-
1
-
-
0021918946
-
Prediction of chain flexibility in proteins - A tool for the selection of peptide antigens
-
Karplus PA, Schulz GE (1985) Prediction of chain flexibility in proteins - A tool for the selection of peptide antigens. Naturwiss 72:212-213.
-
(1985)
Naturwiss
, vol.72
, pp. 212-213
-
-
Karplus, P.A.1
Schulz, G.E.2
-
2
-
-
0028361031
-
Accuracy of protein flexibility predictions
-
Vihinen M, Torkkila E, Riikonen P (1994) Accuracy of protein flexibility predictions. Proteins 19:141-149.
-
(1994)
Proteins
, vol.19
, pp. 141-149
-
-
Vihinen, M.1
Torkkila, E.2
Riikonen, P.3
-
3
-
-
0037407015
-
Improved amino acid flexibility parameters
-
Smith DK, Radivojac P, Obradovic Z, Dunker AK, Zhu G (2003) Improved amino acid flexibility parameters. Protein Sci 12:1060-1072.
-
(2003)
Protein Sci
, vol.12
, pp. 1060-1072
-
-
Smith, D.K.1
Radivojac, P.2
Obradovic, Z.3
Dunker, A.K.4
Zhu, G.5
-
4
-
-
0347364621
-
Protein flexibility and intrinsic disorder
-
Radivojac P, et al. (2004) Protein flexibility and intrinsic disorder. Protein Sci 13:71-80.
-
(2004)
Protein Sci
, vol.13
, pp. 71-80
-
-
Radivojac, P.1
-
5
-
-
13944277320
-
Prediction of protein B-factor profiles
-
Yuan Z, Bailey TL, Teasdale RD (2005) Prediction of protein B-factor profiles. Proteins 58:905-912.
-
(2005)
Proteins
, vol.58
, pp. 905-912
-
-
Yuan, Z.1
Bailey, T.L.2
Teasdale, R.D.3
-
6
-
-
24344503079
-
Protein flexibility and rigidity predicted from sequence
-
Schlessinger A, Rost B (2005) Protein flexibility and rigidity predicted from sequence. Proteins 61:115-126.
-
(2005)
Proteins
, vol.61
, pp. 115-126
-
-
Schlessinger, A.1
Rost, B.2
-
7
-
-
33846965982
-
Prediction of protein B-factors using multiclass bounded SVM
-
Chen P, Wang B, Wong HS, Huang DS (2007) Prediction of protein B-factors using multiclass bounded SVM. Protein Pept Lett 14:185-190.
-
(2007)
Protein Pept Lett
, vol.14
, pp. 185-190
-
-
Chen, P.1
Wang, B.2
Wong, H.S.3
Huang, D.S.4
-
8
-
-
0030623823
-
Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential
-
Bahar I, Atilgan AR, Erman B (1997) Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Fold Des 2:173-181.
-
(1997)
Fold Des
, vol.2
, pp. 173-181
-
-
Bahar, I.1
Atilgan, A.R.2
Erman, B.3
-
9
-
-
0032749098
-
Structure-based analysis of protein dynamics: Comparison of theoretical results for hen lysozyme with X-ray diffraction and NMR relaxation data
-
Haliloglu T, Bahar I (1999) Structure-based analysis of protein dynamics: Comparison of theoretical results for hen lysozyme with X-ray diffraction and NMR relaxation data. Proteins 37:654-667.
-
(1999)
Proteins
, vol.37
, pp. 654-667
-
-
Haliloglu, T.1
Bahar, I.2
-
10
-
-
0035996990
-
Dynamics of proteins in crystals: Comparison of experiment with simple models
-
Kundu S, Melton JS, Sorensen DC, Phillips GN, Jr (2002) Dynamics of proteins in crystals: Comparison of experiment with simple models. Biophys J 83:723-732.
-
(2002)
Biophys J
, vol.83
, pp. 723-732
-
-
Kundu, S.1
Melton, J.S.2
Sorensen, D.C.3
Phillips Jr, G.N.4
-
11
-
-
33747829284
-
oGNM: Online computation of structural dynamics using the Gaussian network model
-
Yang LW, et al. (2006) oGNM: Online computation of structural dynamics using the Gaussian network model. Nucl Acids Res 34:W24-W31.
-
(2006)
Nucl Acids Res
, vol.34
-
-
Yang, L.W.1
-
12
-
-
33748189629
-
The extent of cooperativity of protein motions observed with elastic network models is similar for atomic and coarser-grained models
-
Sen TZ, Feng Y, Garcia JV, Kloczkowski A, Jernigan RL (2006) The extent of cooperativity of protein motions observed with elastic network models is similar for atomic and coarser-grained models. J Chem Theo Comp 2:696-704.
-
(2006)
J Chem Theo Comp
, vol.2
, pp. 696-704
-
-
Sen, T.Z.1
Feng, Y.2
Garcia, J.V.3
Kloczkowski, A.4
Jernigan, R.L.5
-
13
-
-
34248182936
-
vGNM: A better model for understanding the dynamics of proteins in crystals
-
Song G, Jernigan RL (2007) vGNM: A better model for understanding the dynamics of proteins in crystals. J Mol Biol 369:880-893.
-
(2007)
J Mol Biol
, vol.369
, pp. 880-893
-
-
Song, G.1
Jernigan, R.L.2
-
14
-
-
0037173062
-
How to describe protein motion without amino acid sequence and atomic coordinates
-
Ming D, Kong Y, Lambert MA, Huang Z, Ma J (2002) How to describe protein motion without amino acid sequence and atomic coordinates. Proc Natl Acad Sci USA 99:8620-8625.
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 8620-8625
-
-
Ming, D.1
Kong, Y.2
Lambert, M.A.3
Huang, Z.4
Ma, J.5
-
15
-
-
51149211502
-
Improved simulation of liquid water by molecular dynamics
-
Stillinger FH, Rahman A (1974) Improved simulation of liquid water by molecular dynamics. J Chem Phys 60:1545-1557.
-
(1974)
J Chem Phys
, vol.60
, pp. 1545-1557
-
-
Stillinger, F.H.1
Rahman, A.2
-
17
-
-
27344436659
-
Scalable molecular dynamics with NAMD
-
Phillips JC, et al. (2005) Scalable molecular dynamics with NAMD. J Comp Chem 26:1781-1802.
-
(2005)
J Comp Chem
, vol.26
, pp. 1781-1802
-
-
Phillips, J.C.1
-
18
-
-
84986512474
-
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
-
Brooks BR, et al. (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
-
19
-
-
0023613529
-
Normal modes of vibration in bovine pancreatic trypsin inhibitor and its mechanical property
-
Nishikawa T, Go N (1987) Normal modes of vibration in bovine pancreatic trypsin inhibitor and its mechanical property. Proteins 2:308-329.
-
(1987)
Proteins
, vol.2
, pp. 308-329
-
-
Nishikawa, T.1
Go, N.2
-
20
-
-
0022111715
-
Normal modes for specific motions of macromolecules: Application to the hinge-bending mode of lysozyme
-
Brooks B, Karplus M (1985) Normal modes for specific motions of macromolecules: Application to the hinge-bending mode of lysozyme. Proc Natl Acad Sci USA 82:4995-4999.
-
(1985)
Proc Natl Acad Sci USA
, vol.82
, pp. 4995-4999
-
-
Brooks, B.1
Karplus, M.2
-
21
-
-
0001031179
-
Proteins: A theoretical perspective of dynamics, structure, and thermodynamics
-
Brooks CL, Karplus M, Pettitt BM (1988) Proteins: A theoretical perspective of dynamics, structure, and thermodynamics. Adv Chem Phys 71:1-249.
-
(1988)
Adv Chem Phys
, vol.71
, pp. 1-249
-
-
Brooks, C.L.1
Karplus, M.2
Pettitt, B.M.3
-
22
-
-
0028331255
-
Normal mode analysis of protein dynamics
-
Case DA (1994) Normal mode analysis of protein dynamics. Curr Opin Struct Biol 4:285-290.
-
(1994)
Curr Opin Struct Biol
, vol.4
, pp. 285-290
-
-
Case, D.A.1
-
24
-
-
0032483483
-
Vibrational dynamics of transfer RNAs: Comparison of the free and synthetase-bound forms
-
Bahar I, Jernigan RL (1998) Vibrational dynamics of transfer RNAs: Comparison of the free and synthetase-bound forms. J Mol Biol 281:871-884.
-
(1998)
J Mol Biol
, vol.281
, pp. 871-884
-
-
Bahar, I.1
Jernigan, R.L.2
-
25
-
-
0035132230
-
Anisotropy of fluctuation dynamics of proteins with an elastic network model
-
Atilgan AR, et al. (2001) Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophys J 80:505-515.
-
(2001)
Biophys J
, vol.80
, pp. 505-515
-
-
Atilgan, A.R.1
-
26
-
-
66249121357
-
Comparisons of experimental and computed protein anisotropic temperature factors
-
Yang, L, Song, G, Jernigan, RL (2009) Comparisons of experimental and computed protein anisotropic temperature factors. Proteins 76:164-175.
-
(2009)
Proteins
, vol.76
, pp. 164-175
-
-
Yang, L.1
Song, G.2
Jernigan, R.L.3
-
27
-
-
43649085777
-
Toward a molecular understanding of the anisotropic response of proteins to external forces: Insights from elastic network models
-
Eyal E, Bahar I (2008) Toward a molecular understanding of the anisotropic response of proteins to external forces: Insights from elastic network models. Biophys J 94:3424-3435.
-
(2008)
Biophys J
, vol.94
, pp. 3424-3435
-
-
Eyal, E.1
Bahar, I.2
-
28
-
-
34249950182
-
Anisotropic fluctuations of amino acids in protein structures: Insights from X-ray crystallography and elastic network models
-
Eyal E, Chennubhotla C, Yang LW, Bahar I (2007) Anisotropic fluctuations of amino acids in protein structures: Insights from X-ray crystallography and elastic network models. Bioinformatics 23:i175-184.
-
(2007)
Bioinformatics
, vol.23
, Issue.I175-184
-
-
Eyal, E.1
Chennubhotla, C.2
Yang, L.W.3
Bahar, I.4
-
29
-
-
58849116413
-
Application of elastic network models to proteins in the crystalline state
-
Riccardi D, Cui Q, Phillips GN, Jr (2009) Application of elastic network models to proteins in the crystalline state. Biophys J 96:464-475.
-
(2009)
Biophys J
, vol.96
, pp. 464-475
-
-
Riccardi, D.1
Cui, Q.2
Phillips Jr, G.N.3
-
30
-
-
33846818860
-
Protein structural variation in computational models and crystallographic data
-
Kondrashov DA, Van Wynsberghe AW, Bannen RM, Cui Q, Phillips GN, Jr (2007) Protein structural variation in computational models and crystallographic data. Structure 15:169-177.
-
(2007)
Structure
, vol.15
, pp. 169-177
-
-
Kondrashov, D.A.1
Van Wynsberghe, A.W.2
Bannen, R.M.3
Cui, Q.4
Phillips Jr, G.N.5
-
31
-
-
33645019704
-
An enhanced elastic network model to represent the motions of domain-swapped proteins
-
Song G, Jernigan RL (2006) An enhanced elastic network model to represent the motions of domain-swapped proteins. Proteins 63:197-209.
-
(2006)
Proteins
, vol.63
, pp. 197-209
-
-
Song, G.1
Jernigan, R.L.2
-
32
-
-
34547666968
-
How well can we understand large-scale protein motions using normal modes from elastic network models?
-
Yang L, Song G, Jernigan RL (2007) How well can we understand large-scale protein motions using normal modes from elastic network models? Biophys J 93:920-929.
-
(2007)
Biophys J
, vol.93
, pp. 920-929
-
-
Yang, L.1
Song, G.2
Jernigan, R.L.3
-
33
-
-
33751225684
-
The Gaussian network model: Precise prediction of residue fluctuations and application to binding problems
-
Erman B (2006) The Gaussian network model: Precise prediction of residue fluctuations and application to binding problems. Biophys J 91:3589-3599.
-
(2006)
Biophys J
, vol.91
, pp. 3589-3599
-
-
Erman, B.1
-
34
-
-
0032533790
-
Analysis of domain motions by approximate normal mode calculations
-
Hinsen K, Kneller GR (1998) Analysis of domain motions by approximate normal mode calculations. Proteins 33:417-429.
-
(1998)
Proteins
, vol.33
, pp. 417-429
-
-
Hinsen, K.1
Kneller, G.R.2
-
35
-
-
0042503333
-
A simplified force field for describing vibrational protein dynamics over the whole frequency range
-
Hinsen K, Kneller GR (1999) A simplified force field for describing vibrational protein dynamics over the whole frequency range. J Chem Phys 111:10766-10769.
-
(1999)
J Chem Phys
, vol.111
, pp. 10766-10769
-
-
Hinsen, K.1
Kneller, G.R.2
-
36
-
-
0034333103
-
Harmonicity in slow protein dynamics
-
Hinsen K, Petrescu A, Dellerue S, Bellissent-Funel M, Kneller GR (2000) Harmonicity in slow protein dynamics. Chem Phys 261:25-37.
-
(2000)
Chem Phys
, vol.261
, pp. 25-37
-
-
Hinsen, K.1
Petrescu, A.2
Dellerue, S.3
Bellissent-Funel, M.4
Kneller, G.R.5
-
37
-
-
39149108868
-
Structural flexibility in proteins:Impact of the crystal environment
-
Hinsen K (2008) Structural flexibility in proteins:Impact of the crystal environment. Bioinformatics 24:521-528.
-
(2008)
Bioinformatics
, vol.24
, pp. 521-528
-
-
Hinsen, K.1
-
38
-
-
47349097554
-
Deriving protein dynamical properties from weighted protein contact number
-
Lin CP, et al. (2008) Deriving protein dynamical properties from weighted protein contact number. Proteins 72:929-935.
-
(2008)
Proteins
, vol.72
, pp. 929-935
-
-
Lin, C.P.1
-
39
-
-
0037022347
-
Flexibility and packing in proteins
-
Halle B (2002) Flexibility and packing in proteins. Proc Natl Acad Sci USA 99:1274-1279.
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 1274-1279
-
-
Halle, B.1
-
40
-
-
36849087583
-
On the interrelationship between atomic displacement parameters (ADPs) and coordinates in protein structures
-
Weiss MS (2007) On the interrelationship between atomic displacement parameters (ADPs) and coordinates in protein structures. Acta Crystallogr D 63:1235-1242.
-
(2007)
Acta Crystallogr D
, vol.63
, pp. 1235-1242
-
-
Weiss, M.S.1
-
41
-
-
0000197372
-
Large amplitude elastic motions from a single-parameter, atomic analysis
-
Tirion MM (1996) Large amplitude elastic motions from a single-parameter, atomic analysis. Phys Rev Lett 77:1905-1908.
-
(1996)
Phys Rev Lett
, vol.77
, pp. 1905-1908
-
-
Tirion, M.M.1
-
42
-
-
0017021957
-
Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins
-
Tanaka S, Scheraga H (1976) Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins. Macromolecules 9:945-950.
-
(1976)
Macromolecules
, vol.9
, pp. 945-950
-
-
Tanaka, S.1
Scheraga, H.2
-
43
-
-
33845377127
-
Estimation of effective interresidue contact energies from protein crystal structures: Quasi-chemical approximation
-
Miyazawa S, Jernigan RL (1985) Estimation of effective interresidue contact energies from protein crystal structures: Quasi-chemical approximation. Macromolecules 18:534-552.
-
(1985)
Macromolecules
, vol.18
, pp. 534-552
-
-
Miyazawa, S.1
Jernigan, R.L.2
-
44
-
-
0033386039
-
Comparing anisotropic displacement parameters in protein structures
-
Merritt EA (1999) Comparing anisotropic displacement parameters in protein structures. Acta Crystallogr D55:Pt 12:1997-2004.
-
(1999)
Acta Crystallogr
, vol.D55
, Issue.PART 12
, pp. 1997-2004
-
-
Merritt, E.A.1
-
45
-
-
0036708474
-
Efficient generation of feasible pathways for protein conformational transitions
-
Kim MK, Jernigan RL, Chirikjian GS (2002) Efficient generation of feasible pathways for protein conformational transitions. Biophys J 83:1620-1630.
-
(2002)
Biophys J
, vol.83
, pp. 1620-1630
-
-
Kim, M.K.1
Jernigan, R.L.2
Chirikjian, G.S.3
-
47
-
-
23244465157
-
Rigid-cluster models of conformational transitions in macromolecular machines and assemblies
-
Kim MK, Jernigan RL, Chirikjian GS (2005) Rigid-cluster models of conformational transitions in macromolecular machines and assemblies, Biophys J 89:43-55.
-
(2005)
Biophys J
, vol.89
, pp. 43-55
-
-
Kim, M.K.1
Jernigan, R.L.2
Chirikjian, G.S.3
-
48
-
-
0035044995
-
Conformational change of proteins arising from normal mode calculations
-
Tama F, Sanejouand YH (2001) Conformational change of proteins arising from normal mode calculations. Protein Eng 14:1-6.
-
(2001)
Protein Eng
, vol.14
, pp. 1-6
-
-
Tama, F.1
Sanejouand, Y.H.2
-
49
-
-
0036721233
-
Normal mode analysis of macromolecular motions in a database framework: Developing mode concentration as a useful classifying statistic
-
Krebs WG, et al. (2002) Normal mode analysis of macromolecular motions in a database framework: Developing mode concentration as a useful classifying statistic. Proteins 48:682-695.
-
(2002)
Proteins
, vol.48
, pp. 682-695
-
-
Krebs, W.G.1
-
50
-
-
3342877839
-
Collective motions in HIV-1 Reverse Transcriptase: Examination of flexibility and enzyme function
-
Bahar I, Erman B, Jernigan RL, Covell DG (1999) Collective motions in HIV-1 Reverse Transcriptase: Examination of flexibility and enzyme function. J Mol Biol 285:1023-1037.
-
(1999)
J Mol Biol
, vol.285
, pp. 1023-1037
-
-
Bahar, I.1
Erman, B.2
Jernigan, R.L.3
Covell, D.G.4
-
51
-
-
0034029144
-
Proteins with similar architecture exhibit similar large-scale dynamic behavior
-
Keskin O, Jernigan RL, Bahar I (2000) Proteins with similar architecture exhibit similar large-scale dynamic behavior. Biophys J 78:2093-2106.
-
(2000)
Biophys J
, vol.78
, pp. 2093-2106
-
-
Keskin, O.1
Jernigan, R.L.2
Bahar, I.3
-
52
-
-
4344685227
-
Global ribosomemotions revealed with elastic network model
-
Wang Y, Rader AJ, Bahar I, Jernigan RL (2004) Global ribosomemotions revealed with elastic network model. J Struct Biol 147:302-314.
-
(2004)
J Struct Biol
, vol.147
, pp. 302-314
-
-
Wang, Y.1
Rader, A.J.2
Bahar, I.3
Jernigan, R.L.4
-
53
-
-
31544444687
-
Loop motions of triosephosphate isomerase observed with elastic networks
-
Kurkcuoglu O, Jernigan RL, Doruker P (2006) Loop motions of triosephosphate isomerase observed with elastic networks. Biochemistry 45:1173-1182.
-
(2006)
Biochemistry
, vol.45
, pp. 1173-1182
-
-
Kurkcuoglu, O.1
Jernigan, R.L.2
Doruker, P.3
-
54
-
-
78049283691
-
-
Sen TZ, Jernigan RL (2006) Optimizing the parameters of the Gaussian network model for ATP-binding proteins. In Normal Mode Analysis: Theory and Applications to Biological and Chemical Systems, eds Bahar I, Cui Q (Chapman and Hall/CRC, Boca Raton), pp 171-186.
-
Sen TZ, Jernigan RL (2006) Optimizing the parameters of the Gaussian network model for ATP-binding proteins. In Normal Mode Analysis: Theory and Applications to Biological and Chemical Systems, eds Bahar I, Cui Q (Chapman and Hall/CRC, Boca Raton), pp 171-186.
-
-
-
-
55
-
-
0037250308
-
PDB-REPRDB: A database of representative protein chains from the Protein Data Bank (PDB) in 2003
-
Noguchi T, Akiyama Y (2003) PDB-REPRDB: A database of representative protein chains from the Protein Data Bank (PDB) in 2003. Nucleic Acids Res 31:492-493.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 492-493
-
-
Noguchi, T.1
Akiyama, Y.2
-
56
-
-
0033954256
-
The protein data bank
-
Berman HM, et al. (2000) The protein data bank. Nucleic Acids Res 28:235-242.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
|