting protein contact map using evolutionary and physical constraints by integer programming
    • Wang Z, Xu J. Predicting protein contact map using evolutionary and physical constraints by integer programming. Bioinformatics 2013;29:i266–i273.
    • (2013) Bioinformatics , vol.29 , pp. i266-i273
    • Wang, Z.1    Xu, J.2
  • 41
    • 84908542331 scopus 로고    scopus 로고
    • Combining physicochemical and evolutionary information for protein contact prediction
    • Schneider M, Brock O. Combining physicochemical and evolutionary information for protein contact prediction. PLoS One 2014;9:e108438.
    • (2014) PLoS One , vol.9
    • Schneider, M.1    Brock, O.2
  • 42
  • 44
    • 84939515755 scopus 로고    scopus 로고
    • Accurate contact predictions using covariation techniques and machine learning
    • [Epub ahead of print]
    • Kosciolek T, Jones DT. Accurate contact predictions using covariation techniques and machine learning. Proteins 2015. doi:10.1002/prot.24863. [Epub ahead of print].
    • (2015) Proteins
    • Kosciolek, T.1    Jones, D.T.2
  • 45
    • 84898619057 scopus 로고    scopus 로고
    • De novo structure prediction of globular proteins aided by sequence variation-derived contacts
    • Kosciolek T, Jones DT. De novo structure prediction of globular proteins aided by sequence variation-derived contacts. PLoS One 2014;9:e92197.
    • (2014) PLoS One , vol.9
    • Kosciolek, T.1    Jones, D.T.2
  • 46
  • 47
    • 67849103757 scopus 로고    scopus 로고
    • SAM-T08, HMM-based protein structure prediction
    • –W
    • Karplus K. SAM-T08, HMM-based protein structure prediction. Nucleic Acids Res 2009;37:W492–W497.
    • (2009) Nucleic Acids Res , vol.37 , pp. W492-497
    • Karplus, K.1


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