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Volumn 6, Issue 2, 1996, Pages 227-231

Genetic algorithms for protein structure prediction

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; GENETIC MODEL; MOLECULAR MODEL; PREDICTION; PRIORITY JOURNAL; PROTEIN CONFORMATION; SHORT SURVEY;

EID: 0029984690     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(96)80079-0     Document Type: Article
Times cited : (84)

References (40)
  • 1
    • 0028864205 scopus 로고
    • A critical assessment of comparative molecular modeling of tertiary structures of proteins
    • Mosimann S, Meleshko R, James MNG: A critical assessment of comparative molecular modeling of tertiary structures of proteins. Proteins 1995, 23:301-317.
    • (1995) Proteins , vol.23 , pp. 301-317
    • Mosimann, S.1    Meleshko, R.2    James, M.N.G.3
  • 2
    • 0028818340 scopus 로고
    • Protein structure prediction by threading methods: Evaluation of current techniques
    • Lemer CMR, Rooman MJ, Wodak SJ: Protein structure prediction by threading methods: evaluation of current techniques. Proteins 1995, 23:337-355.
    • (1995) Proteins , vol.23 , pp. 337-355
    • Lemer, C.M.R.1    Rooman, M.J.2    Wodak, S.J.3
  • 3
    • 0028849882 scopus 로고
    • Evaluation of current techniques for ab initio protein structure prediction
    • Defay T, Cohen FE: Evaluation of current techniques for ab initio protein structure prediction. Proteins 1995, 23:431-445.
    • (1995) Proteins , vol.23 , pp. 431-445
    • Defay, T.1    Cohen, F.E.2
  • 4
    • 0029094684 scopus 로고
    • Molecular dynamics simulation of cytochrome b5: Implications for protein-protein recognition
    • Storch EM, Daggett V: Molecular dynamics simulation of cytochrome b5: implications for protein-protein recognition. Biochemistry 1995, 34:9682-9693.
    • (1995) Biochemistry , vol.34 , pp. 9682-9693
    • Storch, E.M.1    Daggett, V.2
  • 6
    • 0015859467 scopus 로고
    • Principles that govern the folding of protein chains
    • Anfinsen CB: Principles that govern the folding of protein chains. Science 1973, 181:223-230.
    • (1973) Science , vol.181 , pp. 223-230
    • Anfinsen, C.B.1
  • 7
    • 0018588511 scopus 로고
    • Stability of proteins: Small globular proteins
    • Privalov PL: Stability of proteins: small globular proteins. Adv Protein Chem 1979, 33:167-236.
    • (1979) Adv Protein Chem , vol.33 , pp. 167-236
    • Privalov, P.L.1
  • 11
    • 0009571585 scopus 로고
    • The performance of cooperative processes
    • Huberman BA: The performance of cooperative processes. Physica D 1990, 42:38-47.
    • (1990) Physica D , vol.42 , pp. 38-47
    • Huberman, B.A.1
  • 12
    • 0009611896 scopus 로고
    • Cooperative solution of constraint satisfaction problems
    • Clearwater SH, Huberman BA, Hogg T: Cooperative solution of constraint satisfaction problems. Science 1991, 254:1181-1183.
    • (1991) Science , vol.254 , pp. 1181-1183
    • Clearwater, S.H.1    Huberman, B.A.2    Hogg, T.3
  • 13
    • 0342575592 scopus 로고    scopus 로고
    • Genetic algorithms and their use in chemistry
    • in press
    • Judson RS: Genetic algorithms and their use in chemistry. Rev Comp Chem 1996, 20:in press. An excellent review of the current use of genetic algorithms in chemistry problems.
    • (1996) Rev Comp Chem , vol.20
    • Judson, R.S.1
  • 14
    • 0027245418 scopus 로고
    • Genetic algorithms for protein folding simulations
    • Unger R, Moult J: Genetic algorithms for protein folding simulations. J Mol Biol 1993, 231:75-81
    • (1993) J Mol Biol , vol.231 , pp. 75-81
    • Unger, R.1    Moult, J.2
  • 16
    • 0027503403 scopus 로고
    • Reduced representation of protein structure prediction: Statistical potential and genetic algorithms
    • Sun S: Reduced representation of protein structure prediction: statistical potential and genetic algorithms. Protein Sci 1993, 2:762-785.
    • (1993) Protein Sci , vol.2 , pp. 762-785
    • Sun, S.1
  • 17
    • 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: An evolutionary approach to folding small α-helical proteins that uses sequence information and an empirical guiding fitness function. Proc Natl Acad Sci USA 1994, 91:4436-4440.
    • (1994) Proc Natl Acad Sci USA , vol.91 , pp. 4436-4440
    • Bowie, J.U.1    Eisenberg, D.2
  • 18
    • 0026448484 scopus 로고
    • Potential of genetic algorithms in protein folding and protein engineering simulations
    • Dandekar T, Argos P: Potential of genetic algorithms in protein folding and protein engineering simulations. Protein Eng 1992, 5:637-645.
    • (1992) Protein Eng , vol.5 , pp. 637-645
    • Dandekar, T.1    Argos, P.2
  • 19
    • 0028297304 scopus 로고
    • Folding the main-chain of small proteins with the genetic algorithm
    • Dandekar T, Argos P: Folding the main-chain of small proteins with the genetic algorithm. J Mol Biol 1994, 236:844-861. A bit-string encoding of a simplified protein chain representation is used together with a phenomenological potential to fold a number of helical proteins. All simulations are seeded with secondary structure prediction.
    • (1994) J Mol Biol , vol.236 , pp. 844-861
    • Dandekar, T.1    Argos, P.2
  • 20
    • 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
    • in press
    • Dandekar T, Argos P: 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 1996, in press.
    • (1996) J Mol Biol
    • Dandekar, T.1    Argos, P.2
  • 21
    • 0028841399 scopus 로고
    • Simple protein folding algorithm using a binary code and secondary structure constraints
    • Sun S, Thomas PD, Dill KA: Simple protein folding algorithm using a binary code and secondary structure constraints. Protein Eng 1995, 8:769-778.
    • (1995) Protein Eng , vol.8 , pp. 769-778
    • Sun, S.1    Thomas, P.D.2    Dill, K.A.3
  • 22
    • 0028865590 scopus 로고
    • Ab initio structure prediction for small polypeptides and protein fragments using genetic algorithms
    • Pedersen JT, Moult J: Ab initio structure prediction for small polypeptides and protein fragments using genetic algorithms. Proteins 1995, 23:454-460. A true blind test of a full atom representation torsion based genetic algorithm. A search algorithm was tested on two small protein fragments and a larger (22 residue) membrane associated peptide.
    • (1995) Proteins , vol.23 , pp. 454-460
    • Pedersen, J.T.1    Moult, J.2
  • 24
    • 0004667533 scopus 로고
    • The genetic algorithm and the conformational search of polypeptides and proteins
    • Le-Grand SM, Merz KM Jr: The genetic algorithm and the conformational search of polypeptides and proteins. Mol Simulat 1994, 13:299-320. A full atom representation of the protein together with a rotamer library is used; the AMBER potential is used to evaluate the fitness of the conformations. The method is tested on several small peptides and on the 46-residue protein crambin.
    • (1994) Mol Simulat , vol.13 , pp. 299-320
    • Le-Grand, S.M.1    Merz K.M., Jr.2
  • 25
    • 0000335209 scopus 로고
    • Hierarchical algorithm for computer modeling of protein tertiary structure: Folding of myoglobin to 6.2 å resolution
    • Gunn JR, Monge A, Friesner RA, Marshall CH: Hierarchical algorithm for computer modeling of protein tertiary structure: folding of myoglobin to 6.2 Å resolution. J Phys Chem 1994, 98:702-711.
    • (1994) J Phys Chem , vol.98 , pp. 702-711
    • Gunn, J.R.1    Monge, A.2    Friesner, R.A.3    Marshall, C.H.4
  • 26
    • 0001536737 scopus 로고
    • Conformational searching methods for small molecules. II. Genetic algorithm approach
    • Judson RS, Jaeger EP, Treasurywala AM, Peterson MA: Conformational searching methods for small molecules. II. Genetic algorithm approach. J Comput Chem 1993, 14:1407-1414.
    • (1993) J Comput Chem , vol.14 , pp. 1407-1414
    • Judson, R.S.1    Jaeger, E.P.2    Treasurywala, A.M.3    Peterson, M.A.4
  • 27
    • 84913584731 scopus 로고
    • Analysis of the genetic algorithm method of molecular conformation determination
    • McGarrah DB, Judson RS: Analysis of the genetic algorithm method of molecular conformation determination. J Comput Chem 1993, 14:1385-1395.
    • (1993) J Comput Chem , vol.14 , pp. 1385-1395
    • McGarrah, D.B.1    Judson, R.S.2
  • 28
    • 0343445455 scopus 로고    scopus 로고
    • Minimization of peptide analogues using genetic algorithms
    • in press
    • Herrmann F, Suhai S: Minimization of peptide analogues using genetic algorithms. J Comput Chem 1996, in press.
    • (1996) J Comput Chem
    • Herrmann, F.1    Suhai, S.2
  • 29
    • 0005889794 scopus 로고
    • Genetic algorithms in protein structure prediction
    • Edited by Suhai S. New York: Plenum Press
    • Herrmann F, Suhai S: Genetic algorithms in protein structure prediction. In Computational Methods in Genome Research. Edited by Suhai S. New York: Plenum Press; 1994:173-190.
    • (1994) Computational Methods in Genome Research , pp. 173-190
    • Herrmann, F.1    Suhai, S.2
  • 30
    • 0026179489 scopus 로고
    • A new approach to the rapid determination of protein side-chain conformations
    • Tuffery P, Etchebest C, Hazout S, Lavery R: A new approach to the rapid determination of protein side-chain conformations. J Biomol Struct Dyn 1991, 8:1267-1289.
    • (1991) J Biomol Struct Dyn , vol.8 , pp. 1267-1289
    • Tuffery, P.1    Etchebest, C.2    Hazout, S.3    Lavery, R.4
  • 31
    • 84913539119 scopus 로고
    • A critical comparison of search algorithms applied to the optimization of protein sidechain conformations
    • Tuffery P, Etchebest C, Hazout S, Lavery R: A critical comparison of search algorithms applied to the optimization of protein sidechain conformations. J Comput Chem 1993, 14:790-798.
    • (1993) J Comput Chem , vol.14 , pp. 790-798
    • Tuffery, P.1    Etchebest, C.2    Hazout, S.3    Lavery, R.4
  • 32
    • 85005670823 scopus 로고
    • Conformational sampling of loop structures using genetic algorithms
    • Ring CS, Cohen FE: Conformational sampling of loop structures using genetic algorithms. Isr J Chem 1994, 34:245-252.
    • (1994) Isr J Chem , vol.34 , pp. 245-252
    • Ring, C.S.1    Cohen, F.E.2
  • 33
    • 0025101549 scopus 로고
    • Theory for protein mutability and biogenesis
    • Lau KF, Dill KA: Theory for protein mutability and biogenesis. Proc Natl Acad Sci USA 1990, 87:638-642.
    • (1990) Proc Natl Acad Sci USA , vol.87 , pp. 638-642
    • Lau, K.F.1    Dill, K.A.2
  • 34
    • 0025830469 scopus 로고
    • A method to identify protein sequences that fold into a known three-dimensional structure
    • Bowie JU, Luthy R, Eisenberg D: A method to identify protein sequences that fold into a known three-dimensional structure. Science 1991, 253:164-170.
    • (1991) Science , vol.253 , pp. 164-170
    • Bowie, J.U.1    Luthy, R.2    Eisenberg, D.3
  • 35
    • 0026009212 scopus 로고
    • Prediction of protein backbone conformation based on seven structural assignments
    • Rooman MJ, Kocher J-PA, Wodak SJ: Prediction of protein backbone conformation based on seven structural assignments. J Mol Biol 1991, 221:961-979.
    • (1991) J Mol Biol , vol.221 , pp. 961-979
    • Rooman, M.J.1    Kocher, J.-P.A.2    Wodak, S.J.3
  • 36
    • 0028883794 scopus 로고
    • Determination of the conformation of folding initiation sites in proteins by computer simulation
    • Avbelj F, Moult J: Determination of the conformation of folding initiation sites in proteins by computer simulation. Proteins 1995, 23:129-141.
    • (1995) Proteins , vol.23 , pp. 129-141
    • Avbelj, F.1    Moult, J.2
  • 37
    • 0025906759 scopus 로고
    • An analysis of protein folding pathways
    • Moult J, Unger R: An analysis of protein folding pathways. Biochemistry 1991, 30:3816-3824.
    • (1991) Biochemistry , vol.30 , pp. 3816-3824
    • Moult, J.1    Unger, R.2
  • 38
    • 0343445450 scopus 로고    scopus 로고
    • How similar must a template structure be for homology modeling by sidechain packing methods?
    • in press
    • Chung SY, Subbiah S: How similar must a template structure be for homology modeling by sidechain packing methods? Pacific Biotechnol Symp 1996, in press.
    • (1996) Pacific Biotechnol Symp
    • Chung, S.Y.1    Subbiah, S.2
  • 39
    • 0028220365 scopus 로고
    • De novo protein design using pairwise potentials and a genetic algorithm
    • Jones DT: De novo protein design using pairwise potentials and a genetic algorithm. Protein Sci 1994, 3:567-574.
    • (1994) Protein Sci , vol.3 , pp. 567-574
    • Jones, D.T.1
  • 40
    • 0001686231 scopus 로고    scopus 로고
    • A comparison of a direct search method and a genetic algorithm for conformational searching
    • in press
    • Meza JC, Judson RS, Faulkner TR, Treasurywala AM: A comparison of a direct search method and a genetic algorithm for conformational searching. J Comput Chem 1996, in press.
    • (1996) J Comput Chem
    • Meza, J.C.1    Judson, R.S.2    Faulkner, T.R.3    Treasurywala, A.M.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.