메뉴 건너뛰기




Volumn 43, Issue 2, 2015, Pages e10-

Mechismo: Predicting the mechanistic impact of mutations and modifications on molecular interactions

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

EID: 84941125727     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gku1094     Document Type: Article
Times cited : (75)

References (64)
  • 1
    • 84875552595 scopus 로고    scopus 로고
    • Diagnostic cancer genome sequencing and the contribution of germline variants
    • Kilpivaara,O. and Aaltonen,L. A. (2013) Diagnostic cancer genome sequencing and the contribution of germline variants. Science, 339, 1559-1562.
    • (2013) Science , vol.339 , pp. 1559-1562
    • Kilpivaara, O.1    Aaltonen, L.A.2
  • 2
    • 77952956167 scopus 로고    scopus 로고
    • Decoding signalling networks by mass spectrometry-based proteomics
    • Choudhary,C. and Mann,M. (2010) Decoding signalling networks by mass spectrometry-based proteomics. Nat. Rev. Mol. Cell Biol., 11, 427-439.
    • (2010) Nat. Rev. Mol. Cell Biol. , vol.11 , pp. 427-439
    • Choudhary, C.1    Mann, M.2
  • 4
    • 84871967106 scopus 로고    scopus 로고
    • Interactome3D: Adding structural details to protein networks
    • Mosca,R., Céol,A. and Aloy,P. (2013) Interactome3D: adding structural details to protein networks. Nat. Methods, 10, 47-53.
    • (2013) Nat. Methods , vol.10 , pp. 47-53
    • Mosca, R.1    Céol, A.2    Aloy, P.3
  • 5
    • 47849091218 scopus 로고    scopus 로고
    • Architectures and functional coverage of protein-protein interfaces
    • Tuncbag,N., Gursoy,A., Guney,E., Nussinov,R. and Keskin,O. (2008) Architectures and functional coverage of protein-protein interfaces. J. Mol. Biol., 381, 785-802.
    • (2008) J. Mol. Biol. , vol.381 , pp. 785-802
    • Tuncbag, N.1    Gursoy, A.2    Guney, E.3    Nussinov, R.4    Keskin, O.5
  • 6
    • 33644876493 scopus 로고    scopus 로고
    • SCOPPI: A structural classification of protein-protein interfaces
    • Winter,C., Henschel,A., Kim,W. K. and Schroeder,M. (2006) SCOPPI: a structural classification of protein-protein interfaces. Nucleic Acids Res., 34, D310-D314.
    • (2006) Nucleic Acids Res. , vol.34 , pp. D310-D314
    • Winter, C.1    Henschel, A.2    Kim, W.K.3    Schroeder, M.4
  • 7
    • 0042386609 scopus 로고    scopus 로고
    • The relationship between sequence and interaction divergence in proteins
    • Aloy,P., Ceulemans,H., Stark,A. and Russell,R. B. (2003) The relationship between sequence and interaction divergence in proteins. J. Mol. Biol., 332, 989-998.
    • (2003) J. Mol. Biol. , vol.332 , pp. 989-998
    • Aloy, P.1    Ceulemans, H.2    Stark, A.3    Russell, R.B.4
  • 12
    • 84863010950 scopus 로고    scopus 로고
    • Three-dimensional reconstruction of protein networks provides insight into human genetic disease
    • Wang,X., Wei,X., Thijssen,B., Das,J., Lipkin,S. M. and Yu,H. (2012) Three-dimensional reconstruction of protein networks provides insight into human genetic disease. Nat. Biotechnol., 30, 159-164.
    • (2012) Nat. Biotechnol. , vol.30 , pp. 159-164
    • Wang, X.1    Wei, X.2    Thijssen, B.3    Das, J.4    Lipkin, S.M.5    Yu, H.6
  • 14
    • 78651344377 scopus 로고    scopus 로고
    • 3did: Identification and classification of domain-based interactions of known three-dimensional structure
    • Stein,A., Céol,A. and Aloy,P. (2011) 3did: identification and classification of domain-based interactions of known three-dimensional structure. Nucleic Acids Res., 39, D718-D723.
    • (2011) Nucleic Acids Res. , vol.39 , pp. D718-D723
    • Stein, A.1    Céol, A.2    Aloy, P.3
  • 17
    • 84877109655 scopus 로고    scopus 로고
    • Chapter 7, Unit7. 20
    • Protoc. Hum. Genet., Chapter 7, Unit7. 20, doi:10. 1002/0471142905. hg0720s76.
    • Protoc. Hum. Genet
  • 18
    • 68149165614 scopus 로고    scopus 로고
    • Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm
    • Kumar,P., Henikoff,S. and Ng,P. C. (2009) Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat. Protoc., 4, 1073-1081.
    • (2009) Nat. Protoc. , vol.4 , pp. 1073-1081
    • Kumar, P.1    Henikoff, S.2    Ng, P.C.3
  • 19
    • 80053189298 scopus 로고    scopus 로고
    • Predicting the functional impact of protein mutations: Application to cancer genomics
    • Reva,B., Antipin,Y. and Sander,C. (2011) Predicting the functional impact of protein mutations: application to cancer genomics. Nucleic Acids Res., 39, e118.
    • (2011) Nucleic Acids Res. , vol.39 , pp. e118
    • Reva, B.1    Antipin, Y.2    Sander, C.3
  • 20
    • 84885190937 scopus 로고    scopus 로고
    • The effects of non-synonymous single nucleotide polymorphisms (nsSNPs) on protein-protein interactions
    • Yates,C. M. and Sternberg,M. J. E. (2013) The effects of non-synonymous single nucleotide polymorphisms (nsSNPs) on protein-protein interactions. J. Mol. Biol., 425, 3949-3963.
    • (2013) J. Mol. Biol. , vol.425 , pp. 3949-3963
    • Yates, C.M.1    Sternberg, M.J.E.2
  • 21
    • 79953715693 scopus 로고    scopus 로고
    • Improving the assessment of the outcome of nonsynonymous SNVs with a consensus deleteriousness score, Condel
    • González-Pérez,A. and López-Bigas,N. (2011) Improving the assessment of the outcome of nonsynonymous SNVs with a consensus deleteriousness score, Condel. Am. J. Hum. Genet., 88, 440-449.
    • (2011) Am. J. Hum. Genet , vol.88 , pp. 440-449
    • González-Pérez, A.1    López-Bigas, N.2
  • 22
    • 84857790275 scopus 로고    scopus 로고
    • Protein-protein interaction sites are hot spots for disease-associated nonsynonymous SNPS
    • David,A., Razali,R., Wass,M. N. and Sternberg,M. J. E. (2012) Protein-protein interaction sites are hot spots for disease-associated nonsynonymous SNPs. Hum. Mutat., 33, 359-363.
    • (2012) Hum. Mutat , vol.33 , pp. 359-363
    • David, A.1    Razali, R.2    Wass, M.N.3    Sternberg, M.J.E.4
  • 23
    • 33750353461 scopus 로고    scopus 로고
    • Predicting the effects of amino acid substitutions on protein function
    • Ng,P. C. and Henikoff,S. (2006) Predicting the effects of amino acid substitutions on protein function. Annu. Rev. Genomics Hum. Genet., 7, 61-80.
    • (2006) Annu. Rev. Genomics Hum. Genet , vol.7 , pp. 61-80
    • Ng, P.C.1    Henikoff, S.2
  • 24
    • 67149088375 scopus 로고    scopus 로고
    • Connecting protein interaction data, mutations, and disease using bioinformatics
    • Chen,J. Y., Youn,E. and Mooney,S. D. (2009) Connecting protein interaction data, mutations, and disease using bioinformatics. Methods Mol. Biol., 541, 449-461.
    • (2009) Methods Mol. Biol. , vol.541 , pp. 449-461
    • Chen, J.Y.1    Youn, E.2    Mooney, S.D.3
  • 26
    • 0031683688 scopus 로고    scopus 로고
    • Apert syndrome mutations in fibroblast growth factor receptor 2 exhibit increased affinity for FGF ligand
    • Anderson,J., Burns,H. D., Enriquez-Harris,P.,Wilkie,A. O. and Heath,J. K. (1998) Apert syndrome mutations in fibroblast growth factor receptor 2 exhibit increased affinity for FGF ligand. Hum. Mol. Genet., 7, 1475-1483.
    • (1998) Hum. Mol. Genet , vol.7 , pp. 1475-1483
    • Anderson, J.1    Burns, H.D.2    Enriquez-Harris, P.3    Wilkie, A.O.4    Heath, J.K.5
  • 29
    • 77957371355 scopus 로고    scopus 로고
    • Promoting a structural view of biology for varied audiences: An overview of RCSB PDB resources and experiences
    • Dutta,S., Zardecki,C., Goodsell,D. S. and Berman,H. M. (2010) Promoting a structural view of biology for varied audiences: an overview of RCSB PDB resources and experiences. J. Appl. Crystallogr., 43, 1224-1229.
    • (2010) J. Appl. Crystallogr. , vol.43 , pp. 1224-1229
    • Dutta, S.1    Zardecki, C.2    Goodsell, D.S.3    Berman, H.M.4
  • 31
    • 79958081489 scopus 로고    scopus 로고
    • Combinations of protein-chemical complex structures reveal new targets for established drugs
    • Kalinina,O. V.,Wichmann,O., Apic,G. and Russell,R. B. (2011) Combinations of protein-chemical complex structures reveal new targets for established drugs. PLoS Comput. Biol., 7, e1002043.
    • (2011) PLoS Comput. Biol. , vol.7 , pp. e1002043
    • Kalinina, O.V.1    Wichmann, O.2    Apic, G.3    Russell, R.B.4
  • 37
    • 24044538903 scopus 로고    scopus 로고
    • IUPred: Web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content
    • Dosztányi,Z., Csizmok,V., Tompa,P. and Simon,I. (2005) IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content. Bioinformatics, 21, 3433-3434.
    • (2005) Bioinformatics , vol.21 , pp. 3433-3434
    • Dosztányi, Z.1    Csizmok, V.2    Tompa, P.3    Simon, I.4
  • 38
    • 0037245913 scopus 로고    scopus 로고
    • BIND: The biomolecular interaction network database
    • Bader,G. D., Betel,D. and Hogue,C. W. V. (2003) BIND: the Biomolecular Interaction Network Database. Nucleic Acids Res., 31, 248-250.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 248-250
    • Bader, G.D.1    Betel, D.2    Hogue, C.W.V.3
  • 46
    • 39749166860 scopus 로고    scopus 로고
    • Phosphoproteome analysis of e coli reveals evolutionary conservation of bacterial Ser/Thr/Tyr phosphorylation
    • Macek,B., Gnad,F., Soufi,B., Kumar,C., Olsen,J. V, Mijakovic,I. and Mann,M. (2008) Phosphoproteome analysis of E. coli reveals evolutionary conservation of bacterial Ser/Thr/Tyr phosphorylation. Mol. Cell. Proteomics, 7, 299-307.
    • (2008) Mol. Cell. Proteomics , vol.7 , pp. 299-307
    • Macek, B.1    Gnad, F.2    Soufi, B.3    Kumar, C.4    Olsen, V.J.5    Mijakovic, I.6    Mann, M.7
  • 48
    • 0037197902 scopus 로고    scopus 로고
    • Interrogating protein interaction networks through structural biology
    • Aloy,P. and Russell,R. B. (2002) Interrogating protein interaction networks through structural biology. Proc. Natl. Acad. Sci. U. S. A., 99, 5896-5901.
    • (2002) Proc. Natl. Acad. Sci. U. S. A , vol.99 , pp. 5896-5901
    • Aloy, P.1    Russell, R.B.2
  • 49
    • 84891811692 scopus 로고    scopus 로고
    • Scope: Structural classification of proteins-extended, integrating scop and astral data and classification of new structures
    • Fox,N. K., Brenner,S. E. and Chandonia,J.-M. (2014) SCOPe: Structural Classification of Proteins-extended, integrating SCOP and ASTRAL data and classification of new structures. Nucleic Acids Res., 42, D304-D309.
    • (2014) Nucleic Acids Res. , vol.42 , pp. D304-D309
    • Fox, N.K.1    Brenner, S.E.2    Chandonia, J.-M.3
  • 50
    • 2942610863 scopus 로고    scopus 로고
    • Visualisation and graph-theoretic analysis of a large-scale protein structural interactome
    • Bolser,D., Dafas,P., Harrington,R., Park,J. and Schroeder,M. (2003) Visualisation and graph-theoretic analysis of a large-scale protein structural interactome. BMC Bioinformat., 4, 45.
    • (2003) BMC Bioinformat , vol.4 , pp. 45
    • Bolser, D.1    Dafas, P.2    Harrington, R.3    Park, J.4    Schroeder, M.5
  • 51
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch,W. and Sander,C. (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22, 2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 52
    • 0027136282 scopus 로고
    • Comparative protein modelling by satisfaction of spatial restraints
    • Sali,A. and Blundell,T. L. (1993) Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol., 234, 779-815.
    • (1993) J. Mol. Biol. , vol.234 , pp. 779-815
    • Sali, A.1    Blundell, T.L.2
  • 55
    • 0025341310 scopus 로고
    • Calculation of conformational ensembles from potentials of mean force,an approach to the knowledge-based prediction of local structures in globular proteins
    • Sippl,M. J. (1990) Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins. J. Mol. Biol., 213, 859-883.
    • (1990) J. Mol. Biol. , vol.213 , pp. 859-883
    • Sippl, M.J.1
  • 56
    • 0037229456 scopus 로고    scopus 로고
    • Analysing six types of protein-protein interfaces
    • Ofran,Y. and Rost,B. (2003) Analysing six types of protein-protein interfaces. J. Mol. Biol., 325, 377-387.
    • (2003) J. Mol. Biol. , vol.325 , pp. 377-387
    • Ofran, Y.1    Rost, B.2
  • 57
    • 33745658056 scopus 로고    scopus 로고
    • Acetylation of estrogen receptor alpha by p300 at lysines 266 and 268 enhances the deoxyribonucleic acid binding and transactivation activities of the receptor
    • Kim,M. Y., Woo,E. M., Chong,Y. T. E., Homenko,D. R. and Kraus,W. L. (2006) Acetylation of estrogen receptor alpha by p300 at lysines 266 and 268 enhances the deoxyribonucleic acid binding and transactivation activities of the receptor. Mol. Endocrinol., 20, 1479-1493.
    • (2006) Mol. Endocrinol. , vol.20 , pp. 1479-1493
    • Kim, M.Y.1    Woo, E.M.2    Chong, Y.T.E.3    Homenko, D.R.4    Kraus, W.L.5
  • 58
    • 4644355809 scopus 로고    scopus 로고
    • The architecture of metal coordination groups in proteins
    • Harding,M. M. (2004) The architecture of metal coordination groups in proteins. Acta Crystallogr. D. Biol. Crystallogr., 60, 849-859.
    • (2004) Acta Crystallogr. D. Biol. Crystallogr. , vol.60 , pp. 849-859
    • Harding, M.M.1
  • 60
    • 39749099893 scopus 로고    scopus 로고
    • Exploiting 3D structural templates for detection of metal-binding sites in protein structures
    • Goyal,K. and Mande,S. C. (2008) Exploiting 3D structural templates for detection of metal-binding sites in protein structures. Proteins, 70, 1206-1218.
    • (2008) Proteins , vol.70 , pp. 1206-1218
    • Goyal, K.1    Mande, S.C.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.