메뉴 건너뛰기




Volumn 81, Issue 1, 2013, Pages 81-92

Combining coarse-grained nonbonded and atomistic bonded interactions for protein modeling

Author keywords

Biased force field; Binding site prediction; Docking by energy minimization; Protein protein complex formation; Protein protein interaction

Indexed keywords

HYBRID PROTEIN;

EID: 84871061224     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.24164     Document Type: Article
Times cited : (23)

References (36)
  • 1
    • 84861367246 scopus 로고    scopus 로고
    • Biomolecular simulation: a computational microscope for molecular biology
    • Dror RO, Dirks RM, Grossman JP, Xu H, Shaw DE. Biomolecular simulation: a computational microscope for molecular biology. Annu Rev Biophys 2012; 41: 429-452.
    • (2012) Annu Rev Biophys , vol.41 , pp. 429-452
    • Dror, R.O.1    Dirks, R.M.2    Grossman, J.P.3    Xu, H.4    Shaw, D.E.5
  • 2
    • 0016610491 scopus 로고
    • Computer simulation of protein folding
    • Levitt M, Warshel A. Computer simulation of protein folding. Nature 1975; 253: 694-698.
    • (1975) Nature , vol.253 , pp. 694-698
    • Levitt, M.1    Warshel, A.2
  • 3
    • 14044266389 scopus 로고    scopus 로고
    • Ab initio simulations of protein folding pathways by molecular dynamics with united-residue model of polypeptide chains
    • Liwo A, Khalili M, Scheraga HA. Ab initio simulations of protein folding pathways by molecular dynamics with united-residue model of polypeptide chains. Proc Natl Acad Sci USA 2005; 102: 2362-2367.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 2362-2367
    • Liwo, A.1    Khalili, M.2    Scheraga, H.A.3
  • 4
    • 21144442648 scopus 로고    scopus 로고
    • Physics-based protein-structure prediction using a hierarchical protocol based on the UNRES force field: assessment in two blind tests
    • Gibson KD, Scheraga HA. Physics-based protein-structure prediction using a hierarchical protocol based on the UNRES force field: assessment in two blind tests. Proc Natl Acad Sci USA 2005; 102: 7547-7552.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 7547-7552
    • Gibson, K.D.1    Scheraga, H.A.2
  • 5
    • 34247098754 scopus 로고    scopus 로고
    • Multiscale modeling of biomolecular systems: in serial and in parallel
    • Ayton GS, Noid WG, Voth GA. Multiscale modeling of biomolecular systems: in serial and in parallel. Curr Opin Struct Biol 2007; 17: 192-198.
    • (2007) Curr Opin Struct Biol , vol.17 , pp. 192-198
    • Ayton, G.S.1    Noid, W.G.2    Voth, G.A.3
  • 6
    • 33847116895 scopus 로고    scopus 로고
    • Flap opening dynamics in HIV-1 protease explored with a coarse-grained model
    • Tozzini V, Trylska J, Chang CE, McCammon JA. Flap opening dynamics in HIV-1 protease explored with a coarse-grained model. J Struct Biol 2007; 157: 606-615.
    • (2007) J Struct Biol , vol.157 , pp. 606-615
    • Tozzini, V.1    Trylska, J.2    Chang, C.E.3    McCammon, J.A.4
  • 7
    • 34548809141 scopus 로고    scopus 로고
    • A coarse-grained protein force field for folding and structure prediction
    • Maupetit J, Tuffery P, Derreumaux P. A coarse-grained protein force field for folding and structure prediction. Proteins 2007; 69: 394-408.
    • (2007) Proteins , vol.69 , pp. 394-408
    • Maupetit, J.1    Tuffery, P.2    Derreumaux, P.3
  • 9
    • 84862529711 scopus 로고    scopus 로고
    • Simple model for the simulation of peptide folding and aggregation with different sequences
    • Enisco M, Rey A. Simple model for the simulation of peptide folding and aggregation with different sequences. J Chem Phys 2012; 136: 215103.
    • (2012) J Chem Phys , vol.136 , pp. 215103
    • Enisco, M.1    Rey, A.2
  • 10
    • 68949144755 scopus 로고    scopus 로고
    • Coarse-grained description of protein internal dynamics: an optimal strategy for decomposing proteins in rigid subunits
    • Potestio R, Pontiggia F, Micheletti C. Coarse-grained description of protein internal dynamics: an optimal strategy for decomposing proteins in rigid subunits. Biophys J 2009; 96: 4993-5002.
    • (2009) Biophys J , vol.96 , pp. 4993-5002
    • Potestio, R.1    Pontiggia, F.2    Micheletti, C.3
  • 11
    • 73549096657 scopus 로고    scopus 로고
    • Transferable coarse grain nonbonded interaction model for amino acids
    • DeVane R, Shinoda W, Moore PB, Klein ML. Transferable coarse grain nonbonded interaction model for amino acids. J Chem Theory Comput 2009; 5: 2115-2124.
    • (2009) J Chem Theory Comput , vol.5 , pp. 2115-2124
    • DeVane, R.1    Shinoda, W.2    Moore, P.B.3    Klein, M.L.4
  • 12
    • 72449144639 scopus 로고    scopus 로고
    • Coarse-grained protein model with residue orientation energies derived from atomic force fields
    • Betancourt MR. Coarse-grained protein model with residue orientation energies derived from atomic force fields. J Phys Chem B 2009; 113: 14824-14830.
    • (2009) J Phys Chem B , vol.113 , pp. 14824-14830
    • Betancourt, M.R.1
  • 13
    • 77950477912 scopus 로고    scopus 로고
    • Investigation of protein folding by coarse-grained molecular dynamics with the UNRES force field
    • Maisuradze GG, Senet P, Czaplewski C, Liwo A, Scheraga HA. Investigation of protein folding by coarse-grained molecular dynamics with the UNRES force field. J Phys Chem A 2010; 114: 4471-4485.
    • (2010) J Phys Chem A , vol.114 , pp. 4471-4485
    • Maisuradze, G.G.1    Senet, P.2    Czaplewski, C.3    Liwo, A.4    Scheraga, H.A.5
  • 14
    • 77955487466 scopus 로고    scopus 로고
    • Multiscale coarse-graining of the protein energy landscape
    • Hills RDJr, Lu L, Voth GA. Multiscale coarse-graining of the protein energy landscape. PLoS Comput Biol 2010; 6: e1000827.
    • (2010) PLoS Comput Biol , vol.6
    • Hills Jr, R.D.1    Lu, L.2    Voth, G.A.3
  • 15
    • 79959873730 scopus 로고    scopus 로고
    • Simulation of chaperonin effect on protein folding: a shift from nucleation-condensation to framework mechanism
    • Kmiecik S, Kolinski A. Simulation of chaperonin effect on protein folding: a shift from nucleation-condensation to framework mechanism. J Am Chem Soc 2011; 133: 10283-10289.
    • (2011) J Am Chem Soc , vol.133 , pp. 10283-10289
    • Kmiecik, S.1    Kolinski, A.2
  • 16
    • 39149100599 scopus 로고    scopus 로고
    • Coarse-grained models of protein folding: toy models or predictive tools?
    • Clementi C. Coarse-grained models of protein folding: toy models or predictive tools? Curr Opin Struct Biol 2008; 18: 10-15.
    • (2008) Curr Opin Struct Biol , vol.18 , pp. 10-15
    • Clementi, C.1
  • 18
    • 80053277257 scopus 로고    scopus 로고
    • Coarse-grained force field: general folding theory
    • Liwo A, He Y, Scheraga HA. Coarse-grained force field: general folding theory. Phys Chem Chem Phys 2011; 13: 16890-16901.
    • (2011) Phys Chem Chem Phys , vol.13 , pp. 16890-16901
    • Liwo, A.1    He, Y.2    Scheraga, H.A.3
  • 20
    • 80054031361 scopus 로고    scopus 로고
    • Free energies for coarse-grained proteins by integrating multibody statistical contact potentials with entropies from elastic network models
    • Zimmermann MT, Leelananda SP, Gniewek P, Feng Y, Jernigan RL, Kloczkowski A Free energies for coarse-grained proteins by integrating multibody statistical contact potentials with entropies from elastic network models. J Struct Funct Genomics 2011; 12: 137-147.
    • (2011) J Struct Funct Genomics , vol.12 , pp. 137-147
    • Zimmermann, M.T.1    Leelananda, S.P.2    Gniewek, P.3    Feng, Y.4    Jernigan, R.L.5    Kloczkowski, A.6
  • 21
    • 79955737158 scopus 로고    scopus 로고
    • Multibody coarse-grained potentials for native structure recognition and quality assessment of protein models
    • Gniewek P, Leelananda SP, Kolinski A, Jernigan RL, Kloczkowski A. Multibody coarse-grained potentials for native structure recognition and quality assessment of protein models. Proteins 2011; 79: 1923-1929.
    • (2011) Proteins , vol.79 , pp. 1923-1929
    • Gniewek, P.1    Leelananda, S.P.2    Kolinski, A.3    Jernigan, R.L.4    Kloczkowski, A.5
  • 22
    • 0031585984 scopus 로고    scopus 로고
    • Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions
    • Simons KT, Kooperberg C, Huang E, Baker D. Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J Mol Biol 1997; 268: 209-225.
    • (1997) J Mol Biol , vol.268 , pp. 209-225
    • Simons, K.T.1    Kooperberg, C.2    Huang, E.3    Baker, D.4
  • 23
    • 0038583687 scopus 로고    scopus 로고
    • Protein-protein docking using a reduced model
    • Zacharias, M. Protein-protein docking using a reduced model. Protein Sci 2003; 12: 1271-1282.
    • (2003) Protein Sci , vol.12 , pp. 1271-1282
    • Zacharias, M.1
  • 24
    • 77957958670 scopus 로고    scopus 로고
    • Binding site prediction and improved scoring during flexible protein-protein docking with ATTRACT
    • Fiorucci S, Zacharias M. Binding site prediction and improved scoring during flexible protein-protein docking with ATTRACT. Proteins 2010; 78: 3131-3139.
    • (2010) Proteins , vol.78 , pp. 3131-3139
    • Fiorucci, S.1    Zacharias, M.2
  • 26
    • 36749107785 scopus 로고
    • Molecular dynamics simulations at constant pressure and/or temperature
    • Andersen HC. Molecular dynamics simulations at constant pressure and/or temperature. J Chem Phys 1980; 72: 2384-2393.
    • (1980) J Chem Phys , vol.72 , pp. 2384-2393
    • Andersen, H.C.1
  • 28
    • 84855263403 scopus 로고    scopus 로고
    • Accounting for conformational changes during protein-protein docking
    • Zacharias, M. Accounting for conformational changes during protein-protein docking. Curr Opin Struct Biol 2010; 16: 194-200.
    • (2010) Curr Opin Struct Biol , vol.16 , pp. 194-200
    • Zacharias, M.1
  • 29
    • 0030941458 scopus 로고    scopus 로고
    • P53, the cellular gatekeeper for growth and division
    • Levine AJ. P53, the cellular gatekeeper for growth and division. Cell 1997; 88: 323-331.
    • (1997) Cell , vol.88 , pp. 323-331
    • Levine, A.J.1
  • 31
    • 0034657187 scopus 로고    scopus 로고
    • Structural basis of the Axin-adenomatous polyposis coli interaction
    • Spink KE, Polakis P, Weis WI. Structural basis of the Axin-adenomatous polyposis coli interaction. EMBO J 2000; 19: 2270-2279.
    • (2000) EMBO J , vol.19 , pp. 2270-2279
    • Spink, K.E.1    Polakis, P.2    Weis, W.I.3
  • 32
    • 38549097715 scopus 로고    scopus 로고
    • Energy minimization in low-frequency normal modes to efficiently allow for global flexibility during systematic protein-protein docking
    • May A, Zacharias M. Energy minimization in low-frequency normal modes to efficiently allow for global flexibility during systematic protein-protein docking. Proteins 2008, 70: 794-809.
    • (2008) Proteins , vol.70 , pp. 794-809
    • May, A.1    Zacharias, M.2
  • 33
    • 84855256224 scopus 로고    scopus 로고
    • Scoring optimisation of unbound protein-protein docking including protein binding site predictions
    • Schneider S, Zacharias M. Scoring optimisation of unbound protein-protein docking including protein binding site predictions. J Mol Recognit 2012; 25: 15-23.
    • (2012) J Mol Recognit , vol.25 , pp. 15-23
    • Schneider, S.1    Zacharias, M.2
  • 34
    • 80053999690 scopus 로고    scopus 로고
    • Enhancing systematic protein-protein docking methods using ray casting: application to ATTRACT
    • Li Y, Cortés J, Siméon T. Enhancing systematic protein-protein docking methods using ray casting: application to ATTRACT. Proteins 2011; 79: 3037-3049.
    • (2011) Proteins , vol.79 , pp. 3037-3049
    • Li, Y.1    Cortés, J.2    Siméon, T.3
  • 35
    • 51349091797 scopus 로고    scopus 로고
    • Identification of protein interaction partners and protein-protein interaction sites
    • Sacquin-Mora S, Carbone A, Lavery R. Identification of protein interaction partners and protein-protein interaction sites. J Mol Biol 2008; 382: 1276-1289.
    • (2008) J Mol Biol , vol.382 , pp. 1276-1289
    • Sacquin-Mora, S.1    Carbone, A.2    Lavery, R.3
  • 36
    • 0034283147 scopus 로고    scopus 로고
    • Specificity in protein-protein interactions: the structural basis fordual recognition in endonuclease colicin-immunity protein complexes
    • Kuhlmann UC, Pommer AJ, Moore GR, James R, Kleanthous C. Specificity in protein-protein interactions: the structural basis fordual recognition in endonuclease colicin-immunity protein complexes. J Mol Biol 2000; 301: 1163-1178.
    • (2000) J Mol Biol , vol.301 , pp. 1163-1178
    • Kuhlmann, U.C.1    Pommer, A.J.2    Moore, G.R.3    James, R.4    Kleanthous, C.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.