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Volumn 37, Issue 4, 1999, Pages 554-564

Unit-vector RMS (URMS) as a tool to analyze molecular dynamics trajectories

Author keywords

C peptide; Folding; Order parameter; Root mean square distance; Structure comparison

Indexed keywords

AMINO ACID; C PEPTIDE; MYOGLOBIN;

EID: 0032749097     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19991201)37:4<554::AID-PROT6>3.0.CO;2-1     Document Type: Article
Times cited : (46)

References (20)
  • 2
    • 49049123546 scopus 로고
    • The theory and practice of distance geometry
    • Havel TF, Kuntz ID, Crippen GM. The theory and practice of distance geometry. Bull Math Biol 1983;45:665-720. Kabsch WA. A solution for the best rotation to relate two sets of vectors. Acta Crystallogr A 1976;32:922-923.
    • (1983) Bull Math Biol , vol.45 , pp. 665-720
    • Havel, T.F.1    Kuntz, I.D.2    Crippen, G.M.3
  • 3
    • 84893482610 scopus 로고
    • A solution for the best rotation to relate two sets of vectors
    • Havel TF, Kuntz ID, Crippen GM. The theory and practice of distance geometry. Bull Math Biol 1983;45:665-720. Kabsch WA. A solution for the best rotation to relate two sets of vectors. Acta Crystallogr A 1976;32:922-923.
    • (1976) Acta Crystallogr A , vol.32 , pp. 922-923
    • Kabsch, W.A.1
  • 4
    • 0025339420 scopus 로고
    • Molecular dynamics study of secondary structure motions in proteins: Application to myohemerythrin
    • Rojewska D, Elber R. Molecular dynamics study of secondary structure motions in proteins: application to myohemerythrin. Proteins 1990;7:265-279.
    • (1990) Proteins , vol.7 , pp. 265-279
    • Rojewska, D.1    Elber, R.2
  • 5
    • 0032444334 scopus 로고    scopus 로고
    • Folding nucleus: Specific or multiple? Insights from lattice models and experiments
    • Shakhnovich EI. Folding nucleus: specific or multiple? Insights from lattice models and experiments. Fold Des 1998;3:R108-111. Thirumalai D, Klimov KD. Fishing for folding nuclei in lattice models and proteins. Fold Des 1998;3:R112-118.
    • (1998) Fold Des , vol.3
    • Shakhnovich, E.I.1
  • 6
    • 0032428359 scopus 로고    scopus 로고
    • Fishing for folding nuclei in lattice models and proteins
    • Shakhnovich EI. Folding nucleus: specific or multiple? Insights from lattice models and experiments. Fold Des 1998;3:R108-111. Thirumalai D, Klimov KD. Fishing for folding nuclei in lattice models and proteins. Fold Des 1998;3:R112-118.
    • (1998) Fold Des , vol.3
    • Thirumalai, D.1    Klimov, K.D.2
  • 7
    • 16444370098 scopus 로고    scopus 로고
    • A stochastic path approach to compute atomically detailed trajectories: Application to the folding of C peptide
    • Elber R, Meiler J, Olender R. A stochastic path approach to compute atomically detailed trajectories: application to the folding of C peptide. J Phys Chem B 1999;103:899-911.
    • (1999) J Phys Chem B , vol.103 , pp. 899-911
    • Elber, R.1    Meiler, J.2    Olender, R.3
  • 9
    • 0021757436 scopus 로고
    • A new force field for molecular mechanical simulation of nucleic acids and proteins
    • Weiner SJ, Kollman PA, Case DA, et al. A new force field for molecular mechanical simulation of nucleic acids and proteins. J Am Chem Soc 1984;106:765-784. Jorgensen WL, Tirado-Rives J. The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimization for crystals of cyclic peptides and crambin. J Am Chem Soc 1988;110:1657-1666.
    • (1984) J Am Chem Soc , vol.106 , pp. 765-784
    • Weiner, S.J.1    Kollman, P.A.2    Case, D.A.3
  • 10
    • 33645941402 scopus 로고
    • The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimization for crystals of cyclic peptides and crambin
    • Weiner SJ, Kollman PA, Case DA, et al. A new force field for molecular mechanical simulation of nucleic acids and proteins. J Am Chem Soc 1984;106:765-784. Jorgensen WL, Tirado-Rives J. The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimization for crystals of cyclic peptides and crambin. J Am Chem Soc 1988;110:1657-1666.
    • (1988) J Am Chem Soc , vol.110 , pp. 1657-1666
    • Jorgensen, W.L.1    Tirado-Rives, J.2
  • 13
    • 0000171604 scopus 로고
    • Differential geometry and polymer conformations 1. Comparison of protein conformations
    • Rackovsky S, Scheraga HA. Differential geometry and polymer conformations 1. Comparison of protein conformations. Macromolecules 1978;11:1168-1174. Rackovsky S, Scheraga HA. Differential geometry and polymer conformations 2. Development of a conformational distance function. Macromolecules 1980;12:1440-1453. Rackovsky S, Goldstein DA, Protein comparison and classification: a differential geometric approach. Proc Natl Acad Sci USA 1988;85:777-781.
    • (1978) Macromolecules , vol.11 , pp. 1168-1174
    • Rackovsky, S.1    Scheraga, H.A.2
  • 14
    • 10944266000 scopus 로고
    • Differential geometry and polymer conformations 2. Development of a conformational distance function
    • Rackovsky S, Scheraga HA. Differential geometry and polymer conformations 1. Comparison of protein conformations. Macromolecules 1978;11:1168-1174. Rackovsky S, Scheraga HA. Differential geometry and polymer conformations 2. Development of a conformational distance function. Macromolecules 1980;12:1440-1453. Rackovsky S, Goldstein DA, Protein comparison and classification: a differential geometric approach. Proc Natl Acad Sci USA 1988;85:777-781.
    • (1980) Macromolecules , vol.12 , pp. 1440-1453
    • Rackovsky, S.1    Scheraga, H.A.2
  • 15
    • 0023831683 scopus 로고
    • Protein comparison and classification: A differential geometric approach
    • Rackovsky S, Scheraga HA. Differential geometry and polymer conformations 1. Comparison of protein conformations. Macromolecules 1978;11:1168-1174. Rackovsky S, Scheraga HA. Differential geometry and polymer conformations 2. Development of a conformational distance function. Macromolecules 1980;12:1440-1453. Rackovsky S, Goldstein DA, Protein comparison and classification: a differential geometric approach. Proc Natl Acad Sci USA 1988;85:777-781.
    • (1988) Proc Natl Acad Sci USA , vol.85 , pp. 777-781
    • Rackovsky, S.1    Goldstein, D.A.2
  • 16
    • 0000939821 scopus 로고    scopus 로고
    • What is the probability of a chance prediction of a protein structure with an rmsd of 6 Å?
    • Reva BA, Finkelstein AV, Skolnick J. What is the probability of a chance prediction of a protein structure with an rmsd of 6 Å? Fold Des 1998;3:141-147
    • (1998) Fold Des , vol.3 , pp. 141-147
    • Reva, B.A.1    Finkelstein, A.V.2    Skolnick, J.3
  • 17
    • 0029057126 scopus 로고
    • Size-independent comparison of protein three-dimensional structures
    • Maiorov VN, Grippen GM. Size-independent comparison of protein three-dimensional structures. Proteins 1995;22:273-283.
    • (1995) Proteins , vol.22 , pp. 273-283
    • Maiorov, V.N.1    Grippen, G.M.2
  • 18
    • 0031697713 scopus 로고    scopus 로고
    • A geometric algorithm to find small but highly similar 3D substructures in proteins
    • Pennec X, Ayache N. A geometric algorithm to find small but highly similar 3D substructures in proteins. Bioinformatics 1998; 14:516-522.
    • (1998) Bioinformatics , vol.14 , pp. 516-522
    • Pennec, X.1    Ayache, N.2
  • 20
    • 36449009348 scopus 로고
    • Folding kinetics of proteins: A model study
    • Guo Z, Thirumalai D, Honeycutt JD. Folding kinetics of proteins: a model study. J Chem Phys 1992;97:525-535.
    • (1992) J Chem Phys , vol.97 , pp. 525-535
    • Guo, Z.1    Thirumalai, D.2    Honeycutt, J.D.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.