메뉴 건너뛰기




Volumn 44, Issue 1, 2016, Pages W361-W366

CoinFold: a web server for protein contact prediction and contact-assisted protein folding

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; EVOLUTION; EVOLUTIONARY COUPLING; INFORMATION PROCESSING; PREDICTION; PROTEIN CONTACT; PROTEIN FAMILY; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; PROTEIN TERTIARY STRUCTURE; SOFTWARE; SUPERVISED MACHINE LEARNING; ALGORITHM; CHEMISTRY; COMPUTER GRAPHICS; COMPUTER INTERFACE; GENETICS; INTERNET; MACHINE LEARNING; MOLECULAR MODEL; PROTEIN DOMAIN; SEQUENCE ANALYSIS; STATIC ELECTRICITY;

EID: 84990885355     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/NAR/GKW307     Document Type: Article
Times cited : (52)

References (29)
  • 1
    • 84867316765 scopus 로고    scopus 로고
    • Deep architectures for protein contact map prediction
    • Di Lena,P., Nagata,K. and Baldi,P. (2012) Deep architectures for protein contact map prediction. Bioinformatics, 28, 2449-2457.
    • (2012) Bioinformatics , vol.28 , pp. 2449-2457
    • Di Lena, P.1    Nagata, K.2    Baldi, P.3
  • 2
    • 84892997887 scopus 로고    scopus 로고
    • One contact for every twelve residues allows robust and accurate topology-level protein structure modeling
    • Kim,D.E., DiMaio,F., Yu-Ruei Wang,R., Song,Y. and Baker,D. (2014) One contact for every twelve residues allows robust and accurate topology-level protein structure modeling. Proteins: Struct. Funct. Bioinform., 82, 208-218.
    • (2014) Proteins: Struct. Funct. Bioinform , vol.82 , pp. 208-218
    • Kim, D.E.1    DiMaio, F.2    Yu-Ruei Wang, R.3    Song, Y.4    Baker, D.5
  • 3
    • 84875225476 scopus 로고    scopus 로고
    • Emerging methods in protein co-evolution
    • de Juan,D., Pazos,F. and Valencia,A. (2013) Emerging methods in protein co-evolution. Nat. Rev. Genet., 14, 249-261.
    • (2013) Nat. Rev. Genet , vol.14 , pp. 249-261
    • de Juan, D.1    Pazos, F.2    Valencia, A.3
  • 4
    • 84869447010 scopus 로고    scopus 로고
    • Protein structure prediction from sequence variation
    • Marks,D.S., Hopf,T.A. and Sander,C. (2012) Protein structure prediction from sequence variation. Nat. Biotechnol., 30, 1072-1080.
    • (2012) Nat. Biotechnol , vol.30 , pp. 1072-1080
    • Marks, D.S.1    Hopf, T.A.2    Sander, C.3
  • 7
    • 84856090271 scopus 로고    scopus 로고
    • PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments
    • Jones,D.T., Buchan,D.W., Cozzetto,D. and Pontil,M. (2012) PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments. Bioinformatics, 28, 184-190.
    • (2012) Bioinformatics , vol.28 , pp. 184-190
    • Jones, D.T.1    Buchan, D.W.2    Cozzetto, D.3    Pontil, M.4
  • 8
    • 84872521100 scopus 로고    scopus 로고
    • Improved contact prediction in proteins: using pseudolikelihoods to infer Potts models
    • Ekeberg,M., Lövkvist,C., Lan,Y., Weigt,M. and Aurell,E. (2013) Improved contact prediction in proteins: using pseudolikelihoods to infer Potts models. Phys. Rev. E, 87, 012707.
    • (2013) Phys. Rev. E , vol.87 , pp. 012707
    • Ekeberg, M.1    Lövkvist, C.2    Lan, Y.3    Weigt, M.4    Aurell, E.5
  • 9
    • 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. and Baker,D. (2013) Assessing the utility of coevolution-based residue-residue contact predictions in a sequence-and structure-rich era. Proc. Natl. Acad. Sci., 110, 15674-15679.
    • (2013) Proc. Natl. Acad. Sci , vol.110 , pp. 15674-15679
    • Kamisetty, H.1    Ovchinnikov, S.2    Baker, D.3
  • 10
    • 84911444768 scopus 로고    scopus 로고
    • CCMpred-fast and precise prediction of protein residue-residue contacts from correlated mutations
    • Seemayer,S., Gruber,M. and Söding,J. (2014) CCMpred-fast and precise prediction of protein residue-residue contacts from correlated mutations. Bioinformatics, 30, 3128-3130.
    • (2014) Bioinformatics , vol.30 , pp. 3128-3130
    • Seemayer, S.1    Gruber, M.2    Söding, J.3
  • 11
    • 84893766307 scopus 로고    scopus 로고
    • The joint graphical lasso for inverse covariance estimation across multiple classes
    • Danaher,P., Wang,P. and Witten,D.M. (2014) The joint graphical lasso for inverse covariance estimation across multiple classes. J. Roy. Stat. Soc.: Ser. B (Stat. Methodol.), 76, 373-397.
    • (2014) J. Roy. Stat. Soc.: Ser. B (Stat. Methodol.) , vol.76 , pp. 373-397
    • Danaher, P.1    Wang, P.2    Witten, D.M.3
  • 12
    • 84947552221 scopus 로고    scopus 로고
    • Protein contact prediction by integrating joint evolutionary coupling analysis and supervised learning
    • Ma,J., Wang,S., Wang,Z. and Xu,J. (2015) Protein contact prediction by integrating joint evolutionary coupling analysis and supervised learning. Bioinformatics, btv472.
    • (2015) Bioinformatics , pp. btv472
    • Ma, J.1    Wang, S.2    Wang, Z.3    Xu, J.4
  • 13
    • 84954113329 scopus 로고    scopus 로고
    • Protein secondary structure prediction using deep convolutional neural fields
    • Wang,S., Peng,J., Ma,J. and Xu,J. (2016) Protein secondary structure prediction using deep convolutional neural fields. Sci. Rep., 6, 18962.
    • (2016) Sci. Rep , vol.6 , pp. 18962
    • Wang, S.1    Peng, J.2    Ma, J.3    Xu, J.4
  • 16
    • 84879901270 scopus 로고    scopus 로고
    • Protein threading using context-specific alignment potential
    • Ma,J., Wang,S., Zhao,F. and Xu,J. (2013) Protein threading using context-specific alignment potential. Bioinformatics, 29, i257-i265.
    • (2013) Bioinformatics , vol.29 , pp. i257-i265
    • Ma, J.1    Wang, S.2    Zhao, F.3    Xu, J.4
  • 17
    • 84861977121 scopus 로고    scopus 로고
    • A position-specific distance-dependent statistical potential for protein structure and functional study
    • Zhao,F. and Xu,J. (2012) A position-specific distance-dependent statistical potential for protein structure and functional study. Structure, 20, 1118-1126.
    • (2012) Structure , vol.20 , pp. 1118-1126
    • Zhao, F.1    Xu, J.2
  • 18
    • 84938356212 scopus 로고    scopus 로고
    • AcconPred: Predicting solvent accessibility and contact number simultaneously by a multitask learning framework under the conditional neural fields model
    • Ma,J. and Wang,S. (2015) AcconPred: Predicting solvent accessibility and contact number simultaneously by a multitask learning framework under the conditional neural fields model. BioMed Res. Int., 2015, 1.
    • (2015) BioMed Res. Int , vol.2015 , pp. 1
    • Ma, J.1    Wang, S.2
  • 20
    • 84929144039 scopus 로고    scopus 로고
    • MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins
    • Jones,D.T., Singh,T., Kosciolek,T. and Tetchner,S. (2015) MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins. Bioinformatics, 31, 999-1006.
    • (2015) Bioinformatics , vol.31 , pp. 999-1006
    • Jones, D.T.1    Singh, T.2    Kosciolek, T.3    Tetchner, S.4
  • 22
    • 84856489442 scopus 로고    scopus 로고
    • HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment
    • Remmert,M., Biegert,A., Hauser,A. and Söding,J. (2012) HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nat. Methods, 9, 173-175.
    • (2012) Nat. Methods , vol.9 , pp. 173-175
    • Remmert, M.1    Biegert, A.2    Hauser, A.3    Söding, J.4
  • 23
    • 16344373015 scopus 로고    scopus 로고
    • Protein homology detection by HMM-HMM comparison
    • Söding,J. (2005) Protein homology detection by HMM-HMM comparison. Bioinformatics, 21, 951-960.
    • (2005) Bioinformatics , vol.21 , pp. 951-960
    • Söding, J.1
  • 24
    • 10344232638 scopus 로고    scopus 로고
    • Scoring function for automated assessment of protein structure template quality
    • Zhang,Y. and Skolnick,J. (2004) Scoring function for automated assessment of protein structure template quality. Proteins: Struct. Funct. Bioinform., 57, 702-710.
    • (2004) Proteins: Struct. Funct. Bioinform , vol.57 , pp. 702-710
    • Zhang, Y.1    Skolnick, J.2
  • 26
    • 84883481556 scopus 로고    scopus 로고
    • The Protein Model Portal-a comprehensive resource for protein structure and model information
    • Haas,J., Roth,S., Arnold,K., Kiefer,F., Schmidt,T., Bordoli,L. and Schwede,T. (2013) The Protein Model Portal-a comprehensive resource for protein structure and model information. Database, 2013, bat031.
    • (2013) Database , vol.2013 , pp. bat031
    • Haas, J.1    Roth, S.2    Arnold, K.3    Kiefer, F.4    Schmidt, T.5    Bordoli, L.6    Schwede, T.7
  • 27
    • 84864448769 scopus 로고    scopus 로고
    • Template-based protein structure modeling using the RaptorX web server
    • Källberg,M., Wang,H., Wang,S., Peng,J., Wang,Z., Lu,H. and Xu,J. (2012) Template-based protein structure modeling using the RaptorX web server. Nat. Protoc., 7, 1511-1522.
    • (2012) Nat. Protoc , vol.7 , pp. 1511-1522
    • Källberg, M.1    Wang, H.2    Wang, S.3    Peng, J.4    Wang, Z.5    Lu, H.6    Xu, J.7
  • 28
  • 29
    • 84953267041 scopus 로고    scopus 로고
    • Combining evolutionary information and an iterative sampling strategy for accurate protein structure prediction
    • Braun,T., Leman,J.K. and Lange,O.F. (2015) Combining evolutionary information and an iterative sampling strategy for accurate protein structure prediction. PLoS Comput. Biol., 11, e1004661.
    • (2015) PLoS Comput. Biol , vol.11 , pp. e1004661
    • Braun, T.1    Leman, J.K.2    Lange, O.F.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.