-
1
-
-
0033970022
-
Expectations from structural genomics
-
Brenner, S., Levitt, M. (2000) Expectations from structural genomics. Protein Sci., 9, 197-200.
-
(2000)
Protein Sci
, vol.9
, pp. 197-200
-
-
Brenner, S.1
Levitt, M.2
-
2
-
-
0035487690
-
A tour of structural genomics
-
Brenner, S.E. (2001) A tour of structural genomics. Nat. Genet., 210, 801-809.
-
(2001)
Nat. Genet
, vol.210
, pp. 801-809
-
-
Brenner, S.E.1
-
3
-
-
0033757822
-
An overview of structural genomics
-
Burley, S.K. (2000) An overview of structural genomics. Nat. Struct. Biol., 7 (Suppl), 932-934.
-
(2000)
Nat. Struct. Biol
, vol.7
, Issue.SUPPL.
, pp. 932-934
-
-
Burley, S.K.1
-
4
-
-
0035424346
-
High-throughput three-dimensional protein structure determination
-
Heinemann, U., Illing, G., Oschkinat, H. (2001) High-throughput three-dimensional protein structure determination. Curr. Opin. Biotech., 12, 348-354.
-
(2001)
Curr. Opin. Biotech
, vol.12
, pp. 348-354
-
-
Heinemann, U.1
Illing, G.2
Oschkinat, H.3
-
5
-
-
0034985005
-
Ab initio protein structure prediction: Progress and prospects
-
Bonneau, R., Baker, D. (2001) Ab initio protein structure prediction: progress and prospects. Annu. Rev. Biophys. Biomol. Struct., 30, 173-189.
-
(2001)
Annu. Rev. Biophys. Biomol. Struct
, vol.30
, pp. 173-189
-
-
Bonneau, R.1
Baker, D.2
-
6
-
-
67349189383
-
The kinetics of formation of active ribonuclease during oxidation of the reduced polypeptide chain
-
Anfinsen, C.B., Haber, E., Sela, M., White, F.H., Jr. (1961) The kinetics of formation of active ribonuclease during oxidation of the reduced polypeptide chain. Proc. Natl. Acad. Sci. U. S. A., 47, 1309-1314.
-
(1961)
Proc. Natl. Acad. Sci. U. S. A
, vol.47
, pp. 1309-1314
-
-
Anfinsen, C.B.1
Haber, E.2
Sela, M.3
White Jr., F.H.4
-
7
-
-
0019858614
-
Similar amino acid sequences: Chance or common ancestry?
-
Doolittle, R. (1981) Similar amino acid sequences: chance or common ancestry? Science, 214, 149-159.
-
(1981)
Science
, vol.214
, pp. 149-159
-
-
Doolittle, R.1
-
8
-
-
0026030641
-
Database of homology-derived protein structures and the structural meaning of sequence alignment
-
Sander, C., Schneider, R. (1991) Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins, 9, 56-68.
-
(1991)
Proteins
, vol.9
, pp. 56-68
-
-
Sander, C.1
Schneider, R.2
-
9
-
-
0031302793
-
Distance homology recognition using structural classification of proteins
-
Murzin, A., Bateman, A. (1997) Distance homology recognition using structural classification of proteins. Proteins, 29S, 105-112.
-
(1997)
Proteins
, vol.29 S
, pp. 105-112
-
-
Murzin, A.1
Bateman, A.2
-
10
-
-
0025830469
-
Method to identify protein sequences that fold into a known three-dimensional structure
-
Bowie, J., Luthy, R., Eisenberg, D. (1991) Method to identify protein sequences that fold into a known three-dimensional structure. Science, 253, 164-170.
-
(1991)
Science
, vol.253
, pp. 164-170
-
-
Bowie, J.1
Luthy, R.2
Eisenberg, D.3
-
11
-
-
0026690571
-
A new approach to protein fold recognition
-
Jones, D., Taylor, W., Thornton, J. (1992) A new approach to protein fold recognition. Nature, 258, 86-89.
-
(1992)
Nature
, vol.258
, pp. 86-89
-
-
Jones, D.1
Taylor, W.2
Thornton, J.3
-
12
-
-
0242267517
-
Critical assessment of methods of protein structure prediction (CASP): Round V
-
Moult, J., Fidelis, K., Zemla, A. Hubbard, T. (2003) Critical assessment of methods of protein structure prediction (CASP): round V. Proteins, 53, 334-339.
-
(2003)
Proteins
, vol.53
, pp. 334-339
-
-
Moult, J.1
Fidelis, K.2
Zemla, A.3
Hubbard, T.4
-
13
-
-
30344459116
-
Critical assessment of methods of protein structure prediction (CASP) - round 6
-
Moult, J., Fidelis, K., Rost, B., Hubbard, T., Tramontano, A. (2005) Critical assessment of methods of protein structure prediction (CASP) - round 6. Proteins, 61, 3-7.
-
(2005)
Proteins
, vol.61
, pp. 3-7
-
-
Moult, J.1
Fidelis, K.2
Rost, B.3
Hubbard, T.4
Tramontano, A.5
-
14
-
-
0032605909
-
Calculation of protein conformation by global optimization of a potential energy function
-
S3
-
Lee, J., Liwo, A., Ripoll, D., Pillardy, J., Scheraga, J. (1999) Calculation of protein conformation by global optimization of a potential energy function. Proteins, S3, 204-208.
-
(1999)
Proteins
, pp. 204-208
-
-
Lee, J.1
Liwo, A.2
Ripoll, D.3
Pillardy, J.4
Scheraga, J.5
-
15
-
-
0032606133
-
Ab initio protein structure prediction using a combined hierarchical approach
-
S3
-
Samudrala, R., Xia, Y., Huang, E., Levitt, M. (1999) Ab initio protein structure prediction using a combined hierarchical approach. Proteins, S3, 194-198.
-
(1999)
Proteins
, pp. 194-198
-
-
Samudrala, R.1
Xia, Y.2
Huang, E.3
Levitt, M.4
-
16
-
-
0032612579
-
Ab initio structure prediction of CASP3 targets using ROSETTA
-
S3
-
Simons, K., Bonneau, R., Ruczinski, I., Baker, D. (1999) Ab initio structure prediction of CASP3 targets using ROSETTA. Proteins, S3, 171-176.
-
(1999)
Proteins
, pp. 171-176
-
-
Simons, K.1
Bonneau, R.2
Ruczinski, I.3
Baker, D.4
-
17
-
-
0032611514
-
A combined approach for ab initio construction of low resolution protein tertiary structures from sequence
-
Altman, R. B, Dunker, A.K, Hunter, L, Klein, T.E, Lauderdale, K, eds, World Scientific Press, Singapore, pp
-
Samudrala, R., Xia, Y., Levitt, M., Huang E.S. (1999) A combined approach for ab initio construction of low resolution protein tertiary structures from sequence, in Proceedings of the Pacific Symposium on Biocomputing (Altman, R. B., Dunker, A.K., Hunter, L., Klein, T.E., Lauderdale, K., eds.), World Scientific Press, Singapore, pp. 505-516.
-
(1999)
Proceedings of the Pacific Symposium on Biocomputing
, pp. 505-516
-
-
Samudrala, R.1
Xia, Y.2
Levitt, M.3
Huang, E.S.4
-
18
-
-
3342936478
-
A comprehensive analysis of 40 blind protein structure predictions
-
Samudrala, R., Levitt, M. (2002) A comprehensive analysis of 40 blind protein structure predictions. BMC Struct Biol., 2, 3-18.
-
(2002)
BMC Struct Biol
, vol.2
, pp. 3-18
-
-
Samudrala, R.1
Levitt, M.2
-
19
-
-
0031297386
-
Critical assessment of methods of protein structure prediction (CASP): Round II
-
Moult, J., Hubbard, T., Bryant, S.H., Fidelis, K., Pedersen, J.T. (1997) Critical assessment of methods of protein structure prediction (CASP): round II. Proteins, 29, 2-6.
-
(1997)
Proteins
, vol.29
, pp. 2-6
-
-
Moult, J.1
Hubbard, T.2
Bryant, S.H.3
Fidelis, K.4
Pedersen, J.T.5
-
20
-
-
0032606039
-
Critical assessment, of methods of protein structure prediction (CASP): Round III
-
Moult, J., Hubbard, T., Fidelis, K., Pedersen, J.T. (1999) Critical assessment, of methods of protein structure prediction (CASP): round III. Proteins, 37, 2-6.
-
(1999)
Proteins
, vol.37
, pp. 2-6
-
-
Moult, J.1
Hubbard, T.2
Fidelis, K.3
Pedersen, J.T.4
-
21
-
-
0035702809
-
Critical assessment of methods of protein structure prediction (CASP): Round IV
-
Moult, J., Fidelis, K., Zemla, A., Hubbard, T. (2001) Critical assessment of methods of protein structure prediction (CASP): round IV. Proteins, 45, 2-7.
-
(2001)
Proteins
, vol.45
, pp. 2-7
-
-
Moult, J.1
Fidelis, K.2
Zemla, A.3
Hubbard, T.4
-
22
-
-
84986512474
-
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
-
Brooks, B., Bruccoleri, R., Olafeon, B., States, D., Swaminathan, S., Karplus, M. (1983) CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J. Comp. Chem., 4, 187-217.
-
(1983)
J. Comp. Chem
, vol.4
, pp. 187-217
-
-
Brooks, B.1
Bruccoleri, R.2
Olafeon, B.3
States, D.4
Swaminathan, S.5
Karplus, M.6
-
23
-
-
84988053694
-
An all atom force field foisimulations of proteins and nucleic acids
-
Weiner, S., Kollman P., Nguyen, D., Case, D. (1986) An all atom force field foisimulations of proteins and nucleic acids. J. Comp. Chem., 7, 230-252.
-
(1986)
J. Comp. Chem
, vol.7
, pp. 230-252
-
-
Weiner, S.1
Kollman, P.2
Nguyen, D.3
Case, D.4
-
24
-
-
33645941402
-
The OPLS potential, function for proteins. Energy minimisations for crystals of cyclic peptides and crambin
-
Jorgensen, W., Tirado-Rives, J. (1988) The OPLS potential, function for proteins. Energy minimisations for crystals of cyclic peptides and crambin. J. Amer. Chem. Soc., 110, 1657-1666.
-
(1988)
J. Amer. Chem. Soc
, vol.110
, pp. 1657-1666
-
-
Jorgensen, W.1
Tirado-Rives, J.2
-
25
-
-
0041784950
-
-
MacKerell, A.D., Jr., Bashford, D., Bellott, M., Dunbrack, R.L., Jr., Evanseck, J.D., et al. (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B, 102, 3586-3616.
-
MacKerell, A.D., Jr., Bashford, D., Bellott, M., Dunbrack, R.L., Jr., Evanseck, J.D., et al. (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B, 102, 3586-3616.
-
-
-
-
26
-
-
0029011701
-
A second generation force field for the simulation of proteins and nucleic acids
-
Cornell, W.D., Cieplak, P., Bayly, C.I., Gould, I.R., Merz, K.M., Jr., Fergusson, D.M., Spellmeyer, D.C., Fox, D.C., Caldwell, J.W., Kollman, P.A. (1995) A second generation force field for the simulation of proteins and nucleic acids. J. Amer. Chem. Soc., 117, 5179-5197.
-
(1995)
J. Amer. Chem. Soc
, vol.117
, pp. 5179-5197
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Gould, I.R.4
Merz Jr., K.M.5
Fergusson, D.M.6
Spellmeyer, D.C.7
Fox, D.C.8
Caldwell, J.W.9
Kollman, P.A.10
-
27
-
-
0001731773
-
Energy parameters in peptides: Improved geometrical parameters and non-bonded interactions for use in the ECEPP/3 algorithm, with application to proline-containing peptides
-
Nemethy, G., Gibson, K.D., Palmer, K.A., Yoon, C.N., Paterlini, G., Zagari, A., Rumsey, S., Scheraga, H.A. (1992) Energy parameters in peptides: improved geometrical parameters and non-bonded interactions for use in the ECEPP/3 algorithm, with application to proline-containing peptides. J. Phys. Chem., 96, 6472-6484.
-
(1992)
J. Phys. Chem
, vol.96
, pp. 6472-6484
-
-
Nemethy, G.1
Gibson, K.D.2
Palmer, K.A.3
Yoon, C.N.4
Paterlini, G.5
Zagari, A.6
Rumsey, S.7
Scheraga, H.A.8
-
28
-
-
0027413658
-
Generating and testing protein folds
-
Wodak, S., Rooman, M. (1993) Generating and testing protein folds. Curr. Opin. Struct. Biol., 3, 247-259.
-
(1993)
Curr. Opin. Struct. Biol
, vol.3
, pp. 247-259
-
-
Wodak, S.1
Rooman, M.2
-
29
-
-
0029000696
-
Knowledge based potentials for proteins
-
Sippl, M. (1995) Knowledge based potentials for proteins. Curr. Opin. Struct. Biol., 5, 229-235.
-
(1995)
Curr. Opin. Struct. Biol
, vol.5
, pp. 229-235
-
-
Sippl, M.1
-
30
-
-
0029873155
-
Stability changes upon mutation of solvent-accessible residues in proteins evaluated by database-derived potentials
-
Gilis, D., Rooman, M. (1996) Stability changes upon mutation of solvent-accessible residues in proteins evaluated by database-derived potentials. J. Mol. Biol., 257, 1112-1126.
-
(1996)
J. Mol. Biol
, vol.257
, pp. 1112-1126
-
-
Gilis, D.1
Rooman, M.2
-
31
-
-
0029942661
-
Structure-derived potentials and protein simulations
-
Jernigan, R.L., Bahar I. (1996) Structure-derived potentials and protein simulations. Curr. Opin. Struct. Biol., 6, 195-209.
-
(1996)
Curr. Opin. Struct. Biol
, vol.6
, pp. 195-209
-
-
Jernigan, R.L.1
Bahar, I.2
-
32
-
-
0029844461
-
Evaluation of atomic level mean force potentials via inverse refinement of protein structures: Atomic burial position and pairwise non-bonded interactions
-
DeBolt, S.E., Skolnick, J. (1996) Evaluation of atomic level mean force potentials via inverse refinement of protein structures: atomic burial position and pairwise non-bonded interactions. Protein Eng., 8, 637-655.
-
(1996)
Protein Eng
, vol.8
, pp. 637-655
-
-
DeBolt, S.E.1
Skolnick, J.2
-
33
-
-
0031552370
-
Determination of atomic desolvation energies from the structures of crystallised proteins
-
Zhang, C., Vasmatzis, G., Cornette, J.L., DeLisi, C. (1997) Determination of atomic desolvation energies from the structures of crystallised proteins. J. Mol. Biol., 267, 707-726.
-
(1997)
J. Mol. Biol
, vol.267
, pp. 707-726
-
-
Zhang, C.1
Vasmatzis, G.2
Cornette, J.L.3
DeLisi, C.4
-
34
-
-
0032488962
-
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, 895-916.
-
(1998)
J. Mol. Biol
, vol.275
, pp. 895-916
-
-
Samudrala, R.1
Moult, J.2
-
35
-
-
0034575681
-
Scoring functions for ab initio protein structure prediction
-
Huang, E.S., Samudrala, R., Park, B.H. (2000) Scoring functions for ab initio protein structure prediction. Methods Mol. Biol., 143, 223-245.
-
(2000)
Methods Mol. Biol
, vol.143
, pp. 223-245
-
-
Huang, E.S.1
Samudrala, R.2
Park, B.H.3
-
37
-
-
10644250257
-
Inhomogeneous electron gas
-
Hohenberg, P., Kohn, W. (1964) Inhomogeneous electron gas. Phys. Rev., 136, 864.
-
(1964)
Phys. Rev
, vol.136
, pp. 864
-
-
Hohenberg, P.1
Kohn, W.2
-
38
-
-
0008863560
-
Some factors in the interpretation of protein denaturation
-
Kauzmann, W. (1959) Some factors in the interpretation of protein denaturation. Adv. Protein Chem,, 14, 1-64.
-
(1959)
Adv. Protein Chem
, vol.14
, pp. 1-64
-
-
Kauzmann, W.1
-
39
-
-
0025370815
-
Dominant forces in protein folding
-
Dill, K.A. (1990) Dominant forces in protein folding. Biochemistry, 29, 7133-7155.
-
(1990)
Biochemistry
, vol.29
, pp. 7133-7155
-
-
Dill, K.A.1
-
40
-
-
2342593131
-
Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum, mechanical calculations
-
Morozov, A.V., Kortemme, T., Tsemekhman, K., Baker, D. (2004) Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum, mechanical calculations. Proc. Natl. Acad. Sci. U. S. A., 101, 6946-6951.
-
(2004)
Proc. Natl. Acad. Sci. U. S. A
, vol.101
, pp. 6946-6951
-
-
Morozov, A.V.1
Kortemme, T.2
Tsemekhman, K.3
Baker, D.4
-
41
-
-
84986518863
-
AMBER: Assisted model building with energy refinement. A general program for modeling molecules and their interactions
-
Weiner, P.K., Kollman P.A. (1981) AMBER: Assisted model building with energy refinement. A general program for modeling molecules and their interactions. J. Comp. Chem., 2, 287-303.
-
(1981)
J. Comp. Chem
, vol.2
, pp. 287-303
-
-
Weiner, P.K.1
Kollman, P.A.2
-
42
-
-
84986512474
-
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
-
Brooks, B.R., Bruccoleri, R.E., Olafson, B.D., States, D.J., Swaminathan, S., Karplus, M. (1983) CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J. Comp. Chem., 4, 187-217.
-
(1983)
J. Comp. Chem
, vol.4
, pp. 187-217
-
-
Brooks, B.R.1
Bruccoleri, R.E.2
Olafson, B.D.3
States, D.J.4
Swaminathan, S.5
Karplus, M.6
-
43
-
-
0029633167
-
Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution
-
Levitt, M., Hirshberg, M., Sharon, R., Daggett, V. (1995) Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution. Comp. Phys. Comm., 91, 215-231.
-
(1995)
Comp. Phys. Comm
, vol.91
, pp. 215-231
-
-
Levitt, M.1
Hirshberg, M.2
Sharon, R.3
Daggett, V.4
-
44
-
-
0021104775
-
Molecular dynamics of native protein. I. Computer simulation of trajectories
-
Levitt, M. (1983) Molecular dynamics of native protein. I. Computer simulation of trajectories. J. Mol. Biol., 168, 595-617.
-
(1983)
J. Mol. Biol
, vol.168
, pp. 595-617
-
-
Levitt, M.1
-
45
-
-
0029144222
-
Molecular and functional characterization of recombinant human metabotropic glutamate receptor subtype 5
-
Daggett, L.P., Sacaan, A.I., Akong, M., Rao, S.P., Hess, S.D., Liaw, C., Urrutia, A., Jachec, C., Ellis, S.B., Dreessen J, et al. (1995) Molecular and functional characterization of recombinant human metabotropic glutamate receptor subtype 5. Neuropharmacology, 34, 7133-7155.
-
(1995)
Neuropharmacology
, vol.34
, pp. 7133-7155
-
-
Daggett, L.P.1
Sacaan, A.I.2
Akong, M.3
Rao, S.P.4
Hess, S.D.5
Liaw, C.6
Urrutia, A.7
Jachec, C.8
Ellis, S.B.9
Dreessen, J.10
-
46
-
-
0021095856
-
Protein folding by restrained energy minimization and molecular dynamics
-
Levitt, M. (1983) Protein folding by restrained energy minimization and molecular dynamics. J. Mol. Biol., 170, 723-764.
-
(1983)
J. Mol. Biol
, vol.170
, pp. 723-764
-
-
Levitt, M.1
-
47
-
-
0000870109
-
Three-dimensional structure of proteins determined by molecular dynamics with interproton distance restraints: Application to crambin
-
Brunger, A.T., Clore, G.M., Gronenborn, A.M., Karplus, M. (1986) Three-dimensional structure of proteins determined by molecular dynamics with interproton distance restraints: application to crambin. Proc. Natl. Acad. Sci. U S. A., 83, 3801-3805.
-
(1986)
Proc. Natl. Acad. Sci. U S. A
, vol.83
, pp. 3801-3805
-
-
Brunger, A.T.1
Clore, G.M.2
Gronenborn, A.M.3
Karplus, M.4
-
48
-
-
84986439485
-
Can the Lennard-Jones 6-12 function replace the 10-12 form in molecular mechanics calculations?
-
Ferguson, D.M., Kollman, P.A. (1991) Can the Lennard-Jones 6-12 function replace the 10-12 form in molecular mechanics calculations? J. Comput., Chem., 12, 620-626.
-
(1991)
J. Comput., Chem
, vol.12
, pp. 620-626
-
-
Ferguson, D.M.1
Kollman, P.A.2
-
49
-
-
0001010885
-
Representation of van der Waals (vdW) interactions in molecular mechanics force fields: Potential form, combination rules, and vdW parameters
-
Halgren, T.A. (1992) Representation of van der Waals (vdW) interactions in molecular mechanics force fields: potential form, combination rules, and vdW parameters. J. Am. Chem. Soc., 114, 7827-7843.
-
(1992)
J. Am. Chem. Soc
, vol.114
, pp. 7827-7843
-
-
Halgren, T.A.1
-
50
-
-
0037571112
-
Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94
-
Halgren, T.A. (1996) Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94. J. Comput. Chem., 17, 490-519.
-
(1996)
J. Comput. Chem
, vol.17
, pp. 490-519
-
-
Halgren, T.A.1
-
51
-
-
0001690449
-
van der Waals functional forms for molecular simulations
-
Hart, J.R., Rappe, A.K. (1992) van der Waals functional forms for molecular simulations. J. Chem. Phys., 97, 1109-1115.
-
(1992)
J. Chem. Phys
, vol.97
, pp. 1109-1115
-
-
Hart, J.R.1
Rappe, A.K.2
-
52
-
-
0000378902
-
A model for the geometries of van der Waals complexes
-
Buckingham, A.D., Fowler, P.W. (1985) A model for the geometries of van der Waals complexes. Can. J. Chem., 63, 2018.
-
(1985)
Can. J. Chem
, vol.63
, pp. 2018
-
-
Buckingham, A.D.1
Fowler, P.W.2
-
53
-
-
0027898472
-
Point charge representation of multicenter multipole moments in calculation of electrostatic properties
-
Sokalski, W.A., Shibata, M., Ornstein, R.L., Rein, R. (1993) Point charge representation of multicenter multipole moments in calculation of electrostatic properties. Theor. Chim. Acta, 85, 209-216.
-
(1993)
Theor. Chim. Acta
, vol.85
, pp. 209-216
-
-
Sokalski, W.A.1
Shibata, M.2
Ornstein, R.L.3
Rein, R.4
-
54
-
-
0001475763
-
Distributed multipole analysis, or how to describe a molecular charge distribution
-
Stone, A.J. (1981) Distributed multipole analysis, or how to describe a molecular charge distribution. Chem. Phys. Lett., 83, 233-239.
-
(1981)
Chem. Phys. Lett
, vol.83
, pp. 233-239
-
-
Stone, A.J.1
-
55
-
-
0034245990
-
Atomic partitioning of molecular electrostatic potentials
-
Kosov, D., Popelier, P.L.A. (2000) Atomic partitioning of molecular electrostatic potentials. J. Phys. Chem. A, 104, 7339-7345.
-
(2000)
J. Phys. Chem. A
, vol.104
, pp. 7339-7345
-
-
Kosov, D.1
Popelier, P.L.A.2
-
56
-
-
0035974484
-
Molecular mechanical models for organic and biological systems going beyond the atom centered two body additive approximation: Aqueous solution free energies of methanol and N-methyl acetamide, nucleic acid base, and amide hydrogen bonding and chloroform/water partition coefficients of the nucleic acid bases
-
Cieplak, P., Caldwell, J., Kollman, P. (2001) Molecular mechanical models for organic and biological systems going beyond the atom centered two body additive approximation: aqueous solution free energies of methanol and N-methyl acetamide, nucleic acid base, and amide hydrogen bonding and chloroform/water partition coefficients of the nucleic acid bases. J. Comput. Chem., 22, 1048-1057.
-
(2001)
J. Comput. Chem
, vol.22
, pp. 1048-1057
-
-
Cieplak, P.1
Caldwell, J.2
Kollman, P.3
-
57
-
-
0036882094
-
Development of a polarizable force field for proteins via ab initio quantum chemistry: First generation model and gas phase tests
-
Kaminski, G.A., Stern, H.A., Berne, B.J., Friesner, R.A., Cao, Y.X., Murphy, R.B., Zhou, R., Halgren, T.A. (2002) Development of a polarizable force field for proteins via ab initio quantum chemistry: first generation model and gas phase tests. J. Comput. Chem., 23, 1515-1531.
-
(2002)
J. Comput. Chem
, vol.23
, pp. 1515-1531
-
-
Kaminski, G.A.1
Stern, H.A.2
Berne, B.J.3
Friesner, R.A.4
Cao, Y.X.5
Murphy, R.B.6
Zhou, R.7
Halgren, T.A.8
-
58
-
-
0037899660
-
Polarizable atomic multipole water model for molecular mechanics simulation
-
Ren, P., Ponder, J.W. (2003) Polarizable atomic multipole water model for molecular mechanics simulation. J. Phys. Chem. B, 107, 5933-5947.
-
(2003)
J. Phys. Chem. B
, vol.107
, pp. 5933-5947
-
-
Ren, P.1
Ponder, J.W.2
-
59
-
-
33645858780
-
Transferable intermolecular potential functions for water, alcohols, and ethers. Application to liquid water
-
Jorgensen, W.L. (1981) Transferable intermolecular potential functions for water, alcohols, and ethers. Application to liquid water. J. Am. Chem. Soc., 103, 335-340.
-
(1981)
J. Am. Chem. Soc
, vol.103
, pp. 335-340
-
-
Jorgensen, W.L.1
-
60
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen, W.L., Chandrasekhar, J., Madura, J.D., Impey, R.W., Klein, M.L. (1983) Comparison of simple potential functions for simulating liquid water. J. Chem. Phys., 79, 926-935.
-
(1983)
J. Chem. Phys
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
61
-
-
1242346370
-
The missing term in effective pair potentials
-
Berendsen, H.J.C., Grigera, J.R., Sfraatsma, T.P. (1987) The missing term in effective pair potentials. J. Phys. Chem., 91, 6269-6271.
-
(1987)
J. Phys. Chem
, vol.91
, pp. 6269-6271
-
-
Berendsen, H.J.C.1
Grigera, J.R.2
Sfraatsma, T.P.3
-
62
-
-
0000125216
-
Calibration and testing of a water model for simulation of the molecular dynamics of proteins and nucleic acids in solution
-
Levitt, M., Hirshberg, M., Sharon, R., Laidig, K.E., Daggett, V. (1997) Calibration and testing of a water model for simulation of the molecular dynamics of proteins and nucleic acids in solution. J. Phys. Chem. B, 101, 5051-5061.
-
(1997)
J. Phys. Chem. B
, vol.101
, pp. 5051-5061
-
-
Levitt, M.1
Hirshberg, M.2
Sharon, R.3
Laidig, K.E.4
Daggett, V.5
-
63
-
-
36449007976
-
The effect of long-range electrostatic interactions in simulations of macromolecular crystals: A comparison of the Ewald and truncated list methods
-
York, D.M., Darden, T., Pedersen, L.G. (1993) The effect of long-range electrostatic interactions in simulations of macromolecular crystals: a comparison of the Ewald and truncated list methods. J. Chem. Phys., 99, 8345-8348.
-
(1993)
J. Chem. Phys
, vol.99
, pp. 8345-8348
-
-
York, D.M.1
Darden, T.2
Pedersen, L.G.3
-
64
-
-
33846823909
-
Particle mesh Ewald: An N*log(N) method for Ewald sums in large systems
-
Darden, T., York, D., Pedersen, L. (1993) Particle mesh Ewald: an N*log(N) method for Ewald sums in large systems J. Chem. Phys., 98, 10089-10092.
-
(1993)
J. Chem. Phys
, vol.98
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
65
-
-
0000555535
-
Sur la constitution de la charge électrique a la surface d'un electrolyte
-
Gouy, M. (1910) Sur la constitution de la charge électrique a la surface d'un electrolyte. Journ. Phys., 9, 457-468.
-
(1910)
Journ. Phys
, vol.9
, pp. 457-468
-
-
Gouy, M.1
-
66
-
-
0023779259
-
Calculation of the total electrostatic energy of a macromolecular system: Solvation energies, binding energies, and conformational analysis
-
Gilson, M.K., Honig, B. (1988) Calculation of the total electrostatic energy of a macromolecular system: solvation energies, binding energies, and conformational analysis. Proteins, 4, 7-18.
-
(1988)
Proteins
, vol.4
, pp. 7-18
-
-
Gilson, M.K.1
Honig, B.2
-
67
-
-
84986486656
-
A rapid finite difference algorithm, utilizing successive over-relaxation to solve the Poisson-Boltzmann equation
-
Nicholls, A., Honig, B. (1991) A rapid finite difference algorithm, utilizing successive over-relaxation to solve the Poisson-Boltzmann equation. J. Comp. Chem., 12, 435-445.
-
(1991)
J. Comp. Chem
, vol.12
, pp. 435-445
-
-
Nicholls, A.1
Honig, B.2
-
68
-
-
0033654297
-
Generalized Born models of macromolecular solvation effects
-
Bashford, D., Case, D.A. (2000) Generalized Born models of macromolecular solvation effects. Annu. Rev. Phys. Chem., 51, 129-152.
-
(2000)
Annu. Rev. Phys. Chem
, vol.51
, pp. 129-152
-
-
Bashford, D.1
Case, D.A.2
-
69
-
-
0037375615
-
Ab initio construction of polypeptide fragments: Accuracy of loop decoy discrimination by an all-atom statistical potential and the AMBER force field with the generalized born solvation model
-
de Bakker, P.I.W., DePristo, M.A., Burke, D.F., Blundell, T.L. (2003) Ab initio construction of polypeptide fragments: accuracy of loop decoy discrimination by an all-atom statistical potential and the AMBER force field with the generalized born solvation model. Proteins, 51, 21-40.
-
(2003)
Proteins
, vol.51
, pp. 21-40
-
-
de Bakker, P.I.W.1
DePristo, M.A.2
Burke, D.F.3
Blundell, T.L.4
-
70
-
-
0038650794
-
Protocol for MM/PBSA molecular dynamics simulations of proteins
-
Fogolari, F., Brigo, A., Molinari, H. (2003) Protocol for MM/PBSA molecular dynamics simulations of proteins. Biophys. J., 85, 159-166.
-
(2003)
Biophys. J
, vol.85
, pp. 159-166
-
-
Fogolari, F.1
Brigo, A.2
Molinari, H.3
-
71
-
-
0017100947
-
Theoretical studies of enzymic reactions -dielectric, electrostatic and steric stabilization of carbonium-ion in reaction of lysozyme
-
Warshel, A., Levitt, M. (1976) Theoretical studies of enzymic reactions -dielectric, electrostatic and steric stabilization of carbonium-ion in reaction of lysozyme. J. Mol. Biol., 103, 227-249.
-
(1976)
J. Mol. Biol
, vol.103
, pp. 227-249
-
-
Warshel, A.1
Levitt, M.2
-
72
-
-
0018780591
-
Side-chain torsional, potentials: Effect of dipeptide, protein, and solvent environment
-
Gelin, B.R., Karplus, M. (1979) Side-chain torsional, potentials: effect of dipeptide, protein, and solvent environment. Biochemistry, 18, 1256-1268.
-
(1979)
Biochemistry
, vol.18
, pp. 1256-1268
-
-
Gelin, B.R.1
Karplus, M.2
-
73
-
-
0033135638
-
Effective energy function for proteins in solution
-
Lazaridis, T., Karplus, M. (1999) Effective energy function for proteins in solution. Proteins, 35, 133-152.
-
(1999)
Proteins
, vol.35
, pp. 133-152
-
-
Lazaridis, T.1
Karplus, M.2
-
74
-
-
0036679837
-
Distance and exposure dependent effective dielectric function
-
Mallik, B., Masunov, A., Lazaridis, T. (2002) Distance and exposure dependent effective dielectric function. J. Comp. Chem., 23, 1090-1099.
-
(2002)
J. Comp. Chem
, vol.23
, pp. 1090-1099
-
-
Mallik, B.1
Masunov, A.2
Lazaridis, T.3
-
75
-
-
0030914617
-
Comparison of database potentials and molecular mechanics force fields
-
Moult, J. (1997) Comparison of database potentials and molecular mechanics force fields. Curr. Opin. Struct. Biol., 7, 194-199.
-
(1997)
Curr. Opin. Struct. Biol
, vol.7
, pp. 194-199
-
-
Moult, J.1
-
76
-
-
0019934717
-
The helical hydrophobic moment: A measure of the amphiphilicity of a helix
-
Eisenberg, D., Weiss, R.M., Terwillinger, T.C. (1982) The helical hydrophobic moment: a measure of the amphiphilicity of a helix. Nature, 299, 371-374.
-
(1982)
Nature
, vol.299
, pp. 371-374
-
-
Eisenberg, D.1
Weiss, R.M.2
Terwillinger, T.C.3
-
77
-
-
0026704815
-
-
Sippl, M.W., S. (1992) Detection of native-like models for amino acid sequences of unknown three-dimensional structure in a database of known protein conformations. Proteins, 13, 258-271.
-
Sippl, M.W., S. (1992) Detection of native-like models for amino acid sequences of unknown three-dimensional structure in a database of known protein conformations. Proteins, 13, 258-271.
-
-
-
-
78
-
-
0035698619
-
Predicting novel protein folds by using FRAGFOLD
-
Jones, D.T. (2001) Predicting novel protein folds by using FRAGFOLD. Proteins, 45, 127-132.
-
(2001)
Proteins
, vol.45
, pp. 127-132
-
-
Jones, D.T.1
-
79
-
-
16644386061
-
Tertiary structure predictions on a comprehensive benchmark of medium to large size proteins
-
Zhang, Y., Skolnick, J. (2004) Tertiary structure predictions on a comprehensive benchmark of medium to large size proteins. Biophys. J., 87, 2647-2655.
-
(2004)
Biophys. J
, vol.87
, pp. 2647-2655
-
-
Zhang, Y.1
Skolnick, J.2
-
80
-
-
1842484092
-
Protein fragment reconstruction using various modeling techniques
-
Boniecki, M., Rotkiewicz, P., Skolnick, J., Kolinski, A. (2003) Protein fragment reconstruction using various modeling techniques. J. Comput. Aided Mol. Des., 17, 725-738.
-
(2003)
J. Comput. Aided Mol. Des
, vol.17
, pp. 725-738
-
-
Boniecki, M.1
Rotkiewicz, P.2
Skolnick, J.3
Kolinski, A.4
-
81
-
-
21444448763
-
PROTINFO: New algorithms for enhanced protein structure predictions
-
Hung, L.H., Ngan, S.C., Liu, T., Samudrala, R. (2005) PROTINFO: new algorithms for enhanced protein structure predictions. Nucleic Acids Res., 33, W77-W80.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Hung, L.H.1
Ngan, S.C.2
Liu, T.3
Samudrala, R.4
-
82
-
-
0037248878
-
The Protein Data Bank and structural genomics
-
Westbrook, J., Feng, Z., Chen, L., Yang, H., Berman, H.M. (2003) The Protein Data Bank and structural genomics. Nucleic Acids Res., 31, 489-491.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 489-491
-
-
Westbrook, J.1
Feng, Z.2
Chen, L.3
Yang, H.4
Berman, H.M.5
-
83
-
-
9144251611
-
The distribution and query systems of the RCSB Protein Data Bank
-
Bourne, P.E., Addess, K.J., Bluhm, W.F., Chen, L., Deshpande, N., Feng, Z., Fieri, W., Green, R., Merino-Ott, J.C, Townsend-Merino, W., Weissig, H., Westbrook, J., Berman, H.M. (2004) The distribution and query systems of the RCSB Protein Data Bank. Nucleic Acids Res., 32, D223-D225.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Bourne, P.E.1
Addess, K.J.2
Bluhm, W.F.3
Chen, L.4
Deshpande, N.5
Feng, Z.6
Fieri, W.7
Green, R.8
Merino-Ott, J.C.9
Townsend-Merino, W.10
Weissig, H.11
Westbrook, J.12
Berman, H.M.13
-
84
-
-
0348129526
-
The ASTRAL compendium in 2004
-
Chandonia, J.M., Hon, G., Walker, N.S., LoConte, L., Koehl, P., Levitt, M., Brenner, S.E. (2004) The ASTRAL compendium in 2004. Nucleic Acids Res., 32, D189-D192.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Chandonia, J.M.1
Hon, G.2
Walker, N.S.3
LoConte, L.4
Koehl, P.5
Levitt, M.6
Brenner, S.E.7
-
85
-
-
0030341420
-
Knowledge-based methods for protein structure refinement and prediction
-
States, D, Agarwal, P, Gaasterland, T, Hunter, L. & Simth, R, eds, AAAI Press, Menlo Park, CA, pp
-
Subramaniam, S., Tcheng, D.K., Fenton, J. (1996) Knowledge-based methods for protein structure refinement and prediction, in Proceedings of the Fourth International Conference on Intelligent Systems in Molecular Biology (States, D., Agarwal, P., Gaasterland, T., Hunter, L. & Simth, R., eds.), AAAI Press, Menlo Park, CA, pp. 218-229.
-
(1996)
Proceedings of the Fourth International Conference on Intelligent Systems in Molecular Biology
, pp. 218-229
-
-
Subramaniam, S.1
Tcheng, D.K.2
Fenton, J.3
-
86
-
-
0028960071
-
Role of electrostatic screening in determining protein main chain conformational preferences
-
Avbelj, F., Moult, J. (1995) Role of electrostatic screening in determining protein main chain conformational preferences. Biochemistry, 34, 755-764.
-
(1995)
Biochemistry
, vol.34
, pp. 755-764
-
-
Avbelj, F.1
Moult, J.2
-
87
-
-
0035882533
-
A distance-dependent atomic knowledge-based potential, for improved protein structure selection
-
Lu, H., Skolnick, J. (2001) A distance-dependent atomic knowledge-based potential, for improved protein structure selection. Proteins, 44, 223-232.
-
(2001)
Proteins
, vol.44
, pp. 223-232
-
-
Lu, H.1
Skolnick, J.2
-
88
-
-
0036838311
-
Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction
-
Zhou, H., Zhou, Y. (2002) Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Protein Sci., 11, 2714-2726.
-
(2002)
Protein Sci
, vol.11
, pp. 2714-2726
-
-
Zhou, H.1
Zhou, Y.2
-
89
-
-
0003513556
-
-
2nd ed. Prentice Hall, Upper Saddle River, NJ
-
Oppenheim, A.V., Schafer, R.W., Buck, J.R. (1999) Discrete-Time Signal Processing, 2nd ed. Prentice Hall, Upper Saddle River, NJ.
-
(1999)
Discrete-Time Signal Processing
-
-
Oppenheim, A.V.1
Schafer, R.W.2
Buck, J.R.3
-
90
-
-
0028109886
-
Conservation and prediction of solvent accessibility in protein families
-
Rost, B., Sander, C. (1994) Conservation and prediction of solvent accessibility in protein families. Proteins, 20, 216-226.
-
(1994)
Proteins
, vol.20
, pp. 216-226
-
-
Rost, B.1
Sander, C.2
-
91
-
-
0036303121
-
NETASA: Neural network based prediction of solvent accessibility
-
Ahmad, S., Gromiha, M.M. (2002) NETASA: neural network based prediction of solvent accessibility. Bioinformatics, 18, 819-824.
-
(2002)
Bioinformatics
, vol.18
, pp. 819-824
-
-
Ahmad, S.1
Gromiha, M.M.2
-
92
-
-
1042268067
-
Prediction of protein relative solvent accessibility with support vector machines and long-range interaction 3D local descriptor
-
Kim, H., Park, H. (2004) Prediction of protein relative solvent accessibility with support vector machines and long-range interaction 3D local descriptor. Proteins, 54, 557-562.
-
(2004)
Proteins
, vol.54
, pp. 557-562
-
-
Kim, H.1
Park, H.2
-
93
-
-
0027291015
-
Prediction of protein secondary structure at better than 70% accuracy
-
Rost, B., Sander, C. (1993) Prediction of protein secondary structure at better than 70% accuracy. J. Mol. Biol., 232, 584-599.
-
(1993)
J. Mol. Biol
, vol.232
, pp. 584-599
-
-
Rost, B.1
Sander, C.2
-
94
-
-
0033578684
-
Protein secondary structure prediction based on position-specific scoring matrices
-
Jones, D.T. (1999) Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol., 292, 195-202.
-
(1999)
J. Mol. Biol
, vol.292
, pp. 195-202
-
-
Jones, D.T.1
-
95
-
-
0034663597
-
Application of enhanced multiple sequence alignment profiles to improve protein secondary structure prediction
-
Cuff, J.A., Barton, G.J. (1999) Application of enhanced multiple sequence alignment profiles to improve protein secondary structure prediction. Proteins, 40, 502-511.
-
(1999)
Proteins
, vol.40
, pp. 502-511
-
-
Cuff, J.A.1
Barton, G.J.2
-
96
-
-
0031406438
-
Protein distance constraints predicted by neural networks and probability density functions
-
Lund, O., Frimand, K., Gorodkin, J., Bohr, H., Bohr, J., Hansen, J., Brunak, S. (1997) Protein distance constraints predicted by neural networks and probability density functions. Protein Eng., 10, 1241-1248.
-
(1997)
Protein Eng
, vol.10
, pp. 1241-1248
-
-
Lund, O.1
Frimand, K.2
Gorodkin, J.3
Bohr, H.4
Bohr, J.5
Hansen, J.6
Brunak, S.7
-
97
-
-
0036568293
-
Prediction of coordination number and relative solvent accessibility in proteins
-
Pollastri, G., Baldi, P., Fariselli, P., Casadio, R. (2002) Prediction of coordination number and relative solvent accessibility in proteins. Proteins, 47, 142-153.
-
(2002)
Proteins
, vol.47
, pp. 142-153
-
-
Pollastri, G.1
Baldi, P.2
Fariselli, P.3
Casadio, R.4
-
98
-
-
0030627941
-
Improving contact predictions by the combination of correlated mutations and other sources of sequence information
-
Olmea, O., Valencia, A. (1997) Improving contact predictions by the combination of correlated mutations and other sources of sequence information. Fold Des., 2, S25-32.
-
(1997)
Fold Des
, vol.2
-
-
Olmea, O.1
Valencia, A.2
-
99
-
-
0033047710
-
Neural network based predictor of residue contacts in proteins
-
Fariselli, P., Casadio, R. (1999) Neural network based predictor of residue contacts in proteins. Protein Eng., 12, 15-21.
-
(1999)
Protein Eng
, vol.12
, pp. 15-21
-
-
Fariselli, P.1
Casadio, R.2
-
100
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul, S.F., Madden, T.L., Scharfer, A.A. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Scharfer, A.A.3
-
101
-
-
0022471098
-
Learning representations by back-propagating errors
-
Rumelhart, D.E., Hinton, G.E., Williams, R.J. (1986) Learning representations by back-propagating errors. Nature, 323, 533-536.
-
(1986)
Nature
, vol.323
, pp. 533-536
-
-
Rumelhart, D.E.1
Hinton, G.E.2
Williams, R.J.3
-
102
-
-
0027199670
-
Protein secondary structure prediction using nearest-neighbor methods
-
Yi, T.-M., Lander, E.S. (1993) Protein secondary structure prediction using nearest-neighbor methods. J. Mol. Biol., 232, 1117-1129.
-
(1993)
J. Mol. Biol
, vol.232
, pp. 1117-1129
-
-
Yi, T.-M.1
Lander, E.S.2
-
103
-
-
0020997912
-
Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
-
Kabsch, W., 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
-
104
-
-
37149024156
-
-
manual version 4.1. Available at
-
Zell, A., Mamier, G., Vogt, M., et al. (2005) The SNNS users manual version 4.1. Available at http://www-ra.informatik.uni-tuebingen.de/snns.
-
(2005)
The SNNS users
-
-
Zell, A.1
Mamier, G.2
Vogt, M.3
-
105
-
-
85030289585
-
Energy functions that discriminate x-ray and near native folds from well-constructed decoys
-
Park, B., Levitt, M. (1996) Energy functions that discriminate x-ray and near native folds from well-constructed decoys. J. Mol. Biol., 266, 831-846.
-
(1996)
J. Mol. Biol
, vol.266
, pp. 831-846
-
-
Park, B.1
Levitt, M.2
-
106
-
-
0021691918
-
An analysis of incorrectly folded protein models. Implications for structure predictions
-
Novotny, J., Bruccoleri, R., Karplus, M. (1984) An analysis of incorrectly folded protein models. Implications for structure predictions. J. Mol. Biol., 111, 787-818.
-
(1984)
J. Mol. Biol
, vol.111
, pp. 787-818
-
-
Novotny, J.1
Bruccoleri, R.2
Karplus, M.3
-
107
-
-
0026505184
-
Evaluation of protein models by atomic solvation preference
-
Holm, L., Sander, C. (1992) Evaluation of protein models by atomic solvation preference. J. Mol. Biol., 225, 93-105.
-
(1992)
J. Mol. Biol
, vol.225
, pp. 93-105
-
-
Holm, L.1
Sander, C.2
-
108
-
-
0033853177
-
Decoys 'R' Us: A database of incorrect conformations to improve protein structure prediction
-
Samudrala, R., Levitt, M. (2000) Decoys 'R' Us: a database of incorrect conformations to improve protein structure prediction. Protein Sci., 9, 1399-1401.
-
(2000)
Protein Sci
, vol.9
, pp. 1399-1401
-
-
Samudrala, R.1
Levitt, M.2
-
109
-
-
0038008976
-
An improved protein decoy set for testing energy functions for protein structure prediction
-
Tsai J., B., R., Morozov, A.V., Kuhlman, B., Rohl, C.A., Baker, D. (2003) An improved protein decoy set for testing energy functions for protein structure prediction. Proteins, 53, 76-87.
-
(2003)
Proteins
, vol.53
, pp. 76-87
-
-
Tsai, J.B.R.1
Morozov, A.V.2
Kuhlman, B.3
Rohl, C.A.4
Baker, D.5
-
110
-
-
0031557390
-
Factors affecting the ability of energy functions to discriminate correct from incorrect folds
-
Park, B.H., Huang, E.S., 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
-
111
-
-
0026519315
-
A lattice model for protein structure prediction at low resolution
-
Hinds, D.A., Levitt, M. (1992) A lattice model for protein structure prediction at low resolution. Proc. Natl. Acad. Sci. U. S. A., 89, 2536-2540.
-
(1992)
Proc. Natl. Acad. Sci. U. S. A
, vol.89
, pp. 2536-2540
-
-
Hinds, D.A.1
Levitt, M.2
-
112
-
-
0029063717
-
The complexity and accuracy of discrete state models of protein structure
-
Park, B., Levitt, M. (1995) The complexity and accuracy of discrete state models of protein structure. J. Mol. Biol., 249, 493-507.
-
(1995)
J. Mol. Biol
, vol.249
, pp. 493-507
-
-
Park, B.1
Levitt, M.2
-
113
-
-
0031585984
-
Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions
-
Simons, K.T., 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
-
114
-
-
0042622449
-
PROTINFO: Secondary and tertiary protein structure prediction
-
Hung, L.H., Samudrala, R. (2003) PROTINFO: secondary and tertiary protein structure prediction. Nucleic Acids Res., 31, 3296-3299.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3296-3299
-
-
Hung, L.H.1
Samudrala, R.2
-
115
-
-
0037452894
-
Discrimination of native protein structures using atom-atom contact scoring
-
McConkey, B.J., Sobolev, V., Edelman, M. (2003) Discrimination of native protein structures using atom-atom contact scoring. Proc. Natl. Acad. Sci. U. S. A., 100, 3215-3220.
-
(2003)
Proc. Natl. Acad. Sci. U. S. A
, vol.100
, pp. 3215-3220
-
-
McConkey, B.J.1
Sobolev, V.2
Edelman, M.3
-
116
-
-
0035943455
-
Four-body potentials reveal protein-specific correlations to stability changes caused by hydrophobic core mutations
-
Carter, C.W., Jr., LeFebvre, B.C., Cammer, S.A., Tropsha, A., Edgell, M.H. (2001) Four-body potentials reveal protein-specific correlations to stability changes caused by hydrophobic core mutations. J. Mol., Biol., 311, 625-638.
-
(2001)
J. Mol., Biol
, vol.311
, pp. 625-638
-
-
Carter Jr., C.W.1
LeFebvre, B.C.2
Cammer, S.A.3
Tropsha, A.4
Edgell, M.H.5
-
117
-
-
0042889108
-
Development of a four-body statistical pseudo-potential to discriminate native from non-native protein conformations
-
Krishnamoorthy, B., Tropsha, A. (2003) Development of a four-body statistical pseudo-potential to discriminate native from non-native protein conformations. Bioinformatics, 19, 1540-1548.
-
(2003)
Bioinformatics
, vol.19
, pp. 1540-1548
-
-
Krishnamoorthy, B.1
Tropsha, A.2
-
118
-
-
33646238690
-
A knowledge-based scoring function based on residue triplets for protein structure prediction
-
Ngan, S.-C., Inonye, M.T, Samudrala, R. (2006) A knowledge-based scoring function based on residue triplets for protein structure prediction. Protein Eng., 19, 187-193.
-
(2006)
Protein Eng
, vol.19
, pp. 187-193
-
-
Ngan, S.-C.1
Inonye, M.T.2
Samudrala, R.3
-
119
-
-
0344980731
-
Simplicial edge representation of protein structures and alpha contact potential with confidence measure
-
Li, X., Hu, C., Liang, J. (2003) Simplicial edge representation of protein structures and alpha contact potential with confidence measure. Proteins, 53, 792-805.
-
(2003)
Proteins
, vol.53
, pp. 792-805
-
-
Li, X.1
Hu, C.2
Liang, J.3
-
120
-
-
4544355522
-
Improved protein structure selection using decoy-dependent discriminatory functions
-
Wang, K., Fain, B., Levitt, M., Samudrala, R. (2004) Improved protein structure selection using decoy-dependent discriminatory functions. BMC Struct. Biol., 4, 8.
-
(2004)
BMC Struct. Biol
, vol.4
, pp. 8
-
-
Wang, K.1
Fain, B.2
Levitt, M.3
Samudrala, R.4
-
121
-
-
1942519275
-
SPICKER: A clustering approach to identify near-native protein folds
-
Zhang, Y., Skolnick, J. (2004) SPICKER: a clustering approach to identify near-native protein folds. J. Comput. Chem., 25, 865-871.
-
(2004)
J. Comput. Chem
, vol.25
, pp. 865-871
-
-
Zhang, Y.1
Skolnick, J.2
-
122
-
-
37149025388
-
-
Available at
-
Samudrala, R. (2006). RAMP Howto. Available at http://software.compbio. washington.edu/ramp/ramp.html
-
(2006)
RAMP Howto
-
-
Samudrala, R.1
-
123
-
-
14644438345
-
Progress and challenges in high-resolution refinement of protein structure models
-
Misura, K.M.S., Baker, D. (2005) Progress and challenges in high-resolution refinement of protein structure models. Proteins, 59, 15-29.
-
(2005)
Proteins
, vol.59
, pp. 15-29
-
-
Misura, K.M.S.1
Baker, D.2
-
124
-
-
24944493938
-
Toward high-resolution de novo structure prediction for small proteins
-
Bradley, P., Misura, K.M.S., Baker, D. (2005) Toward high-resolution de novo structure prediction for small proteins. Science, 309, 1868-1871.
-
(2005)
Science
, vol.309
, pp. 1868-1871
-
-
Bradley, P.1
Misura, K.M.S.2
Baker, D.3
-
125
-
-
0037470581
-
An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes
-
Kortemme, T., Morozov, A.V., Baker, D. (2003) An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes. J. Mol. Biol., 326, 1239-1259.
-
(2003)
J. Mol. Biol
, vol.326
, pp. 1239-1259
-
-
Kortemme, T.1
Morozov, A.V.2
Baker, D.3
-
126
-
-
0036073603
-
Contact order and ab initio protein structure prediction
-
Bonneau, R., Ruczinski, I., Tsai, J., Baker, D. (2002) Contact order and ab initio protein structure prediction. Protein Sci., 11, 1937-1944.
-
(2002)
Protein Sci
, vol.11
, pp. 1937-1944
-
-
Bonneau, R.1
Ruczinski, I.2
Tsai, J.3
Baker, D.4
-
127
-
-
30344483607
-
Free modeling with Rosetta in CASP6
-
Bradley, P., Malmsfrom, L., Qian, B., Schonburn, J., Chivian, D., Kim, D.E., Meiler, J., Misura, K.M., Baker D. (2005) Free modeling with Rosetta in CASP6. Proteins, 61, 128-134.
-
(2005)
Proteins
, vol.61
, pp. 128-134
-
-
Bradley, P.1
Malmsfrom, L.2
Qian, B.3
Schonburn, J.4
Chivian, D.5
Kim, D.E.6
Meiler, J.7
Misura, K.M.8
Baker, D.9
|