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Volumn 7, Issue 9, 1998, Pages 1998-2003

Distance geometry generates native-like folds for small helical proteins using the consensus distances of predicted protein structures

Author keywords

Ab initio folding; Distance geometry; Energy functions; Protein structure prediction

Indexed keywords

CALBINDIN; HOMEODOMAIN PROTEIN; PROTEIN; PROTEIN A; REPRESSOR PROTEIN;

EID: 0031687654     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1002/pro.5560070916     Document Type: Article
Times cited : (28)

References (37)
  • 1
    • 0029097099 scopus 로고
    • Global fold determination from a small number of distance restraints
    • Aszodi A, Gradwell MJ, Taylor WR. 1995. Global fold determination from a small number of distance restraints. J Mol Biol 251:308-326.
    • (1995) J Mol Biol , vol.251 , pp. 308-326
    • Aszodi, A.1    Gradwell, M.J.2    Taylor, W.R.3
  • 3
    • 0031576989 scopus 로고    scopus 로고
    • Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: A new homology modeling tool
    • Bower MJ, Cohen FE, Dunbrack RL Jr. 1997. Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: A new homology modeling tool. J Mol Biol 267:1268-1282.
    • (1997) J Mol Biol , vol.267 , pp. 1268-1282
    • Bower, M.J.1    Cohen, F.E.2    Dunbrack Jr., R.L.3
  • 4
    • 0028328263 scopus 로고
    • An evolutionary approach to folding small α-helical proteins that uses sequence information and an empirical guiding fitness function
    • Bowie JU, Eisenberg D. 1994. An evolutionary approach to folding small α-helical proteins that uses sequence information and an empirical guiding fitness function. Proc Natl Acad Sci USA 91:4436-4440.
    • (1994) Proc Natl Acad Sci USA , vol.91 , pp. 4436-4440
    • Bowie, J.U.1    Eisenberg, D.2
  • 7
    • 0026761547 scopus 로고
    • Folding protein a-carbon chains into compact forms by Monte Carlo methods
    • Covell DG. 1992. Folding protein a-carbon chains into compact forms by Monte Carlo methods. Proteins Struct Funct Genet 14:409-420.
    • (1992) Proteins Struct Funct Genet , vol.14 , pp. 409-420
    • Covell, D.G.1
  • 8
    • 0028049306 scopus 로고
    • Lattice model simulations of polypeptide chain folding
    • Covell DG. 1994. Lattice model simulations of polypeptide chain folding. J Mol Biol 235:1032-1043.
    • (1994) J Mol Biol , vol.235 , pp. 1032-1043
    • Covell, D.G.1
  • 9
    • 0028297304 scopus 로고
    • Folding the main chain of small proteins with the genetic algorithm
    • Dandekar T, Argos P. 1994. Folding the main chain of small proteins with the genetic algorithm. J Mol Biol 236:844-861.
    • (1994) J Mol Biol , vol.236 , pp. 844-861
    • Dandekar, T.1    Argos, P.2
  • 10
    • 0029980527 scopus 로고    scopus 로고
    • Identifying the tertiary fold of small proteins with different topologies from sequence and secondary structure using the genetic algorithm and extended criteria specific for strand regions
    • Dandekar T, Argos P. 1996. Identifying the tertiary fold of small proteins with different topologies from sequence and secondary structure using the genetic algorithm and extended criteria specific for strand regions. J Mol Biol 256:645-660.
    • (1996) J Mol Biol , vol.256 , pp. 645-660
    • Dandekar, T.1    Argos, P.2
  • 11
    • 0013165834 scopus 로고
    • Étude et extension d'un algorithme de Murchland
    • Dionne R. 1978. Étude et extension d'un algorithme de Murchland. Infor 16:132-146.
    • (1978) Infor , vol.16 , pp. 132-146
    • Dionne, R.1
  • 12
    • 0027160197 scopus 로고
    • Backbone-dependent rotamer library for proteins: Application to side-chain prediction
    • Dunbrack RL Jr, Karplus M. 1993. Backbone-dependent rotamer library for proteins: Application to side-chain prediction. J Mol Biol 230:543-574.
    • (1993) J Mol Biol , vol.230 , pp. 543-574
    • Dunbrack Jr., R.L.1    Karplus, M.2
  • 14
    • 0028238582 scopus 로고
    • Pattern recognition and self-correcting distance geometry calculations applied to myohemerythrin
    • Hanggi G, Braun W. 1994. Pattern recognition and self-correcting distance geometry calculations applied to myohemerythrin. FEBS Lett 344:147-153.
    • (1994) FEBS Lett , vol.344 , pp. 147-153
    • Hanggi, G.1    Braun, W.2
  • 15
    • 0025294066 scopus 로고
    • The sampling properties of some distance geometry algorithms applied to unconstrained polypeptide chains: A study of 1830 independently computed conformations
    • Havel TF. 1990. The sampling properties of some distance geometry algorithms applied to unconstrained polypeptide chains: A study of 1830 independently computed conformations. Biopolymers 29:1565-1585.
    • (1990) Biopolymers , vol.29 , pp. 1565-1585
    • Havel, T.F.1
  • 16
    • 49049123546 scopus 로고
    • The theory and practice of distance geometry
    • Havel TF, Kuntz ID, Crippen GM. 1983. The theory and practice of distance geometry. Bull Math Biol 45:665-720.
    • (1983) Bull Math Biol , vol.45 , pp. 665-720
    • Havel, T.F.1    Kuntz, I.D.2    Crippen, G.M.3
  • 18
    • 0026519315 scopus 로고
    • A lattice model for protein structure prediction at low resolution
    • Hinds DA, Levitt M. 1992. A lattice model for protein structure prediction at low resolution. Proc Natl Acad Sci USA 89:2536-2540.
    • (1992) Proc Natl Acad Sci USA , vol.89 , pp. 2536-2540
    • Hinds, D.A.1    Levitt, M.2
  • 19
    • 0028149160 scopus 로고
    • Exploring conformational space with a simple lattice model for protein structure
    • Hinds DA, Levitt M. 1994. Exploring conformational space with a simple lattice model for protein structure. J Mol Biol 245:668-682.
    • (1994) J Mol Biol , vol.245 , pp. 668-682
    • Hinds, D.A.1    Levitt, M.2
  • 20
    • 0030573021 scopus 로고    scopus 로고
    • The NMR solution structure of intestinal fatty acid binding protein complexed with palmitate: Application of a novel distance geometry algorithm
    • Hodsdon ME, Ponder JW, Cistola DP. 1996. The NMR solution structure of intestinal fatty acid binding protein complexed with palmitate: Application of a novel distance geometry algorithm. J Mol Biol 264:585-602.
    • (1996) J Mol Biol , vol.264 , pp. 585-602
    • Hodsdon, M.E.1    Ponder, J.W.2    Cistola, D.P.3
  • 21
    • 0031720234 scopus 로고    scopus 로고
    • Accuracy of side-chain prediction upon near-native protein backbones generated by ab initio folding methods
    • Forthcoming
    • Huang ES, Koehl P, Levitt M, Pappu RV, Ponder JW. 1998. Accuracy of side-chain prediction upon near-native protein backbones generated by ab initio folding methods. Proteins Struct Fund Genet. Forthcoming.
    • (1998) Proteins Struct Fund Genet
    • Huang, E.S.1    Koehl, P.2    Levitt, M.3    Pappu, R.V.4    Ponder, J.W.5
  • 22
    • 0028203492 scopus 로고
    • Monte Carlo simulations of protein folding. I. Lattice model and interaction scheme
    • Kolinski A, Skolnick J. 1994. Monte Carlo simulations of protein folding. I. Lattice model and interaction scheme. Proteins Struct Funct Genet 18:338-352.
    • (1994) Proteins Struct Funct Genet , vol.18 , pp. 338-352
    • Kolinski, A.1    Skolnick, J.2
  • 23
    • 84985641589 scopus 로고
    • Application of distance geometry to protein tertiary structure calculations
    • Kuntz ID, Crippen GM, Kollman PA. 1979. Application of distance geometry to protein tertiary structure calculations. Biopolymers 18:939-957.
    • (1979) Biopolymers , vol.18 , pp. 939-957
    • Kuntz, I.D.1    Crippen, G.M.2    Kollman, P.A.3
  • 24
    • 0028897718 scopus 로고
    • Computer modeling of protein folding: Conformational and energy analysis of reduced and detailed protein models
    • Monge A, Lathrop EJP, Gunn JR, Shenkin PS, Friesner RA. 1995. Computer modeling of protein folding: Conformational and energy analysis of reduced and detailed protein models. J Mol Biol 247:995-1012.
    • (1995) J Mol Biol , vol.247 , pp. 995-1012
    • Monge, A.1    Lathrop, E.J.P.2    Gunn, J.R.3    Shenkin, P.S.4    Friesner, R.A.5
  • 25
    • 0028955505 scopus 로고
    • Predicting the helix packing of globular proteins by self-correcting distance geometry
    • Mumenthaler C, Braun W. 1995. Predicting the helix packing of globular proteins by self-correcting distance geometry. Protein Sci 4:863-871.
    • (1995) Protein Sci , vol.4 , pp. 863-871
    • Mumenthaler, C.1    Braun, W.2
  • 26
    • 0026203784 scopus 로고
    • Effects of limited input distance constraints upon the distance geometry algorithm
    • Oshiro CM, Thomason J, Kuntz ID. 1991. Effects of limited input distance constraints upon the distance geometry algorithm. Biopolymers 31:1049-1064.
    • (1991) Biopolymers , vol.31 , pp. 1049-1064
    • Oshiro, C.M.1    Thomason, J.2    Kuntz, I.D.3
  • 27
    • 0031557390 scopus 로고    scopus 로고
    • Factors affecting the ability of energy functions to discriminate correct from incorrect folds
    • Park BH, Huang ES, Levitt M. 1997. Factors affecting the ability of energy functions to discriminate correct from incorrect folds. J Mol Biol 266:831-846.
    • (1997) J Mol Biol , vol.266 , pp. 831-846
    • Park, B.H.1    Huang, E.S.2    Levitt, M.3
  • 29
    • 0032488962 scopus 로고    scopus 로고
    • An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction
    • Samudrala R, Moult J. 1998. An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction. J Mol Biol 275:893-914.
    • (1998) J Mol Biol , vol.275 , pp. 893-914
    • Samudrala, R.1    Moult, J.2
  • 30
    • 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. 1997. Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J Mol Biol 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
  • 31
    • 0031575423 scopus 로고    scopus 로고
    • MONSSTER: A method for folding globular proteins with a small number of distance restraints
    • Skolnick J, Kolinski A, Ortiz AR. 1997. MONSSTER: A method for folding globular proteins with a small number of distance restraints. J Mol Biol 265:217-241.
    • (1997) J Mol Biol , vol.265 , pp. 217-241
    • Skolnick, J.1    Kolinski, A.2    Ortiz, A.R.3
  • 32
    • 0029055313 scopus 로고
    • LINUS: A hierarchic procedure to predict the fold of a protein
    • Srinivasan R, Rose GD. 1995. LINUS: A hierarchic procedure to predict the fold of a protein. Proteins Struct Funct Genet 22:81-99.
    • (1995) Proteins Struct Funct Genet , vol.22 , pp. 81-99
    • Srinivasan, R.1    Rose, G.D.2
  • 33
    • 0028841399 scopus 로고
    • A simple protein folding algorithm using a binary code and secondary structure constraints
    • Sun S, Thomas PD, Dill KA. 1995. A simple protein folding algorithm using a binary code and secondary structure constraints. Protein Eng 8:769-778.
    • (1995) Protein Eng , vol.8 , pp. 769-778
    • Sun, S.1    Thomas, P.D.2    Dill, K.A.3
  • 34
    • 0142140800 scopus 로고    scopus 로고
    • Prediction of protein side chain conformations: A study on the influence of backbone accuracy on conformation stability in the rotamer space
    • Tuffery P, Etchebest C, Hazout S. 1997. Prediction of protein side chain conformations: A study on the influence of backbone accuracy on conformation stability in the rotamer space. Protein Eng 10:361-372.
    • (1997) Protein Eng , vol.10 , pp. 361-372
    • Tuffery, P.1    Etchebest, C.2    Hazout, S.3
  • 35
    • 0028290433 scopus 로고
    • Prediction of the folding pathways and structure of the GCN4 leucine zipper
    • Vieth M, Kolinski A, Brooks CL 3rd, Skolnick J. 1994. Prediction of the folding pathways and structure of the GCN4 leucine zipper. J Mol Biol 237:361-367.
    • (1994) J Mol Biol , vol.237 , pp. 361-367
    • Vieth, M.1    Kolinski, A.2    Brooks III, C.L.3    Skolnick, J.4
  • 36
    • 0024435638 scopus 로고
    • A computer model to dynamically simulate protein folding: Studies with crambin
    • Wilson C, Doniach S. 1989. A computer model to dynamically simulate protein folding: Studies with crambin. Proteins Struct Funct Genet 6:193-209.
    • (1989) Proteins Struct Funct Genet , vol.6 , pp. 193-209
    • Wilson, C.1    Doniach, S.2
  • 37
    • 0030048675 scopus 로고    scopus 로고
    • Folding proteins with a simple energy function and extensive conformational searching
    • Yue K, Dill KA. 1996. Folding proteins with a simple energy function and extensive conformational searching. Protein Sci 5:254-261.
    • (1996) Protein Sci , vol.5 , pp. 254-261
    • Yue, K.1    Dill, K.A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.