메뉴 건너뛰기




Volumn 83, Issue 8, 2015, Pages 1436-1449

CONFOLD: Residue-residue contact-guided ab initio protein folding

Author keywords

Ab initio protein folding; Contact assisted protein structure prediction; Optimization; Protein residue residue contacts; Protein structure modeling

Indexed keywords

HYDROGEN; PROTEIN; AMINO ACID;

EID: 84937727830     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.24829     Document Type: Article
Times cited : (129)

References (49)
  • 3
    • 34247247779 scopus 로고    scopus 로고
    • Improved residue contact prediction using support vector machines and a large feature set
    • Cheng J, Baldi P. Improved residue contact prediction using support vector machines and a large feature set. BMC Bioinformatics 2007;8:113.
    • (2007) BMC Bioinformatics , vol.8 , pp. 113
    • Cheng, J.1    Baldi, P.2
  • 4
    • 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
  • 5
    • 0035663988 scopus 로고    scopus 로고
    • Prediction of contact maps with neural networks and correlated mutations
    • Fariselli P, Olmea O, Valencia A, Casadio R. Prediction of contact maps with neural networks and correlated mutations. Protein Eng 2001;14:835-843.
    • (2001) Protein Eng , vol.14 , pp. 835-843
    • Fariselli, P.1    Olmea, O.2    Valencia, A.3    Casadio, R.4
  • 6
    • 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
  • 7
    • 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
  • 8
    • 80051490632 scopus 로고    scopus 로고
    • Improving protein structure prediction using multiple sequence-based contact predictions. Structure
    • Wu S, Szilagyi A, Zhang Y. Improving protein structure prediction using multiple sequence-based contact predictions. Structure 2011;19:1182-1191.
    • (2011) , vol.19 , pp. 1182-1191
    • Wu, S.1    Szilagyi, A.2    Zhang, Y.3
  • 11
    • 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
  • 12
    • 84911444768 scopus 로고    scopus 로고
    • CCMpred-fast and precise prediction of protein residue-residue contacts from correlated mutations
    • Seemayer S, Gruber M, Söding J. CCMpred-fast and precise prediction of protein residue-residue contacts from correlated mutations. Bioinformatics 2014;30:3128-3130.
    • (2014) Bioinformatics , vol.30 , pp. 3128-3130
    • Seemayer, S.1    Gruber, M.2    Söding, J.3
  • 13
    • 84899072164 scopus 로고    scopus 로고
    • FreeContact: fast and free software for protein contact prediction from residue co-evolution
    • Kaján L, Hopf TA, 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
    • Kaján, L.1    Hopf, T.A.2    Marks, D.S.3    Rost, B.4
  • 14
    • 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
  • 15
    • 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
  • 16
    • 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 , pp. e1003889
    • Skwark, M.J.1    Raimondi, D.2    Michel, M.3    Elofsson, A.4
  • 19
    • 77952748293 scopus 로고    scopus 로고
    • In Carugo O, Eisenhaber F editors. Data mining techniques for the life sciences. New York: Springer
    • Pirovano W, Heringa J. Protein secondary structure prediction. In Carugo O, Eisenhaber F editors. Data mining techniques for the life sciences. New York: Springer; 2010. pp 327-348.
    • (2010) Protein secondary structure prediction , pp. 327-348
    • Pirovano, W.1    Heringa, J.2
  • 20
    • 48449106792 scopus 로고    scopus 로고
    • The jpred 3 secondary structure prediction server
    • Cole C, Barber JD, Barton GJ. The jpred 3 secondary structure prediction server. Nucl Acids Res 2008;36:W197-W201.
    • (2008) Nucl Acids Res , vol.36 , pp. W197-W201
    • Cole, C.1    Barber, J.D.2    Barton, G.J.3
  • 21
    • 23144465987 scopus 로고    scopus 로고
    • SCRATCH: a protein structure and structural feature prediction server
    • Cheng J, Randall AZ, Sweredoski MJ, Baldi P. SCRATCH: a protein structure and structural feature prediction server. Nucl Acids Res 2005;33:W72-W76.
    • (2005) Nucl Acids Res , vol.33 , pp. W72-W76
    • Cheng, J.1    Randall, A.Z.2    Sweredoski, M.J.3    Baldi, P.4
  • 22
    • 83855162773 scopus 로고    scopus 로고
    • SPINE X: improving protein secondary structure prediction by multistep learning coupled with prediction of solvent accessible surface area and backbone torsion angles
    • Faraggi E, Zhang T, Yang Y, Kurgan L, Zhou Y. SPINE X: improving protein secondary structure prediction by multistep learning coupled with prediction of solvent accessible surface area and backbone torsion angles. J Comput Chem 2012;33:259-267.
    • (2012) J Comput Chem , vol.33 , pp. 259-267
    • Faraggi, E.1    Zhang, T.2    Yang, Y.3    Kurgan, L.4    Zhou, Y.5
  • 23
    • 0033578684 scopus 로고    scopus 로고
    • Protein secondary structure prediction based on position-specific scoring matrices
    • Jones DT. Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 1999;292:195-202.
    • (1999) J Mol Biol , vol.292 , pp. 195-202
    • Jones, D.T.1
  • 26
    • 43349102979 scopus 로고    scopus 로고
    • FT-COMAR: fault tolerant three-dimensional structure reconstruction from protein contact maps
    • Vassura M, Margara L, Di Lena P, Medri F, Fariselli P, Casadio R. FT-COMAR: fault tolerant three-dimensional structure reconstruction from protein contact maps. Bioinformatics 2008;24:1313-1315.
    • (2008) Bioinformatics , vol.24 , pp. 1313-1315
    • Vassura, M.1    Margara, L.2    Di Lena, P.3    Medri, F.4    Fariselli, P.5    Casadio, R.6
  • 27
    • 0030627407 scopus 로고    scopus 로고
    • Recovery of protein structure from contact maps
    • Vendruscolo M, Kussell E, Domany E. Recovery of protein structure from contact maps. Fold Des 1997;2:295-306.
    • (1997) Fold Des , vol.2 , pp. 295-306
    • Vendruscolo, M.1    Kussell, E.2    Domany, E.3
  • 29
    • 0000935435 scopus 로고    scopus 로고
    • Distance geometry optimization for protein structures
    • Moré JJ, Wu Z. Distance geometry optimization for protein structures. J Global Optim 1999;15:219-234.
    • (1999) J Global Optim , vol.15 , pp. 219-234
    • Moré, J.J.1    Wu, Z.2
  • 30
    • 79952789413 scopus 로고    scopus 로고
    • On the reconstruction of three-dimensional protein structures from contact maps
    • Di Lena P, Vassura M, Margara L, Fariselli P, Casadio R. On the reconstruction of three-dimensional protein structures from contact maps. Algorithms 2009;2:76-92.
    • (2009) Algorithms , vol.2 , pp. 76-92
    • Di Lena, P.1    Vassura, M.2    Margara, L.3    Fariselli, P.4    Casadio, R.5
  • 32
    • 84988112508 scopus 로고
    • TINKER molecular modeling package
    • Ponder J, Richards F. TINKER molecular modeling package. J Comput Chem 1987;8:1016-1024.
    • (1987) J Comput Chem , vol.8 , pp. 1016-1024
    • Ponder, J.1    Richards, F.2
  • 33
    • 84898854997 scopus 로고    scopus 로고
    • Automated procedure for contact-map-based protein structure reconstruction
    • Konopka BM, Ciombor M, Kurczynska M, Kotulska M. Automated procedure for contact-map-based protein structure reconstruction. J Membr Biol 2014;247:409-420.
    • (2014) J Membr Biol , vol.247 , pp. 409-420
    • Konopka, B.M.1    Ciombor, M.2    Kurczynska, M.3    Kotulska, M.4
  • 38
    • 37049014272 scopus 로고    scopus 로고
    • Version 1.2 of the crystallography and NMR system
    • Brunger AT. Version 1.2 of the crystallography and NMR system. Nat Protoc 2007;2:2728-2733.
    • (2007) Nat Protoc , vol.2 , pp. 2728-2733
    • Brunger, A.T.1
  • 39
    • 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 , pp. e92197
    • Kosciolek, T.1    Jones, D.T.2
  • 40
    • 16344394781 scopus 로고    scopus 로고
    • SABmark-a benchmark for sequence alignment that covers the entire known fold space
    • Van Walle I, Lasters I, Wyns L. SABmark-a benchmark for sequence alignment that covers the entire known fold space. Bioinformatics 2005;21:1267-1268.
    • (2005) Bioinformatics , vol.21 , pp. 1267-1268
    • Van Walle, I.1    Lasters, I.2    Wyns, L.3
  • 41
    • 0020991935 scopus 로고
    • Structural properties of protein β-sheets
    • Salemme F. Structural properties of protein β-sheets. Prog Biophys Mol Biol 1983;42:95-133.
    • (1983) Prog Biophys Mol Biol , vol.42 , pp. 95-133
    • Salemme, F.1
  • 42
    • 0019880377 scopus 로고
    • Conformational geometrical properties of β-sheets in proteins: II. Antiparallel and mixed β-sheets
    • Salemme F, Weatherford D. Conformational geometrical properties of β-sheets in proteins: II. Antiparallel and mixed β-sheets. J Mol Biol 1981;146:119-141.
    • (1981) J Mol Biol , vol.146 , pp. 119-141
    • Salemme, F.1    Weatherford, D.2
  • 44
    • 84860507958 scopus 로고    scopus 로고
    • Three-stage prediction of protein β-sheets by neural networks, alignments and graph algorithms
    • Cheng J, Baldi P. Three-stage prediction of protein β-sheets by neural networks, alignments and graph algorithms. Bioinformatics 2005;21:i75-i84.
    • (2005) Bioinformatics , vol.21 , pp. i75-i84
    • Cheng, J.1    Baldi, P.2
  • 45
    • 0025890946 scopus 로고
    • Influence of proline residues on protein conformation
    • MacArthur MW, Thornton JM. Influence of proline residues on protein conformation. J Mol Biol 1991;218:397-412.
    • (1991) J Mol Biol , vol.218 , pp. 397-412
    • MacArthur, M.W.1    Thornton, J.M.2
  • 47
    • 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
  • 48
    • 17644392830 scopus 로고    scopus 로고
    • TM-align: a protein structure alignment algorithm based on the TM-score
    • Zhang Y, Skolnick J. TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res 2005;33:2302-2309.
    • (2005) Nucleic Acids Res , vol.33 , pp. 2302-2309
    • Zhang, Y.1    Skolnick, J.2
  • 49
    • 0034780030 scopus 로고    scopus 로고
    • Pcons: a neural-network-based consensus predictor that improves fold recognition
    • Lundström J, Rychlewski L, Bujnicki J, Elofsson A. Pcons: a neural-network-based consensus predictor that improves fold recognition. Protein Sci 2001;10:2354-2362.
    • (2001) Protein Sci , vol.10 , pp. 2354-2362
    • Lundström, J.1    Rychlewski, L.2    Bujnicki, J.3    Elofsson, A.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.