-
1
-
-
0020655246
-
Structural domains in proteins and their role in the dynamics of protein function
-
Janin, J., Wodak, S.J. Structural domains in proteins and their role in the dynamics of protein function. Prog. Biophys. Mol. Biol. 42:21-78, 1983.
-
(1983)
Prog. Biophys. Mol. Biol.
, vol.42
, pp. 21-78
-
-
Janin, J.1
Wodak, S.J.2
-
2
-
-
0021314461
-
Structural and functional aspects of domain motions in proteins
-
Bennett, W.S., Huber, R. Structural and functional aspects of domain motions in proteins. Crit. Rev. Biochem. 15:291-384, 1984.
-
(1984)
Crit. Rev. Biochem.
, vol.15
, pp. 291-384
-
-
Bennett, W.S.1
Huber, R.2
-
3
-
-
0023488997
-
Flexibility and rigidity, requirements of the function of proteins and protein pigment complexes
-
Huber, R. Flexibility and rigidity, requirements of the function of proteins and protein pigment complexes. Biochem. Soc. Trans. 15:1009-1020, 1987.
-
(1987)
Biochem. Soc. Trans.
, vol.15
, pp. 1009-1020
-
-
Huber, R.1
-
4
-
-
0000453761
-
Domain motions in proteins
-
Schulz, G.E. Domain motions in proteins. Curr. Opin. Struct. Biol. 1:883-888, 1991.
-
(1991)
Curr. Opin. Struct. Biol.
, vol.1
, pp. 883-888
-
-
Schulz, G.E.1
-
5
-
-
0028335096
-
Structural mechanisms for domain movements in proteins
-
Gerstein, M., Lesk, A.M., Chothia, C. Structural mechanisms for domain movements in proteins. Biochemistry 33:6739-7649, 1994.
-
(1994)
Biochemistry
, vol.33
, pp. 6739-7649
-
-
Gerstein, M.1
Lesk, A.M.2
Chothia, C.3
-
6
-
-
0002638513
-
Protein data bank in crystallographic databases: Information content, software systems, scientific applications
-
Abola, E.E., Bernstein, E.C., Bryant, S.H., Koetzle, T.F., Weng, J. Protein data bank in crystallographic databases: information content, software systems, scientific applications. Data Commission Int Union Crystallogr. 107-132, 1987.
-
(1987)
Data Commission Int Union Crystallogr.
, pp. 107-132
-
-
Abola, E.E.1
Bernstein, E.C.2
Bryant, S.H.3
Koetzle, T.F.4
Weng, J.5
-
7
-
-
0017411710
-
The protein data bank: A computer-based archival file for macromolecular structures
-
Bernstein, F.C., Koetzle, T.F., Williams, G.J.B., Meyer, E.F., Brice, M.D., Rodgers, J.R., Kennard, O., Shimanouchi, T., Tasumi, M. The protein data bank: A computer-based archival file for macromolecular structures. J. Mol. Biol. 112:535-542, 1977.
-
(1977)
J. Mol. Biol.
, vol.112
, pp. 535-542
-
-
Bernstein, F.C.1
Koetzle, T.F.2
Williams, G.J.B.3
Meyer, E.F.4
Brice, M.D.5
Rodgers, J.R.6
Kennard, O.7
Shimanouchi, T.8
Tasumi, M.9
-
8
-
-
0024573351
-
Structure of a second crystal form of Bence-Jones protein Loc: Strikingly different domain associations in two crystal forms of a single protein
-
Schiffer, M., Ainsworth, C., Xu, Z.-B., Carperos, W., Olsen, K., Solomon, A., Stevens, F.J., Chang, C.-H. Structure of a second crystal form of Bence-Jones protein Loc: Strikingly different domain associations in two crystal forms of a single protein. Biochemistry 28:4066-4072, 1989.
-
(1989)
Biochemistry
, vol.28
, pp. 4066-4072
-
-
Schiffer, M.1
Ainsworth, C.2
Xu, Z.-B.3
Carperos, W.4
Olsen, K.5
Solomon, A.6
Stevens, F.J.7
Chang, C.-H.8
-
9
-
-
0025047629
-
A mutant T4 lysozyme displays five different crystal conformations
-
Faber, H.R., Matthews, B.W. A mutant T4 lysozyme displays five different crystal conformations. Nature 348:263-266, 1990.
-
(1990)
Nature
, vol.348
, pp. 263-266
-
-
Faber, H.R.1
Matthews, B.W.2
-
10
-
-
0026802277
-
Structure of a hinge-bending bacteriophage T4 lysozyme mutant, Ile3 → Prog
-
Dixon, M.M., Nicholson, H., Shewchuk, L., Baase, W.A., Matthews, B.W. Structure of a hinge-bending bacteriophage T4 lysozyme mutant, Ile3 → Prog. J. Mol. Biol. 227:917-933, 1992.
-
(1992)
J. Mol. Biol.
, vol.227
, pp. 917-933
-
-
Dixon, M.M.1
Nicholson, H.2
Shewchuk, L.3
Baase, W.A.4
Matthews, B.W.5
-
11
-
-
0026489329
-
Structural comparison suggests that thermolysin and related neural proteases undergo hinge-bending motion during catalysis
-
Holland, D.R., Tronrud, D.E., Pley, H.W., Flaherty, K.M., Stark, W., Jansonius, J.N., McKay, D.B., Matthews, B.W. Structural comparison suggests that thermolysin and related neural proteases undergo hinge-bending motion during catalysis. Biochemistry 31:11310-11316, 1992.
-
(1992)
Biochemistry
, vol.31
, pp. 11310-11316
-
-
Holland, D.R.1
Tronrud, D.E.2
Pley, H.W.3
Flaherty, K.M.4
Stark, W.5
Jansonius, J.N.6
McKay, D.B.7
Matthews, B.W.8
-
12
-
-
0026595547
-
Domain flexibility in aspartic proteinases
-
Sali, A., Veerapandian, B., Cooper, J.B., Moss, D.S., Hofmann, T., Blundell, T.L. Domain flexibility in aspartic proteinases. Proteins 12:158-170, 1992.
-
(1992)
Proteins
, vol.12
, pp. 158-170
-
-
Sali, A.1
Veerapandian, B.2
Cooper, J.B.3
Moss, D.S.4
Hofmann, T.5
Blundell, T.L.6
-
13
-
-
0025716317
-
Atomic structures of periplasmic binding proteins and the high-affinity active transport systems in bacteria
-
Quiocho, F.A. Atomic structures of periplasmic binding proteins and the high-affinity active transport systems in bacteria. Phil. Trans. R. Soc. Lond. [Biol.] 326:341-351, 1990.
-
(1990)
Phil. Trans. R. Soc. Lond. [Biol.]
, vol.326
, pp. 341-351
-
-
Quiocho, F.A.1
-
14
-
-
0027326717
-
Crystal structure of hemoprotein domain of P450BM-3, a prototype for microsomal P450's
-
Ravichandran, K.G., Boddupalli, S.S., Hasemann, C.A., Peterson, J.A., Deisenhofer, J. Crystal structure of hemoprotein domain of P450BM-3, a prototype for microsomal P450's. Science 261:731-736, 1993.
-
(1993)
Science
, vol.261
, pp. 731-736
-
-
Ravichandran, K.G.1
Boddupalli, S.S.2
Hasemann, C.A.3
Peterson, J.A.4
Deisenhofer, J.5
-
15
-
-
0029644728
-
Movie of the structural changes during a catalytic cycle of nucleoside monophosphate kinases
-
Vonrhein, C., Schlauderer, G.J., Schulz, G.E. Movie of the structural changes during a catalytic cycle of nucleoside monophosphate kinases. Structure 3:483-490, 1995.
-
(1995)
Structure
, vol.3
, pp. 483-490
-
-
Vonrhein, C.1
Schlauderer, G.J.2
Schulz, G.E.3
-
16
-
-
0027528934
-
Domain closure in adenylate kinase: Joints on either side of two helices close like neighboring fingers
-
Gerstein, M., Schulz, G., Chothia, C. Domain closure in adenylate kinase: Joints on either side of two helices close like neighboring fingers. J. Mol. Biol. 229:494-501, 1993.
-
(1993)
J. Mol. Biol.
, vol.229
, pp. 494-501
-
-
Gerstein, M.1
Schulz, G.2
Chothia, C.3
-
17
-
-
0027438949
-
Domain closure in lactoferrin: Two hinges produce a see-saw motion between alternative close-packed interfaces
-
Gerstein, M., Anderson, B.F., Norris, G.E., Baker, E.N., Lesk, A.M., Chothia, C. Domain closure in lactoferrin: Two hinges produce a see-saw motion between alternative close-packed interfaces. J. Mol. Biol. 234:357-372, 1994.
-
(1994)
J. Mol. Biol.
, vol.234
, pp. 357-372
-
-
Gerstein, M.1
Anderson, B.F.2
Norris, G.E.3
Baker, E.N.4
Lesk, A.M.5
Chothia, C.6
-
18
-
-
0021604916
-
Mechanisms of domain closure in proteins
-
Lesk, A.M., Chothia, C. Mechanisms of domain closure in proteins. J. Mol. Biol. 174:175-191, 1984.
-
(1984)
J. Mol. Biol.
, vol.174
, pp. 175-191
-
-
Lesk, A.M.1
Chothia, C.2
-
19
-
-
0028826992
-
Automatic analysis of protein conformational changes by multiple linkage clustering
-
Boutonnett, N.S., Rooman, M.J., Wodak, S.J. Automatic analysis of protein conformational changes by multiple linkage clustering. J. Mol. Biol. 253:633-647, 1995.
-
(1995)
J. Mol. Biol.
, vol.253
, pp. 633-647
-
-
Boutonnett, N.S.1
Rooman, M.J.2
Wodak, S.J.3
-
20
-
-
0017163950
-
The hinge-bending mode in lysozyme
-
McCammon, J.A., Gelin, B.R., Karplus, M., Wolynes, P.G. The hinge-bending mode in lysozyme. Nature 262:325-326, 1976.
-
(1976)
Nature
, vol.262
, pp. 325-326
-
-
McCammon, J.A.1
Gelin, B.R.2
Karplus, M.3
Wolynes, P.G.4
-
21
-
-
0021347272
-
Structural study of hinge bending in L-arabinose-binding protein
-
Mao, B., McCammon, J.A. Structural study of hinge bending in L-arabinose-binding protein. J. Biol. Chem. 59:964-4970, 1984.
-
(1984)
J. Biol. Chem.
, vol.59
, pp. 964-4970
-
-
Mao, B.1
McCammon, J.A.2
-
22
-
-
0023035967
-
Interdomain motion in liver alcohol dehydrogenase: Structural and energetic analysis of the hinge bending mode
-
Colonna-Cesari, F., Perahia, D., Karplus, M., Eklund, H., Braden, C.I., Tapia, O. Interdomain motion in liver alcohol dehydrogenase: Structural and energetic analysis of the hinge bending mode. J. Biol. Chem. 261:15273-15280, 1986.
-
(1986)
J. Biol. Chem.
, vol.261
, pp. 15273-15280
-
-
Colonna-Cesari, F.1
Perahia, D.2
Karplus, M.3
Eklund, H.4
Braden, C.I.5
Tapia, O.6
-
23
-
-
0026459304
-
A molecular dynamics simulation of bacteriophage T4 lysozyme
-
Arnold, G.E., Ornstein, R.L. A molecular dynamics simulation of bacteriophage T4 lysozyme. Protein Eng. 5:703-714, 1992.
-
(1992)
Protein Eng.
, vol.5
, pp. 703-714
-
-
Arnold, G.E.1
Ornstein, R.L.2
-
24
-
-
0028061638
-
Investigation of domain motions in baeteriophage T4 lysozyme
-
Arnold, G.E., Manchester, J.I., Townsend, B.D., Ornstein, R.L. Investigation of domain motions in baeteriophage T4 lysozyme. J. Biomol. Struct. Dyn. 12:457-474, 1994.
-
(1994)
J. Biomol. Struct. Dyn.
, vol.12
, pp. 457-474
-
-
Arnold, G.E.1
Manchester, J.I.2
Townsend, B.D.3
Ornstein, R.L.4
-
25
-
-
0028956684
-
Dramatic differences in the motions of the mouth of open and closed cytochrome P450BM-3 by molecular dynamics simulations
-
Paulsen, M.D., Ornstein, R.L. Dramatic differences in the motions of the mouth of open and closed cytochrome P450BM-3 by molecular dynamics simulations. Proteins 21:237-243, 1995.
-
(1995)
Proteins
, vol.21
, pp. 237-243
-
-
Paulsen, M.D.1
Ornstein, R.L.2
-
26
-
-
0029916115
-
DNA binding by TATA-box binding protein (TBP): A molecular dynamics computational study
-
Miaskiewicz, K., Ornstein, R.L. DNA binding by TATA-box binding protein (TBP): A molecular dynamics computational study. J. Biomol. Struct. Dyn. 13:593-600, 1996.
-
(1996)
J. Biomol. Struct. Dyn.
, vol.13
, pp. 593-600
-
-
Miaskiewicz, K.1
Ornstein, R.L.2
-
27
-
-
0025913645
-
Structural dynamics of calmodulin and troponin C
-
Mehler, E.L., Pascual-Ahuir, J.L., Weinstein, H. Structural dynamics of calmodulin and troponin C. Protein Eng. 4:625-637, 1991.
-
(1991)
Protein Eng.
, vol.4
, pp. 625-637
-
-
Mehler, E.L.1
Pascual-Ahuir, J.L.2
Weinstein, H.3
-
28
-
-
0029020507
-
Functional role of arginine-11 in the N-terminal helix of skeletal troponin C: Combined mutagenesis and molecular dynamics investigation
-
Gulati, J., Akella, A.B., Su, H., Mehler, E.L., Weinstein, H. Functional role of arginine-11 in the N-terminal helix of skeletal troponin C: Combined mutagenesis and molecular dynamics investigation. Biochemistry 34:7348-7355, 1995.
-
(1995)
Biochemistry
, vol.34
, pp. 7348-7355
-
-
Gulati, J.1
Akella, A.B.2
Su, H.3
Mehler, E.L.4
Weinstein, H.5
-
29
-
-
0029886930
-
Study of global motions in proteins by weighted masses molecular dynamics: Adenilate kinase as a test case
-
Elamrani, S., Berry, M.B., Phillips Jr., G.N., McCammon, J.A. Study of global motions in proteins by weighted masses molecular dynamics: Adenilate kinase as a test case. Proteins 25:79-88, 1996.
-
(1996)
Proteins
, vol.25
, pp. 79-88
-
-
Elamrani, S.1
Berry, M.B.2
Phillips Jr., G.N.3
McCammon, J.A.4
-
30
-
-
0025292904
-
Langevin modes of macromolecules: Applications to crambin and DNA haxamers
-
Kottlam, J., Case, D.A. Langevin modes of macromolecules: Applications to crambin and DNA haxamers. Biopolymers 29:1409-1421, 1990.
-
(1990)
Biopolymers
, vol.29
, pp. 1409-1421
-
-
Kottlam, J.1
Case, D.A.2
-
31
-
-
0024609784
-
New methodology for computer-aided modelling of biomolecular structure and dynamics. 1. Non-cyclic structures
-
Mazur, A.K., Abagyan, R.A. New methodology for computer-aided modelling of biomolecular structure and dynamics. 1. Non-cyclic structures. J. Biomol. Struct. Dyn. 6:815-832, 1989.
-
(1989)
J. Biomol. Struct. Dyn.
, vol.6
, pp. 815-832
-
-
Mazur, A.K.1
Abagyan, R.A.2
-
32
-
-
0000253286
-
Derivation and testing of explicit equations of motion for polymers described by internal coordinates
-
Mazur, A.K., Dorofeyef, V.E., Abagyan, R.A. Derivation and testing of explicit equations of motion for polymers described by internal coordinates. J. Comp. Phys. 92:261-272, 1991.
-
(1991)
J. Comp. Phys.
, vol.92
, pp. 261-272
-
-
Mazur, A.K.1
Dorofeyef, V.E.2
Abagyan, R.A.3
-
33
-
-
0027163648
-
Investigation of conformational equilibrium of polypeptides by internal coordinate stochastic dynamics
-
Dorofeyef, V.E., Mazur, A.K. Investigation of conformational equilibrium of polypeptides by internal coordinate stochastic dynamics. J. Biomol. Struct. Dyn. 10:143-167, 1993.
-
(1993)
J. Biomol. Struct. Dyn.
, vol.10
, pp. 143-167
-
-
Dorofeyef, V.E.1
Mazur, A.K.2
-
34
-
-
0028063256
-
Protein simulations using techniques suitable for very large systems: The cell multipole method for nonbond interactions and the Newton-Euler inverse mass operator method for internal coordinate dynamics
-
Mathiowetz, A.M., Jain, A., Karasawa, N., Goddar III, W.A. Protein simulations using techniques suitable for very large systems: The cell multipole method for nonbond interactions and the Newton-Euler inverse mass operator method for internal coordinate dynamics. Proteins 20:227-247, 1994.
-
(1994)
Proteins
, vol.20
, pp. 227-247
-
-
Mathiowetz, A.M.1
Jain, A.2
Karasawa, N.3
Goddar III, W.A.4
-
36
-
-
0028367073
-
Simulation of enzyme-substrate encounter with gated active sites
-
Wade, R.C., Luty, B.A., Demchuk, E., Madura, J.D., Davis, M.E., Briggs, J.M., McCammon, J.A. Simulation of enzyme-substrate encounter with gated active sites. Nat. Struct. Biol. 1:65-69, 1994.
-
(1994)
Nat. Struct. Biol.
, vol.1
, pp. 65-69
-
-
Wade, R.C.1
Luty, B.A.2
Demchuk, E.3
Madura, J.D.4
Davis, M.E.5
Briggs, J.M.6
McCammon, J.A.7
-
37
-
-
0022036264
-
Efficient Monte Carlo method for simulation of fluctuating conformations of native proteins
-
Noguti, T., Gõ, N. Efficient Monte Carlo method for simulation of fluctuating conformations of native proteins. Biopolymers 24:527-546, 1985.
-
(1985)
Biopolymers
, vol.24
, pp. 527-546
-
-
Noguti, T.1
Gõ, N.2
-
38
-
-
0027441950
-
Essential dynamics of proteins
-
Amadei, A., Linssen, A.B.M., Berendsen, H.J.C. Essential dynamics of proteins. Proteins 17:412-425, 1993.
-
(1993)
Proteins
, vol.17
, pp. 412-425
-
-
Amadei, A.1
Linssen, A.B.M.2
Berendsen, H.J.C.3
-
39
-
-
1842383159
-
The essential dynamics of thermolysin: Comparison of simulations in vacuum and water
-
van Aalten, D.M.F., Amadei, A., Linssen, A.B.M., Eijsink, V.G.H., Vriend, G., Berendsen, H.J.C. The essential dynamics of thermolysin: Comparison of simulations in vacuum and water. Proteins 22:43-54, 1993.
-
(1993)
Proteins
, vol.22
, pp. 43-54
-
-
Van Aalten, D.M.F.1
Amadei, A.2
Linssen, A.B.M.3
Eijsink, V.G.H.4
Vriend, G.5
Berendsen, H.J.C.6
-
40
-
-
84986522918
-
ICM: A new method for protein modeling and design: Applications to docking and structure prediction from the disordered native conformation
-
Abagyan, R.A., Totrov, M.M., Kuznetsov, D.A. ICM: A new method for protein modeling and design: Applications to docking and structure prediction from the disordered native conformation. J. Comp. Chem. 15:488-506, 1994.
-
(1994)
J. Comp. Chem.
, vol.15
, pp. 488-506
-
-
Abagyan, R.A.1
Totrov, M.M.2
Kuznetsov, D.A.3
-
41
-
-
0027955787
-
Biased probability Monte Carlo conformational search and electrostatic calculations for peptide and proteins
-
Abagyan, R.A., Totrov, M.M. Biased probability Monte Carlo conformational search and electrostatic calculations for peptide and proteins. J. Mol. Biol. 235:983-1002, 1994.
-
(1994)
J. Mol. Biol.
, vol.235
, pp. 983-1002
-
-
Abagyan, R.A.1
Totrov, M.M.2
-
42
-
-
0027146064
-
The crystal structure of an engineered monomeric triosephosphate isomerase, monoTIM: The correct modeling of an eight-residue loop
-
Borchert, T.V., Abagyan, R.A., Kishan, K.V.R., Zeelen, J.P., Wierenga, R.K. The crystal structure of an engineered monomeric triosephosphate isomerase, monoTIM: The correct modeling of an eight-residue loop. Structure 1:205-213, 1993.
-
(1993)
Structure
, vol.1
, pp. 205-213
-
-
Borchert, T.V.1
Abagyan, R.A.2
Kishan, K.V.R.3
Zeelen, J.P.4
Wierenga, R.K.5
-
43
-
-
0027185404
-
A method to configure protein side-chains from the main-chain trace in homology modeling
-
Eisenmenger, F., Argos, P., Abagyan, R.A. A method to configure protein side-chains from the main-chain trace in homology modeling. J. Mol. Biol. 231:849-860, 1993.
-
(1993)
J. Mol. Biol.
, vol.231
, pp. 849-860
-
-
Eisenmenger, F.1
Argos, P.2
Abagyan, R.A.3
-
44
-
-
0028410583
-
Detailed ab initio prediction of lysozyme-antibody complex with 1.6 a accuracy
-
Totrov, M.M., Abagyan, R.A. Detailed ab initio prediction of lysozyme-antibody complex with 1.6 A accuracy. Nature Struct. Biol. 1:259-263, 1994.
-
(1994)
Nature Struct. Biol.
, vol.1
, pp. 259-263
-
-
Totrov, M.M.1
Abagyan, R.A.2
-
45
-
-
0028304890
-
Recognition of distantly related proteins through energy calculations
-
Abagyan, R.A., Frishman, D., Argos, P. Recognition of distantly related proteins through energy calculations. Proteins 19:132-140, 1994.
-
(1994)
Proteins
, vol.19
, pp. 132-140
-
-
Abagyan, R.A.1
Frishman, D.2
Argos, P.3
-
46
-
-
0028849881
-
Homology modeling by the ICM method
-
Cardozo, T., Totrov, M.M., Abagyan, R.A. Homology modeling by the ICM method. Proteins 23:403-414, 1995.
-
(1995)
Proteins
, vol.23
, pp. 403-414
-
-
Cardozo, T.1
Totrov, M.M.2
Abagyan, R.A.3
-
47
-
-
0027235488
-
Three-dimensional structures of the periplasmic lysine/arginine/ornithine-binding protein with and without a ligand
-
Oh, B.-H., Pandit, J., Kang, C.-H., Nikaido, K., Gokcen, S., Ames, G.F.-L., Kim, S.-H. Three-dimensional structures of the periplasmic lysine/arginine/ornithine-binding protein with and without a ligand. J. Biol. Chem. 268:11348-11355, 1993.
-
(1993)
J. Biol. Chem.
, vol.268
, pp. 11348-11355
-
-
Oh, B.-H.1
Pandit, J.2
Kang, C.-H.3
Nikaido, K.4
Gokcen, S.5
Ames, G.F.-L.6
Kim, S.-H.7
-
48
-
-
5944250450
-
Energy parameters in polypeptides. VII. Geometric parameters, partial atomic charges, nonbonded interactions, hydrogen bond interactions, and intrinsic torsional potentials for the naturally occurring amino acids
-
Momany, F.A., McGuire, R.F., Burgess, A.W., Scheraga, H.A. Energy parameters in polypeptides. VII. Geometric parameters, partial atomic charges, nonbonded interactions, hydrogen bond interactions, and intrinsic torsional potentials for the naturally occurring amino acids. J. Phys. Chem. 79:2361-2381, 1975.
-
(1975)
J. Phys. Chem.
, vol.79
, pp. 2361-2381
-
-
Momany, F.A.1
McGuire, R.F.2
Burgess, A.W.3
Scheraga, H.A.4
-
49
-
-
33845550595
-
Energy parameters in polypeptides. 9. Updating of geometric parameters, nonbonded interactions and hydrogen bond interactions for the naturally occurring amino acids
-
Nemethy, G., Pottle, M.S., Scheraga, H.A. Energy parameters in polypeptides. 9. Updating of geometric parameters, nonbonded interactions and hydrogen bond interactions for the naturally occurring amino acids. J. Phys. Chem. 87:1883-1887, 1983.
-
(1983)
J. Phys. Chem.
, vol.87
, pp. 1883-1887
-
-
Nemethy, G.1
Pottle, M.S.2
Scheraga, H.A.3
-
50
-
-
0001731773
-
Energy parameters in polypeptides. 10. Improved geometric parameters and nonbonded 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. Energy parameters in polypeptides. 10. Improved geometric parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with application to proline-containing peptides. J. Phys. Chem. 96:6472-6484, 1992.
-
(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
-
51
-
-
0027080909
-
Atomic solvation parameters applied to molecular dynamics of proteins in solution
-
Wesson, L., Eisenberg, D. Atomic solvation parameters applied to molecular dynamics of proteins in solution. Protein Sci. 1:227-235, 1992.
-
(1992)
Protein Sci.
, vol.1
, pp. 227-235
-
-
Wesson, L.1
Eisenberg, D.2
-
52
-
-
0023430366
-
Monte Carlo-minimization approach to the multiple-minima problem in protein folding
-
Li, Z., Scheraga, H.A. Monte Carlo-minimization approach to the multiple-minima problem in protein folding. Proc. Natl. Acad. Sci. USA 84:6611-6615, 1987.
-
(1987)
Proc. Natl. Acad. Sci. USA
, vol.84
, pp. 6611-6615
-
-
Li, Z.1
Scheraga, H.A.2
-
53
-
-
5744249209
-
Equation of state calculation by fast computing machines
-
Metropolis, N.A., Rosenbluth, A.W., Rosenbluth, N.M., Teller, A.H., Teller, E. Equation of state calculation by fast computing machines. J. Chem. Phys. 21:1087-1092, 1953.
-
(1953)
J. Chem. Phys.
, vol.21
, pp. 1087-1092
-
-
Metropolis, N.A.1
Rosenbluth, A.W.2
Rosenbluth, N.M.3
Teller, A.H.4
Teller, E.5
-
54
-
-
0026680831
-
Empirical solvation models in the context of conformational energy searches: Application to bovine pancreatic trypsin inhibitor
-
Williams, R.L., Vila, J., Perrot, G., Scheraga, H.A. Empirical solvation models in the context of conformational energy searches: Application to bovine pancreatic trypsin inhibitor. Proteins 14:110-119, 1992.
-
(1992)
Proteins
, vol.14
, pp. 110-119
-
-
Williams, R.L.1
Vila, J.2
Perrot, G.3
Scheraga, H.A.4
-
55
-
-
0026716409
-
Monte Carlo minimization with thermalization for global optimization of polypeptide conformations in cartesian coordinate space
-
Caflisch, A., Niederer, P., Anliker, M. Monte Carlo minimization with thermalization for global optimization of polypeptide conformations in cartesian coordinate space. Proteins 14:110-119, 1992.
-
(1992)
Proteins
, vol.14
, pp. 110-119
-
-
Caflisch, A.1
Niederer, P.2
Anliker, M.3
-
56
-
-
0028171884
-
2+-bound conformations of morphine and Met-enkephalin: A computational study
-
2+-bound conformations of morphine and Met-enkephalin: a computational study. FEBS Lett. 354:131-134, 1994.
-
(1994)
FEBS Lett.
, vol.354
, pp. 131-134
-
-
Zhorov, B.S.1
Ananthabarayanan, V.S.2
-
57
-
-
0029643787
-
Model for the complex between protein G and an antibody Fc fragment in solution
-
Kato, K., Lian, L.Y., Barsukov, I.L., Derrick, J.P., Kim, H., Tanaka, R., Yoshino, A., Shiraishi, M., Shimada, I., Arata, Y., Roberts, G.C.K. Model for the complex between protein G and an antibody Fc fragment in solution. Structure 3:79-85, 1995.
-
(1995)
Structure
, vol.3
, pp. 79-85
-
-
Kato, K.1
Lian, L.Y.2
Barsukov, I.L.3
Derrick, J.P.4
Kim, H.5
Tanaka, R.6
Yoshino, A.7
Shiraishi, M.8
Shimada, I.9
Arata, Y.10
Roberts, G.C.K.11
-
58
-
-
0026681839
-
Optimal protocol and trajectory visualization for conformational searches of peptides and proteins
-
Abagyan, R.A., Argos, P. Optimal protocol and trajectory visualization for conformational searches of peptides and proteins. J. Mol. Biol. 225:519-532, 1992.
-
(1992)
J. Mol. Biol.
, vol.225
, pp. 519-532
-
-
Abagyan, R.A.1
Argos, P.2
-
59
-
-
0015222647
-
The interpretation of protein structures: Estimation of static accessibility
-
Lee, B., Richards, F.M. The interpretation of protein structures: Estimation of static accessibility. J. Mol. Biol. 55:379-400, 1971.
-
(1971)
J. Mol. Biol.
, vol.55
, pp. 379-400
-
-
Lee, B.1
Richards, F.M.2
-
60
-
-
0018270134
-
The tree structural organization of proteins
-
Crippen, G.M. The tree structural organization of proteins. J. Mol. Biol. 126:315-321, 1978.
-
(1978)
J. Mol. Biol.
, vol.126
, pp. 315-321
-
-
Crippen, G.M.1
-
61
-
-
0019874608
-
Location of domains in globular proteins
-
Rashin, A.A. Location of domains in globular proteins. Nature 291:85-86, 1981.
-
(1981)
Nature
, vol.291
, pp. 85-86
-
-
Rashin, A.A.1
-
62
-
-
0019877668
-
Location of structural domains in proteins
-
Wodak, S.J., Janin, J. Location of structural domains in proteins. Biochemistry 20:6544-6552, 1981.
-
(1981)
Biochemistry
, vol.20
, pp. 6544-6552
-
-
Wodak, S.J.1
Janin, J.2
-
64
-
-
0023055758
-
Compact units in proteins
-
Zehfus, M.H., Rose, G.D. Compact units in proteins. Biochemistry 25:5759-5765, 1986.
-
(1986)
Biochemistry
, vol.25
, pp. 5759-5765
-
-
Zehfus, M.H.1
Rose, G.D.2
-
65
-
-
0028290005
-
Parser for protein folding units
-
Holm, L., Sander, C. Parser for protein folding units. Proteins 19:256-268, 1994.
-
(1994)
Proteins
, vol.19
, pp. 256-268
-
-
Holm, L.1
Sander, C.2
-
66
-
-
0028914725
-
An automatic method involving cluster analysis of secondary structure for the identification of domains in proteins
-
Sowdhamini, R., Blundell, T.L. An automatic method involving cluster analysis of secondary structure for the identification of domains in proteins. Protein Sci. 4:506-520, 1995.
-
(1995)
Protein Sci.
, vol.4
, pp. 506-520
-
-
Sowdhamini, R.1
Blundell, T.L.2
-
67
-
-
0028937153
-
A procedure for detecting structural domains in proteins
-
Swindells, M.B. A procedure for detecting structural domains in proteins. Protein Sci. 4:103-112, 1995.
-
(1995)
Protein Sci.
, vol.4
, pp. 103-112
-
-
Swindells, M.B.1
-
68
-
-
0028891784
-
Identification and analysis of domains in proteins
-
Islam, S.A., Luo, J., Sternberg, M.J.E. Identification and analysis of domains in proteins. Protein Eng. 8:513-525, 1995.
-
(1995)
Protein Eng.
, vol.8
, pp. 513-525
-
-
Islam, S.A.1
Luo, J.2
Sternberg, M.J.E.3
-
69
-
-
0028943588
-
Continuous and discontinuous domains: An algorithm for the automatic generation of reliable protein domain definition
-
Siddiqui, A.S., Barton, G.J. Continuous and discontinuous domains: An algorithm for the automatic generation of reliable protein domain definition. Protein Sci. 4:872-884, 1995.
-
(1995)
Protein Sci.
, vol.4
, pp. 872-884
-
-
Siddiqui, A.S.1
Barton, G.J.2
-
70
-
-
0002336164
-
Ring closure and local conformational deformations of chain molecules
-
Gõ, N., Scheraga, H.A. Ring closure and local conformational deformations of chain molecules. Macromolecules 3:178-187, 1970.
-
(1970)
Macromolecules
, vol.3
, pp. 178-187
-
-
Gõ, N.1
Scheraga, H.A.2
-
71
-
-
0024609825
-
New methodology for computer-aided modelling of biomolecular structure and dynamics. 2. Local deformations and cycles
-
Abagyan, R.A., Mazur, A.K. New methodology for computer-aided modelling of biomolecular structure and dynamics. 2. Local deformations and cycles. J. Biomol. Struct. Dyn. 6:833-845, 1989.
-
(1989)
J. Biomol. Struct. Dyn.
, vol.6
, pp. 833-845
-
-
Abagyan, R.A.1
Mazur, A.K.2
-
72
-
-
0026482961
-
Tracking conformational states in allosteric transitions of phosphorylase
-
Browner, M.F., Fauman, E.B., Fletterick, R.J. Tracking conformational states in allosteric transitions of phosphorylase. Biochemistry 31:11297-11304, 1992.
-
(1992)
Biochemistry
, vol.31
, pp. 11297-11304
-
-
Browner, M.F.1
Fauman, E.B.2
Fletterick, R.J.3
-
73
-
-
0029150760
-
Protein flexibility and adaptability seen in 25 crystal forms of T4 lysozyme
-
Zhang, X.-J., Wozniak, J.A., Matthews, B.W. Protein flexibility and adaptability seen in 25 crystal forms of T4 lysozyme. J. Mol. Biol. 250:527-552, 1995.
-
(1995)
J. Mol. Biol.
, vol.250
, pp. 527-552
-
-
Zhang, X.-J.1
Wozniak, J.A.2
Matthews, B.W.3
-
74
-
-
0022373792
-
Novel arrangement of immunoglobulin variable domains: X-ray crystallographic analysis of the lambda-chain dimer Bence-Jones protein Loc
-
Chang, C.-H., Short, M.T., Westholm, F.A., Stevens, F.J., Wang, B.-C., Furey, W., Solomon, A., Schiffer, M. Novel arrangement of immunoglobulin variable domains: X-ray crystallographic analysis of the lambda-chain dimer Bence-Jones protein Loc. Biochemistry 24:4890-4898, 1985.
-
(1985)
Biochemistry
, vol.24
, pp. 4890-4898
-
-
Chang, C.-H.1
Short, M.T.2
Westholm, F.A.3
Stevens, F.J.4
Wang, B.-C.5
Furey, W.6
Solomon, A.7
Schiffer, M.8
-
75
-
-
0025294114
-
Conformational sampling using high-temperature molecular dynamics
-
Bruccoleri, R.E., Karplus, M. Conformational sampling using high-temperature molecular dynamics. Biopolymers 29:1847-1862, 1990.
-
(1990)
Biopolymers
, vol.29
, pp. 1847-1862
-
-
Bruccoleri, R.E.1
Karplus, M.2
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