-
1
-
-
0001031179
-
Proteins: A theoretical perspective of dynamics, structure, and thermodynamics
-
Brooks, C.L. III, Karplus, M., and Pettitt, B.M., Proteins: A theoretical perspective of dynamics, structure, and thermodynamics, Adv. Chem. Phys.,71,1,1988.
-
(1988)
Adv. Chem. Phys
, vol.71
, pp. 1
-
-
Brooks, C.L.1
Karplus, M.2
Pettitt, B.M.3
-
4
-
-
0004003691
-
-
McGraw-Hill, New York
-
Wilson, E.B., Decius, J.C., and Cross, P.C., Molecular Vibrations, McGraw-Hill, New York, 1955.
-
(1955)
Molecular Vibrations
-
-
Wilson, E.B.1
Decius, J.C.2
Cross, P.C.3
-
5
-
-
0000885331
-
Harmonic analysis of large systems. I. Methodology
-
Brooks, B.R., Janezic, D., and Karplus, M., Harmonic analysis of large systems. I. Methodology, J. Comput. Chem.,16, 1522, 1995.
-
(1995)
J. Comput. Chem
, vol.16
, pp. 1522
-
-
Brooks, B.R.1
Janezic, D.2
Karplus, M.3
-
6
-
-
0032555216
-
The allosteric mechanism of the chaperonin groel: A dynamic analysis
-
Ma, J. and Karplus, M., The allosteric mechanism of the chaperonin GroEL: A dynamic analysis, Proc. Natl Acad. Sci. USA,95, 8502,1998.
-
(1998)
Proc. Natl Acad. Sci. USA
, vol.95
, pp. 8502
-
-
Ma, J.1
Karplus, M.2
-
7
-
-
0029560322
-
Hinge-bending motion in citrate synthase arising from normal mode calculations
-
Marques, O. and Sanejouand, Y., Hinge-bending motion in citrate synthase arising from normal mode calculations, Proteins,23, 557, 1995.
-
(1995)
Proteins
, vol.23
, pp. 557
-
-
Marques, O.1
Sanejouand, Y.2
-
8
-
-
0027576952
-
Diagonalization in a mixed basis: A method to compute low-frequency normal-modes for large macromolecules
-
Mouawad, L. and Perahia, D., Diagonalization in a mixed basis: A method to compute low-frequency normal-modes for large macromolecules, Biopolymers, 33, 599,1993.
-
(1993)
Biopolymers
, vol.33
, pp. 599
-
-
Mouawad, L.1
Perahia, D.2
-
10
-
-
0028454915
-
New approach for determining low-frequency normal-modes in macromolecules
-
Durand, P., Trinquier, G., and Sanejouand, Y.H., New approach for determining low-frequency normal-modes in macromolecules, Biopolymers,34, 759,1994.
-
(1994)
Biopolymers
, vol.34
, pp. 759
-
-
Durand, P.1
Trinquier, G.2
Sanejouand, Y.H.3
-
11
-
-
0034308140
-
Building-block approach for determining low-frequency normal modes of macromolecules
-
Tama, F., Gadea, F.X., Marques, O., and Sanejouand, Y., Building-block approach for determining low-frequency normal modes of macromolecules, Proteins,41,1, 2000.
-
(2000)
Proteins
, vol.41
, pp. 1
-
-
Tama, F.1
Gadea, F.X.2
Marques, O.3
Sanejouand, Y.4
-
12
-
-
0036840202
-
A coarse-grained normal mode approach for macromolecules: An efficient implementation and application to ca2+-atpase
-
2+-ATPase, Biophys.J.,83,2457, 2002.
-
(2002)
Biophys.J
, vol.83
, pp. 2457
-
-
Li, G.1
Cui, Q.2
-
13
-
-
84986469420
-
Harmonic analysis of large systems. Ii. Comparison of different protein models
-
Janezic, D. and Brooks, B.R., Harmonic analysis of large systems. II. Comparison of different protein models, J. Comput. Chem.,16, 1543, 1995.
-
(1995)
J. Comput. Chem
, vol.16
, pp. 1543
-
-
Janezic, D.1
Brooks, B.R.2
-
14
-
-
84986473952
-
Harmonic analysis of large systems. Iii. Comparison with molecular dynamics
-
Janezic, D., Venable, R.M., and Brooks, B.R., Harmonic analysis of large systems. III. Comparison with molecular dynamics, J. Comput. Chem.,16, 1554, 1995.
-
(1995)
J. Comput. Chem
, vol.16
, pp. 1554
-
-
Janezic, D.1
Venable, R.M.2
Brooks, B.R.3
-
15
-
-
0042769222
-
Normal-mode analysis without the hessian: A driven molecular-dynamics approach
-
Bowman, J.M., Zhang, X., and Brown, A., Normal-mode analysis without the Hessian: A driven molecular-dynamics approach, J. Chem. Phys.,119, 646,2003.
-
(2003)
J. Chem. Phys
, vol.119
, pp. 646
-
-
Bowman, J.M.1
Zhang, X.2
Brown, A.3
-
16
-
-
5444269159
-
Normal mode analysis using the driven molecular dynamics method: Ii. An application to biological macromolecules
-
Kaledin, M., Brown, A., Kaledin, A.L., and Bowman, J.M., Normal mode analysis using the driven molecular dynamics method: II. An application to biological macromolecules, J. Chem. Phys.,121, 5646,2004.
-
(2004)
J. Chem. Phys
, vol.121
, pp. 5646
-
-
Kaledin, M.1
Brown, A.2
Kaledin, A.L.3
Bowman, J.M.4
-
17
-
-
0042151935
-
Classical trajectory studies of multi-photon and overtone absorption of hf
-
Christoffel, K.M. and Bowman, J.M., Classical trajectory studies of multi-photon and overtone absorption of HF, J. Phys. Chem.,85, 2159,1981.
-
(1981)
J. Phys. Chem
, vol.85
, pp. 2159
-
-
Christoffel, K.M.1
Bowman, J.M.2
-
18
-
-
0001434097
-
Classical trajectory study of internal energy distributions in unimolecular processes
-
McDonald, J.D. and Marcus, R.A., Classical trajectory study of internal energy distributions in unimolecular processes, J. Chem. Phys.,65,2180, 1976.
-
(1976)
J. Chem. Phys
, vol.65
, pp. 2180
-
-
McDonald, J.D.1
Marcus, R.A.2
-
19
-
-
85057244037
-
-
Version 4.1, Washington University School of Medicine, June
-
McDonald, J.D. and Marcus, R.A., TINKER: software tools for molecular design, Version 4.1, Washington University School of Medicine, June 2003, available from http://dasher.wustl.edu/tinker.
-
(2003)
TINKER: Software Tools for Molecular Design
-
-
McDonald, J.D.1
Marcus, R.A.2
-
20
-
-
0036264492
-
Designing a 20-residue protein
-
Neidigh, J.W., Fesinmeyer, R.M., and Andersen, N.H., Designing a 20-residue protein, Nat. Struct. Biol.,9, 425,2002.
-
(2002)
Nat. Struct. Biol
, vol.9
, pp. 425
-
-
Neidigh, J.W.1
Fesinmeyer, R.M.2
Andersen, N.H.3
-
21
-
-
0029011701
-
A second generation force field for the simulation of proteins, nucleic acids, and organic molecules
-
Cornell, W.D., Cieplak, P., Bayly, C.I., Gould, I.R., Merz, K.M. Jr., Ferguson, D.M., Spellmeyer, D.C., Fox, T., Caldwell, J.W., and Kollman, P.A., A second generation force field for the simulation of proteins, nucleic acids, and organic molecules, J. Am. Chem. Soc.,117,5179,1995
-
(1995)
J. Am. Chem. Soc
, vol.117
, pp. 5179
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Gould, I.R.4
Merz, K.M.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
22
-
-
0032922174
-
A modified version of the cornell et al. Force field with improved sugar pucker phases an helical repeat
-
Cheatham, T.E. III, Cieplak, P., and Kollman, P.A., A modified version of the Cornell et al. force field with improved sugar pucker phases an helical repeat, J. Biomol. Struct. Dyn.,16, 845, 1999.
-
(1999)
J. Biomol. Struct. Dyn
, vol.16
, pp. 845
-
-
Cheatham, T.1
Cieplak, P.2
Kollman, P.A.3
-
23
-
-
0003982971
-
-
Springer-Verlag, New York, (Section 9.1)
-
Nocedal, J. and Wright, S.J., Numerical Optimization, Springer-Verlag, New York, 1999 (Section 9.1).
-
(1999)
Numerical Optimization
-
-
Nocedal, J.1
Wright, S.J.2
-
24
-
-
0022111715
-
Normal modes for specific motions of macromolecules: Application to the hinge-bending mode of lysosome
-
Brooks, B.R. and Karplus, M., Normal modes for specific motions of macromolecules: Application to the hinge-bending mode of lysosome, Proc. Natl Acad. Sci. USA,82, 4995, 1985.
-
(1985)
Proc. Natl Acad. Sci. USA
, vol.82
, pp. 4995
-
-
Brooks, B.R.1
Karplus, M.2
-
25
-
-
0035956502
-
Conformational preferences and vibrational frequency distributions of short peptides in relation to multidimensional infrared spectroscopy
-
Gnanakaran, S. and Hochstrasser, R.M., Conformational preferences and vibrational frequency distributions of short peptides in relation to multidimensional infrared spectroscopy, J. Am. Chem. Soc.,123,12886, 2001.
-
(2001)
J. Am. Chem. Soc
, vol.123
, pp. 12886
-
-
Gnanakaran, S.1
Hochstrasser, R.M.2
-
26
-
-
0348244547
-
All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data
-
Foloppe, N. and MacKerell, Jr., A.D. All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data, J. Comput. Chem.,21, 86, 2000.
-
(2000)
J. Comput. Chem
, vol.21
, pp. 86
-
-
Foloppe, N.1
MacKerell, A.D.2
-
27
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
MacKerell, A.D., Jr., Bashford, D., Bellott, R.L., Dunbrack, R.L., Jr., Evanseck, J.D., Field, M.J., Fischer, S., Gao, J., Guo, H., Ha, S., Joseph-McCarthy, D., Kuch-nir, L., Kuczera, K., Lau, F.T.K., Mattos, C., Michnick, S., Ngo, T., Nguyen, D.T., Prodhom, B., Reiher, W.E., III, Roux, B., Schlenkrich, M., Smith, J.C., Stote, R., Straub, J., Watanabe, M., Wiorkiewicz-Kuczera, J., Yin, D., and Karplus, M., All-atom empirical potential for molecular modeling and dynamics studies of proteins, J. Phys. Chem. B,102, 3586,1998.
-
(1998)
J. Phys. Chem. B
, vol.102
, pp. 3586
-
-
MacKerell, A.D.1
Bashford, D.2
Bellott, R.L.3
Dunbrack, R.L.4
Evanseck, J.D.5
Field, M.J.6
Fischer, S.7
Gao, J.8
Guo, H.9
Ha, S.10
Joseph-McCarthy, D.11
Kuch-Nir, L.12
Kuczera, K.13
Lau, F.T.K.14
Mattos, C.15
Michnick, S.16
Ngo, T.17
Nguyen, D.T.18
Prodhom, B.19
Reiher, W.E.20
Roux, B.21
Schlenkrich, M.22
Smith, J.C.23
Stote, R.24
Straub, J.25
Watanabe, M.26
Wiorkiewicz-Kuczera, J.27
Yin, D.28
Karplus, M.29
more..
-
29
-
-
36449006911
-
Extraction, through filter-diagonalization, of general quantum eigenvalues or classical normal mode frequencies from a small number of residues or a short-time segment of a signal. I. Theory and application to a quantum-dynamics model
-
Wall, M.R. and Neuhauser, D., Extraction, through filter-diagonalization, of general quantum eigenvalues or classical normal mode frequencies from a small number of residues or a short-time segment of a signal. I. Theory and application to a quantum-dynamics model, J. Chem. Phys.,102, 8011,1995.
-
(1995)
J. Chem. Phys
, vol.102
, pp. 8011
-
-
Wall, M.R.1
Neuhauser, D.2
-
30
-
-
0032484774
-
Anharmonic vibrations via filter diagonalization of ab initio dynamics trajectories
-
Da Silva, A.J.R., Pang, J.W., Carter, E.A., and Neuhauser, D., Anharmonic vibrations via filter diagonalization of ab initio dynamics trajectories, J. Phys. Chem. A, 102, 881,1998.
-
(1998)
J. Phys. Chem. A
, vol.102
, pp. 881
-
-
Da Silva, A.J.R.1
Pang, J.W.2
Carter, E.A.3
Neuhauser, D.4
-
31
-
-
0034681238
-
Decimation and harmonic inversion of periodic orbit signals
-
Main, J., Dando, P.A., Belkic, D., and Taylor, H.S., Decimation and harmonic inversion of periodic orbit signals, J. Phys. Math. Gen.,33, 1247,2000.
-
(2000)
J. Phys. Math. Gen
, vol.33
, pp. 1247
-
-
Main, J.1
Dando, P.A.2
Belkic, D.3
Taylor, H.S.4
-
33
-
-
84962367344
-
Methods and applications of combined quantum mechanical and molecular mechanical potentials
-
Lipkowitz, K.B. and Boyd, D.B. (Eds.), VCH Publishers, New York
-
Gao, J., Methods and applications of combined quantum mechanical and molecular mechanical potentials, in Reviews in Computational Chemistry, Lipkowitz, K.B. and Boyd, D.B. (Eds.), VCH Publishers, New York, 1995, Vol. 7, p. 119.
-
(1995)
Reviews in Computational Chemistry
, vol.7
, pp. 119
-
-
Gao, J.1
-
34
-
-
0345986014
-
Linear scaling computation of the hartreefock exchange matrix
-
Schwegler, E. and Challacombe, M., Linear scaling computation of the HartreeFock exchange matrix, J. Chem. Phys.,105, 2726, 1996
-
(1996)
J. Chem. Phys
, vol.105
, pp. 2726
-
-
Schwegler, E.1
Challacombe, M.2
-
35
-
-
0242289628
-
Density matrix search using direct inversion in the iterative subspace as a linear scaling alternative to diagonalization in electronic structure calculations
-
Li, X.S., Millam, J.M., Scuseria, G.E., Frisch, M.J., and Schlegel, H.B., Density matrix search using direct inversion in the iterative subspace as a linear scaling alternative to diagonalization in electronic structure calculations, J. Chem. Phys.,119, 7651, 2003.
-
(2003)
J. Chem. Phys
, vol.119
, pp. 7651
-
-
Li, X.S.1
Millam, J.M.2
Scuseria, G.E.3
Frisch, M.J.4
Schlegel, H.B.5
|