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, vol.48
, pp. 15-30
-
-
Shimizu, S.1
Chan, H.S.2
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46
-
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0842333152
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Implicit solvation based on generalized Born theory in different dielectric environments
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The effect of different dielectric environments on the calculation of GB radii is investigated. The GB/MV implementation is extended in order to accurately reproduce reaction field energies as a function of the internal and external dielectric constants.
-
Feig M., Im W., Brooks C.L. III Implicit solvation based on generalized Born theory in different dielectric environments. J Chem Phys. 120:2004;903-911 The effect of different dielectric environments on the calculation of GB radii is investigated. The GB/MV implementation is extended in order to accurately reproduce reaction field energies as a function of the internal and external dielectric constants.
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(2004)
J Chem Phys
, vol.120
, pp. 903-911
-
-
Feig, M.1
Im, W.2
Brooks III, C.L.3
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47
-
-
0037167860
-
Accurate transferable model for water, n-octanol, and n-hexadecane solvation free energies
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Bordner A.J., Cavasotto C.N., Abagyan R.A. Accurate transferable model for water, n-octanol, and n-hexadecane solvation free energies. J Phys Chem B. 106:2002;11009-11015.
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(2002)
J Phys Chem B
, vol.106
, pp. 11009-11015
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Bordner, A.J.1
Cavasotto, C.N.2
Abagyan, R.A.3
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48
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0036536998
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Theoretical and computational models of ion channels
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Roux B. Theoretical and computational models of ion channels. Curr Opin Struct Biol. 12:2002;182-189.
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(2002)
Curr Opin Struct Biol
, vol.12
, pp. 182-189
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-
Roux, B.1
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49
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0037194983
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Introducing an implicit membrane in generalized Born/solvent accessibility continuum solvent models
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The first report of extending the GB/SA method to include an implicit membrane.
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Spassov V.Z., Yan L., Szalma S. Introducing an implicit membrane in generalized Born/solvent accessibility continuum solvent models. J Phys Chem B. 106:2002;8726-8738 The first report of extending the GB/SA method to include an implicit membrane.
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(2002)
J Phys Chem B
, vol.106
, pp. 8726-8738
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-
Spassov, V.Z.1
Yan, L.2
Szalma, S.3
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50
-
-
0242322528
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An implicit membrane generalized born theory for the study of structure, stability, and interactions of membrane proteins
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An implicit treatment for membrane environments is introduced to GB methods by modeling the membrane as a solvent-inaccessible infinite planar slab, effectively extending the cavity of the solute into the membrane.
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Im W., Feig M., Brooks C.L. III An implicit membrane generalized born theory for the study of structure, stability, and interactions of membrane proteins. Biophys J. 85:2003;2900-2918 An implicit treatment for membrane environments is introduced to GB methods by modeling the membrane as a solvent-inaccessible infinite planar slab, effectively extending the cavity of the solute into the membrane.
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(2003)
Biophys J
, vol.85
, pp. 2900-2918
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Im, W.1
Feig, M.2
Brooks III, C.L.3
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51
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-
1942439372
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De novo folding of integral membrane proteins
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in press.
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Im W, Brooks CL III: De novo folding of integral membrane proteins. J Mol Biol 2004, in press. This study utilizes the IM/implicit solvent GB theory to explore the folding and solid-state NMR properties of the fd coat protein from bacteriophage. The results indicate that experimentally measured properties of the folded protein in a membrane environment are well reproduced in the conformational ensemble from replica-exchange simulations using the GB model.
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(2004)
J Mol Biol
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-
Im, W.1
Brooks III, C.L.2
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52
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-
0038675609
-
Effective energy function for proteins in lipid membranes
-
This paper describes a generalization of the highly successful EEF approach to modeling protein solvation of aqueous/membrane-resident protein molecules. Differing from the continuum electrostatic based approaches built on the GB formalism, this model employs an empirical solvation methodology, with a simple dielectric function, to account for the influence of the heterogeneous aqueous/lipid environment.
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Lazaridis T. Effective energy function for proteins in lipid membranes. Proteins. 52:2003;176-192 This paper describes a generalization of the highly successful EEF approach to modeling protein solvation of aqueous/membrane- resident protein molecules. Differing from the continuum electrostatic based approaches built on the GB formalism, this model employs an empirical solvation methodology, with a simple dielectric function, to account for the influence of the heterogeneous aqueous/lipid environment.
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(2003)
Proteins
, vol.52
, pp. 176-192
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-
Lazaridis, T.1
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53
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0037079585
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Identifying native-like protein structures using physics-based potentials
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Dominy B.N., Brooks C.L. III Identifying native-like protein structures using physics-based potentials. J Comp Chem. 23:2001;147-160.
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(2001)
J Comp Chem
, vol.23
, pp. 147-160
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-
Dominy, B.N.1
Brooks III, C.L.2
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54
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0036681394
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Distinguishing native conformations of proteins from decoys with an effective free energy estimator based on the OPLS all-atom force field and the surface generalized born solvent model
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The OPLS all-atom force-field, in combination with a GB variant, was used successfully as a scoring function for distinguishing native and near-native structures in a large number of test sets.
-
Felts A.K., Gallicchio E., Wallqvist A., Levy R.M. Distinguishing native conformations of proteins from decoys with an effective free energy estimator based on the OPLS all-atom force field and the surface generalized born solvent model. Proteins. 48:2002;404-422 The OPLS all-atom force-field, in combination with a GB variant, was used successfully as a scoring function for distinguishing native and near-native structures in a large number of test sets.
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(2002)
Proteins
, vol.48
, pp. 404-422
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-
Felts, A.K.1
Gallicchio, E.2
Wallqvist, A.3
Levy, R.M.4
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55
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0036836611
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Evaluating CASP4 predictions with physical energy functions
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Feig M., Brooks C.L. III Evaluating CASP4 predictions with physical energy functions. Proteins. 49:2002;232-245.
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(2002)
Proteins
, vol.49
, pp. 232-245
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-
Feig, M.1
Brooks III, C.L.2
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56
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0042921442
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How well can we predict native contacts in proteins based on decoy structures and their energies?
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Zhu J., Zhu Q., Shi Y., Liu H. How well can we predict native contacts in proteins based on decoy structures and their energies? Proteins. 52:2003;598-608.
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(2003)
Proteins
, vol.52
, pp. 598-608
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Zhu, J.1
Zhu, Q.2
Shi, Y.3
Liu, H.4
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57
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0041919601
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Discrimination of native loop conformations in membrane proteins: Decoy library design and evaluation of effective energy scoring functions
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Forrest L.R., Woolf T.B. Discrimination of native loop conformations in membrane proteins: decoy library design and evaluation of effective energy scoring functions. Proteins. 52:2003;492-509.
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(2003)
Proteins
, vol.52
, pp. 492-509
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-
Forrest, L.R.1
Woolf, T.B.2
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58
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0036283048
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Evolution and physics in comparative protein structure modeling
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Fiser A., Feig M., Brooks C.L. III, Sali A. Evolution and physics in comparative protein structure modeling. Acc Chem Res. 35:2002;413-421.
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(2002)
Acc Chem Res
, vol.35
, pp. 413-421
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Fiser, A.1
Feig, M.2
Brooks III, C.L.3
Sali, A.4
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59
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0037422359
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Evaluation of models of electrostatic interactions in proteins
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The evaluation of physical scoring functions for the discrimination of native and native-like protein conformations with and without implicit solvent. The study finds that estimates of solvation energy contributions from PB or GB are not essential, and that a combined electrostatics/hydrogen bonding potential performs better.
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Morozov A.V., Kortemme T., Baker D. Evaluation of models of electrostatic interactions in proteins. J Phys Chem B. 107:2003;2075-2090 The evaluation of physical scoring functions for the discrimination of native and native-like protein conformations with and without implicit solvent. The study finds that estimates of solvation energy contributions from PB or GB are not essential, and that a combined electrostatics/hydrogen bonding potential performs better.
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(2003)
J Phys Chem B
, vol.107
, pp. 2075-2090
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Morozov, A.V.1
Kortemme, T.2
Baker, D.3
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60
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0942266531
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Calculation of affinities of peptides for proteins
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Donnini S., Juffer A.H. Calculation of affinities of peptides for proteins. J Comp Chem. 25:2004;393-411.
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(2004)
J Comp Chem
, vol.25
, pp. 393-411
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Donnini, S.1
Juffer, A.H.2
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61
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0036890285
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Binding affinity and specificity from computational studies
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Lazaridis T. Binding affinity and specificity from computational studies. Curr Org Chem. 6:2002;1319-1332.
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(2002)
Curr Org Chem
, vol.6
, pp. 1319-1332
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Lazaridis, T.1
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62
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0035367150
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Interpreting trends in the binding of cyclic ureas to HIV-1 protease
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Mardis K.L., Luo R., Gilson M.K. Interpreting trends in the binding of cyclic ureas to HIV-1 protease. J Mol Biol. 309:2001;507-517.
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(2001)
J Mol Biol
, vol.309
, pp. 507-517
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-
Mardis, K.L.1
Luo, R.2
Gilson, M.K.3
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63
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1942471391
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Assessing scoring functions for protein-ligand interactions
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in press.
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Ferrara P, Gohlke H, Price D, Klebe G, Brooks CL III: Assessing scoring functions for protein-ligand interactions. J Med Chem 2004, in press. A number of scoring/docking energy functions, including implicit solvent 'physics-based' models, are assessed for their ability to pick native-like protein-ligand complexes from docking decoys.
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(2004)
J Med Chem
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Ferrara, P.1
Gohlke, H.2
Price, D.3
Klebe, G.4
Brooks III, C.L.5
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64
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0347602124
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Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf
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Gohlke H., Case D.A. Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf. J Comp Chem. 25:2003;238-250.
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(2003)
J Comp Chem
, vol.25
, pp. 238-250
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Gohlke, H.1
Case, D.A.2
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65
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84961985307
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Development of a generalized Born model parametrization for proteins and nucleic acids
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Dominy B.N., Brooks C.L. III Development of a generalized Born model parametrization for proteins and nucleic acids. J Phys Chem B. 103:1999;3765-3773.
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(1999)
J Phys Chem B
, vol.103
, pp. 3765-3773
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Dominy, B.N.1
Brooks III, C.L.2
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66
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0035501755
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Protein molecular dynamics with the generalized Born/ACE solvent model
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Calimet N., Schaefer M., Simonson T. Protein molecular dynamics with the generalized Born/ACE solvent model. Proteins. 2001:2001;144-158.
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(2001)
Proteins
, vol.2001
, pp. 144-158
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Calimet, N.1
Schaefer, M.2
Simonson, T.3
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67
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0036217783
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Long time dynamics of met-enkephalin: Comparison of explicit and implicit solvent models
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Molecular dynamics simulations of met-enkephalin are compared for explicit solvent and implicit descriptions based on atomic solvent-accessible surface area formulations.
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Shen M.Y., Freed K.F. Long time dynamics of met-enkephalin: comparison of explicit and implicit solvent models. Biophys J. 82:2002;1791-1808 Molecular dynamics simulations of met-enkephalin are compared for explicit solvent and implicit descriptions based on atomic solvent-accessible surface area formulations.
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(2002)
Biophys J
, vol.82
, pp. 1791-1808
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Shen, M.Y.1
Freed, K.F.2
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68
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0141677983
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Comparison of various implicit solvent models in molecular dynamics simulations of immunoglobulin G light chain dimer
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Molecular dynamics simulations of the immunoglobulin G light chain dimer are compared for explicit solvent, distance-dependent dielectric models, EEF1 and ACE (a GB variant based on Gaussian volume overlap). All of the implicit solvent models were found to introduce varying degrees of divergence from the explicit solvent simulations.
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Krol M. Comparison of various implicit solvent models in molecular dynamics simulations of immunoglobulin G light chain dimer. J Comp Chem. 24:2003;531-546 Molecular dynamics simulations of the immunoglobulin G light chain dimer are compared for explicit solvent, distance-dependent dielectric models, EEF1 and ACE (a GB variant based on Gaussian volume overlap). All of the implicit solvent models were found to introduce varying degrees of divergence from the explicit solvent simulations.
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(2003)
J Comp Chem
, vol.24
, pp. 531-546
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-
Krol, M.1
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69
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0037230970
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Implicit solvent models for flexible protein-protein docking by molecular dynamics simulation
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Molecular dynamics simulations of barnase, barstar, the B1 domain of protein G, WW domains and barnase-barstar docking with Amber and distance-dependent dielectric, solvent-accessible surface area or GB/SA-based implicit solvent models.
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Wang T., Wade R.C. Implicit solvent models for flexible protein-protein docking by molecular dynamics simulation. Proteins. 50:2003;158-169 Molecular dynamics simulations of barnase, barstar, the B1 domain of protein G, WW domains and barnase-barstar docking with Amber and distance-dependent dielectric, solvent-accessible surface area or GB/SA-based implicit solvent models.
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(2003)
Proteins
, vol.50
, pp. 158-169
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-
Wang, T.1
Wade, R.C.2
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70
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0042561888
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Solvent viscosity dependence of the folding rate of a small protein: Distributed computing study
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The relationship between solvent viscosity and folding rates is investigated with implicit solvent simulations of a 20-residue miniprotein. Results obtained in this study suggest that implicit solvent simulations with no or very low solvent viscosity may lead to erroneous estimates of kinetic rates.
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Zagrovic B., Pande V. Solvent viscosity dependence of the folding rate of a small protein: distributed computing study. J Comp Chem. 24:2003;1432-1436 The relationship between solvent viscosity and folding rates is investigated with implicit solvent simulations of a 20-residue miniprotein. Results obtained in this study suggest that implicit solvent simulations with no or very low solvent viscosity may lead to erroneous estimates of kinetic rates.
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(2003)
J Comp Chem
, vol.24
, pp. 1432-1436
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-
Zagrovic, B.1
Pande, V.2
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71
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0034510764
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Comparative study of the folding free energy landscape of a three-stranded β-sheet protein with explicit and implicit solvent models
-
Bursulaya B.D., Brooks C.L. III Comparative study of the folding free energy landscape of a three-stranded β-sheet protein with explicit and implicit solvent models. J Phys Chem B. 104:2000;12378-12383.
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(2000)
J Phys Chem B
, vol.104
, pp. 12378-12383
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-
Bursulaya, B.D.1
Brooks III, C.L.2
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72
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0037397987
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Peptide folding simulations
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Gnanakaran S., Nymeyer H., Portman J., Sanbonmatsu K.Y., Garcia A.E. Peptide folding simulations. Curr Opin Struct Biol. 13:2003;168-174.
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(2003)
Curr Opin Struct Biol
, vol.13
, pp. 168-174
-
-
Gnanakaran, S.1
Nymeyer, H.2
Portman, J.3
Sanbonmatsu, K.Y.4
Garcia, A.E.5
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73
-
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0036789950
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Can a continuum solvent model reproduce the free energy landscape of a b-hairpin folding in water?
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Zhou R., Berne B.J. Can a continuum solvent model reproduce the free energy landscape of a b-hairpin folding in water? Proc Natl Acad Sci USA. 99:2002;12777-12782.
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(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 12777-12782
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Zhou, R.1
Berne, B.J.2
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74
-
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0037934616
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Understanding folding and design: Replica-exchange simulations of "trp-cage" miniproteins
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Ab initio folding studies of 20-residue miniproteins with Amber and GB/SA implicit solvent using replica-exchange sampling are reported and compared to experimental data.
-
Pitera J.W., Swope W.C. Understanding folding and design: replica-exchange simulations of "Trp-cage" miniproteins. Proc Natl Acad Sci USA. 100:2003;7587-7592 Ab initio folding studies of 20-residue miniproteins with Amber and GB/SA implicit solvent using replica-exchange sampling are reported and compared to experimental data.
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(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 7587-7592
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-
Pitera, J.W.1
Swope, W.C.2
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75
-
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0042378853
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Efficiently explore the energy landscape of proteins in molecular dynamics simulations by amplifying collective motions
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He J., Zhang Z., Shi Y., Liu H. Efficiently explore the energy landscape of proteins in molecular dynamics simulations by amplifying collective motions. J Chem Phys. 119:2003;4005-4017.
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(2003)
J Chem Phys
, vol.119
, pp. 4005-4017
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He, J.1
Zhang, Z.2
Shi, Y.3
Liu, H.4
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76
-
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0035850758
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B-Hairpin folding simulations in atomistic detail using an implicit solvent model
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Zagrovic B., Sorin E.J., Pande V. b-Hairpin folding simulations in atomistic detail using an implicit solvent model. J Mol Biol. 313:2001;151-169.
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(2001)
J Mol Biol
, vol.313
, pp. 151-169
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Zagrovic, B.1
Sorin, E.J.2
Pande, V.3
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77
-
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0141704162
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Free energy landscape of protein folding in water: Explicit vs. implicit solvent
-
Folding free energy landscapes are compared between explicit solvent and implicit solvent in a number of force-field/GB combinations. Apart from differences between different force-fields, overly strong salt bridges and enhanced sampling of α-helical conformations are reported.
-
Zhou R. Free energy landscape of protein folding in water: explicit vs. implicit solvent. Proteins. 53:2003;148-161 Folding free energy landscapes are compared between explicit solvent and implicit solvent in a number of force-field/GB combinations. Apart from differences between different force-fields, overly strong salt bridges and enhanced sampling of α-helical conformations are reported.
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(2003)
Proteins
, vol.53
, pp. 148-161
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-
Zhou, R.1
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78
-
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0041375556
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Replica-exchange molecular dynamics simulations for a small-sized protein folding with implicit solvent
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Suenaga A. Replica-exchange molecular dynamics simulations for a small-sized protein folding with implicit solvent. J Mol Struct (Theochem). 634:2003;235-241.
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(2003)
J Mol Struct (Theochem)
, vol.634
, pp. 235-241
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Suenaga, A.1
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79
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0036137805
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Exploratory studies of ab initio protein structure prediction: Multiple copy simulated annealing amber energy functions, and a Generalized born/solvent accessibility solvation model
-
Liu Y., Beveridge D.L. Exploratory studies of ab initio protein structure prediction: multiple copy simulated annealing amber energy functions, and a Generalized born/solvent accessibility solvation model. Proteins. 46:2002;128-146.
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(2002)
Proteins
, vol.46
, pp. 128-146
-
-
Liu, Y.1
Beveridge, D.L.2
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80
-
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0345564821
-
Exploring Flory's isolated-pair hypothesis: Statistical mechanics of helix-coil transitions in polyalanine and the C peptide for RNase a
-
This study explores the nature of helix-to-coil folding entropy using replica-exchange molecular dynamics and first-generation GB models. The peptide entropy is found to increase linearly with the peptide length, in general agreement with Flory's ideas.
-
Ohkubo Y.Z., Brooks C.L. III Exploring Flory's isolated-pair hypothesis: statistical mechanics of helix-coil transitions in polyalanine and the C peptide for RNase A. Proc Natl Acad Sci USA. 100:2003;13916-13921 This study explores the nature of helix-to-coil folding entropy using replica-exchange molecular dynamics and first-generation GB models. The peptide entropy is found to increase linearly with the peptide length, in general agreement with Flory's ideas.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 13916-13921
-
-
Ohkubo, Y.Z.1
Brooks III, C.L.2
-
81
-
-
1542723482
-
Integrating folding kinetics and protein function: Biphasic kinetics and dual binding specificity in a WW domain
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in press.
-
Karanicolas J, Brooks CL III: Integrating folding kinetics and protein function: Biphasic kinetics and dual binding specificity in a WW domain. Proc Natl Acad Sci USA 2004, in press. In this paper, the authors explore the relationship between protein folding kinetics and protein function. Using folding free energy landscapes computed with implicit solvent GB models, they develop the hypothesis that, when function requires multiple conformational substates for ligand/substrate selectivity, folding will proceed via multiphase kinetics, with functionally important alternative conformational substates leading to folding intermediates.
-
(2004)
Proc Natl Acad Sci USA
-
-
Karanicolas, J.1
Brooks III, C.L.2
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82
-
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0042171838
-
Parallel tempering simulations of HP-36
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Lin C-Y., Hu C-K., Hansmann U.H.E. Parallel tempering simulations of HP-36. Proteins. 52:2003;436-445.
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(2003)
Proteins
, vol.52
, pp. 436-445
-
-
Lin, C.-Y.1
Hu, C.-K.2
Hansmann, U.H.E.3
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83
-
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0141794038
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Solution effects and the folding of an artificial peptide
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Alves N.A., Hansmann U.H.E. Solution effects and the folding of an artificial peptide. J Phys Chem B. 107:2003;10284-10291.
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(2003)
J Phys Chem B
, vol.107
, pp. 10284-10291
-
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Alves, N.A.1
Hansmann, U.H.E.2
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84
-
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0041877561
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Replica exchange molecular dynamics simulations of reversible folding
-
Rao F., Caflisch A. Replica exchange molecular dynamics simulations of reversible folding. J Chem Phys. 119:2003;4035-4042.
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(2003)
J Chem Phys
, vol.119
, pp. 4035-4042
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Rao, F.1
Caflisch, A.2
-
85
-
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0344702698
-
Simulation of the folding equilibrium of α-helical peptides: A comparison of the generalized Born approximation with explicit solvent
-
Folding free energy landscapes for two α-helical peptides are compared between explicit and implicit solvent. Differences in sampling non-native conformations are reported, in particular a preference for α-helical conformations when implicit solvent is used.
-
Nymeyer H., Garcia A.E. Simulation of the folding equilibrium of α-helical peptides: a comparison of the generalized Born approximation with explicit solvent. Proc Natl Acad Sci USA. 100:2003;13934-13939 Folding free energy landscapes for two α-helical peptides are compared between explicit and implicit solvent. Differences in sampling non-native conformations are reported, in particular a preference for α-helical conformations when implicit solvent is used.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 13934-13939
-
-
Nymeyer, H.1
Garcia, A.E.2
-
86
-
-
0036234027
-
Comparison of protein solution structures refined by molecular dynamics simulation in vacuum, with a generalized Born model, and with explicit water
-
The inclusion of GB in the molecular dynamics refinement of NMR structures is found to provide significant improvement over refinement in vacuum, with resulting structures comparable to structures obtained from explicit water calculations.
-
Xia B., Tsui V., Case D.A., Dyson H.J., Wright P.E. Comparison of protein solution structures refined by molecular dynamics simulation in vacuum, with a generalized Born model, and with explicit water. J Biomol NMR. 22:2002;317-331 The inclusion of GB in the molecular dynamics refinement of NMR structures is found to provide significant improvement over refinement in vacuum, with resulting structures comparable to structures obtained from explicit water calculations.
-
(2002)
J Biomol NMR
, vol.22
, pp. 317-331
-
-
Xia, B.1
Tsui, V.2
Case, D.A.3
Dyson, H.J.4
Wright, P.E.5
-
87
-
-
0347062349
-
Reintroducing electrostatics into protein X-ray structure refinement: Bulk solvent treated as a dielectric continuum
-
Moulinier L., Case D.A., Simonson T. Reintroducing electrostatics into protein X-ray structure refinement: bulk solvent treated as a dielectric continuum. Acta Crystallog. D59:2003;2094-2103.
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(2003)
Acta Crystallog
, vol.59
, pp. 2094-2103
-
-
Moulinier, L.1
Case, D.A.2
Simonson, T.3
-
88
-
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0036708447
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Bridging implicit and explicit solvent approaches for membrane electrostatics
-
Lin J-H., Baker N.A., McCammon J.A. Bridging implicit and explicit solvent approaches for membrane electrostatics. Biophys J. 83:2002;1374-1379.
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(2002)
Biophys J
, vol.83
, pp. 1374-1379
-
-
Lin, J.-H.1
Baker, N.A.2
McCammon, J.A.3
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89
-
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0036708445
-
Continuum electrostatics fails to describe ion permeation in the gramicidin channel
-
Edwards S., Corry B., Kuyucak S., Chung S-H. Continuum electrostatics fails to describe ion permeation in the gramicidin channel. Biophys J. 83:2002;1348-1360.
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(2002)
Biophys J
, vol.83
, pp. 1348-1360
-
-
Edwards, S.1
Corry, B.2
Kuyucak, S.3
Chung, S.-H.4
-
90
-
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0032539561
-
Molecular picture of folding of a small α/β protein
-
Sheinerman F.B., Brooks C.L. III Molecular picture of folding of a small α/β protein. Proc Natl Acad Sci USA. 95:1998;1562-1567.
-
(1998)
Proc Natl Acad Sci USA
, vol.95
, pp. 1562-1567
-
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Sheinerman, F.B.1
Brooks III, C.L.2
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91
-
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0032080053
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Calculations on folding of segment B1 of streptococcal protein G
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Sheinerman F.B., Brooks C.L. III Calculations on folding of segment B1 of streptococcal protein G. J Mol Biol. 278:1998;439-456.
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(1998)
J Mol Biol
, vol.278
, pp. 439-456
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Sheinerman, F.B.1
Brooks III, C.L.2
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92
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0037058992
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Probing the folding free energy landscape of the src-SH3 protein domain
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This study extended the earlier work of Sheinerman and Brooks [90,91], and identified key water-protein interactions late in the folding of the all-β SH3 domain. The authors note that water plays an explicit role in modulating hydrophobic interactions late in folding and that the expulsion of water gives rise to a free energy barrier late in the folding process.
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Shea J.-E., Onuchic J.N., Brooks C.L. III Probing the folding free energy landscape of the src-SH3 protein domain. Proc Natl Acad Sci USA. 99:2002;16064-16068 This study extended the earlier work of Sheinerman and Brooks [90,91], and identified key water-protein interactions late in the folding of the all-β SH3 domain. The authors note that water plays an explicit role in modulating hydrophobic interactions late in folding and that the expulsion of water gives rise to a free energy barrier late in the folding process.
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(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 16064-16068
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Shea, J.-E.1
Onuchic, J.N.2
Brooks III, C.L.3
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94
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4043132337
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Constant pH molecular dynamics using continuous titration coordinates
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in press.
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Lee MS, Salsbury FRJ, Brooks CL III: Constant pH molecular dynamics using continuous titration coordinates. Proteins 2004, in press. This is one of the first studies to explore the coupling of molecular dynamics with pH-modulated sidechain titration using GB models. Although the accuracy of the results presented in this study is not on a par with the best empirical PB-based calculations, they demonstrate how the new dimension of pH can be effectively coupled with conformational sampling in molecular simulations.
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(2004)
Proteins
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Lee, M.S.1
Salsbury, F.R.J.2
Brooks III, C.L.3
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