Solution conformations and thermodynamics of structured peptides: molecular dynamics simulation with an implicit solvation model

Canonical dynamics: Equilibrium phase-space distributions

1985 • 20,411 citations

A unified formulation of the constant temperature molecular dynamics methods

1984 • 16,207 citations

Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features

1983 • 14,802 citations

<scp>CHARMM</scp>: A program for macromolecular energy, minimization, and dynamics calculations

1983 • 14,615 citations

All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins

1998 • 13,827 citations

NMR with Proteins and Nucleic Acids

1986 • 7,896 citations

MOLMOL: A program for display and analysis of macromolecular structures

1996 • 7,169 citations

THE weighted histogram analysis method for free‐energy calculations on biomolecules. I. The method

1992 • 6,255 citations

Semianalytical treatment of solvation for molecular mechanics and dynamics

1990 • 3,585 citations

Contact Electron-Spin Coupling of Nuclear Magnetic Moments

1959 • 2,920 citations

Volumen und Hydratationswärme der Ionen

1920 • 2,234 citations

Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models

1994 • 2,072 citations

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1987 • 2,022 citations

Common core structure of amyloid fibrils by synchrotron X-ray diffraction 1 1Edited by F. E. Cohen

1997 • 1,648 citations

Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation

1985 • 1,570 citations

Multicanonical ensemble: A new approach to simulate first-order phase transitions

1992 • 1,528 citations

Simulation of activation free energies in molecular systems

1996 • 1,279 citations

Calculation of conformational ensembles from potentials of mena force

1990 • 1,091 citations

Instability, unfolding and aggregation of human lysozyme variants underlying amyloid fibrillogenesis

1997 • 1,041 citations

Energetics of Protein Structure

1995 • 1,040 citations

Finite representation of an infinite bulk system: Solvent boundary potential for computer simulations

1994 • 1,009 citations

Group contributions to the thermodynamic properties of non-ionic organic solutes in dilute aqueous solution

1981 • 971 citations

Biased Probability Monte Carlo Conformational Searches and Electrostatic Calculations for Peptides and Proteins

1994 • 954 citations

Prion Diseases and the BSE Crisis

1997 • 952 citations

Hydrophobic bonding and accessible surface area in proteins

1974 • 887 citations

Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides.

1987 • 737 citations

Theory of hydrophobic bonding. II. Correlation of hydrocarbon solubility in water with solvent cavity surface area

1972 • 694 citations

Optimized δ expansion for relativistic nuclear models

1998 • 652 citations

Human lysozyme gene mutations cause hereditary systemic amyloidosis

1993 • 646 citations

Tests of the helix dipole model for stabilization of α-helices

1987 • 598 citations

New Monte Carlo algorithm: Entropic sampling

1993 • 559 citations

A Comprehensive Analytical Treatment of Continuum Electrostatics

1996 • 552 citations

"New View" of Protein Folding Reconciled with the Old Through Multiple Unfolding Simulations

1997 • 514 citations

Conformation of peptide fragments of proteins in aqueous solution: implications for initiation of protein folding

1988 • 463 citations

The Electrostatic Influence of Substituents on the Dissociation Constants of Organic Acids. I

1938 • 417 citations

Context-dependent secondary structure formation of a designed protein sequence

1996 • 395 citations

Multicanonical Ensemble Generated by Molecular Dynamics Simulation for Enhanced Conformational Sampling of Peptides

1997 • 394 citations

On the use of sequence homologies to predict protein structure: identical pentapeptides can have completely different conformations.

1984 • 386 citations

Multidimensional adaptive umbrella sampling: Applications to main chain and side chain peptide conformations

1997 • 320 citations

Nature of the charged-group effect on the stability of the C-peptide helix.

1985 • 313 citations

Molecular dynamics, Langevin and hydrid Monte Carlo simulations in a multicanonical ensemble

1996 • 286 citations

De novo design and structural analysis of a model β-hairpin peptide system

1996 • 273 citations

Theoretical studies of protein folding and unfolding

1995 • 261 citations

The energetics of ion-pair and hydrogen-bonding interactions in a helical peptide

1993 • 260 citations

Statistical clustering techniques for the analysis of long molecular dynamics trajectories: analysis of 2.2-ns trajectories of YPGDV

1993 • 226 citations

Free Energy Determinants of Secondary Structure Formation: I. α-Helices

1995 • 220 citations

Molecular dynamics simulations of the unfolding of an .alpha.-helical analog of ribonuclease A S-peptide in water

1991 • 217 citations

Simulations of peptide conformational dynamics and thermodynamics

1993 • 212 citations

Configurational entropy of native proteins

1987 • 211 citations

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1990 • 206 citations

Free energies, enthalpies, and entropies of solution of gaseous nonpolar nonelectrolytes in water and nonaqueous solvents. The hydrophobic effect

1982 • 206 citations

Minimization of polypeptide energy. I. Preliminary structures of bovine pancreatic ribonuclease S-peptide.

1967 • 200 citations

Electrostatic contributions to solvation energies: comparison of free energy perturbation and continuum calculations

1991 • 192 citations

A helix stop signal in the isolated S-peptide of ribonuclease A

1984 • 189 citations

Solvation Free Energies Estimated from Macroscopic Continuum Theory: An Accuracy Assessment

1994 • 186 citations

Probability Distributions for Complex Systems: Adaptive Umbrella Sampling of the Potential Energy

1998 • 185 citations

Free Energy Determinants of Secondary Structure Formation: II. Antiparallel β-Sheets

1995 • 160 citations

Proton NMR studies of the solution conformations of an analog of the C-peptide of ribonuclease A

1989 • 154 citations

Solubility of nonelectrolytes in polar solvents. V. Estimation of the solubility of aliphatic monofunctional compounds in water using a molecular surface area approach

1975 • 150 citations

Protein folding simulations with genetic algorithms and a detailed molecular description

1997 • 147 citations

The Meaning of Component Analysis: Decomposition of the Free Energy in Terms of Specific Interactions

1995 • 144 citations

A neutral, water-soluble, .alpha.-helical peptide: the effect of ionic strength on the helix-coil equilibrium

1991 • 144 citations

Folding of Protein G B1 Domain Studied by the Conformational Characterization of Fragments Comprising Its Secondary Structure Elements

1995 • 142 citations

Folding of Protein G B1 Domain Studied by the Conformational Characterization of Fragments Comprising Its Secondary Structure Elements

1995 • 124 citations

Studying the Stability of a Helical β‐Heptapeptide by Molecular Dynamics Simulations

1997 • 121 citations

A Microscopic View of Helix Propagation: N and C-terminal Helix Growth in Alanine Helices

1996 • 120 citations

Conformational Properties of Four Peptides Spanning the Sequence of Hen Lysozyme

1995 • 111 citations

Molecular dynamics and Monte Carlo simulations favor the .alpha.-helical form for alanine-based peptides in water

1993 • 100 citations

Engineering peptides and proteins that undergo α-to-β transitions

1997 • 75 citations

THE MULTICANONICAL ENSEMBLE: A NEW APPROACH TO COMPUTER SIMULATIONS

1992 • 73 citations

Search for Nucleation Sites in Smaller Fragments of Chymotrypsin Inhibitor 2

1995 • 68 citations

Statistical Mechanics

1990 • 63 citations

Molecular dynamics simulations of synthetic peptide folding

1996 • 59 citations

Structural diversity of sequentially identical subsequences of proteins: Identical octapeptides can have different conformations

1998 • 48 citations

The C-peptide Helix from Ribonuclease A Considered as an Autonomous Folding Unit

1987 • 44 citations

The Glu 2− ⋯ Arg 10+ side-chain interaction in the C-peptide helix of ribonuclease A

1990 • 42 citations

Tertiary Structure Prediction of C-Peptide of Ribonuclease A by Multicanonical Algorithm

1998 • 41 citations

Folding simulations and computer redesign of protein A three-helix bundle motifs

1996 • 38 citations

[10] Neural networks for protein structure prediction

1991 • 35 citations

Folding simulations and computer redesign of protein A three‐helix bundle motifs

1996 • 30 citations

Structural and Dynamic Properties of a .beta.-Hairpin-Forming Linear Peptide. 2. 13C NMR Relaxation Analysis

1995 • 27 citations

Energetic decomposition of the α-helix-coil equilibrium of a dynamic model system

1998 • 21 citations

Extensive molecular dynamics simulations of a β-hairpin-forming peptide

1998 • 16 citations

Adaptive umbrella sampling of the potential energy: modified updating procedure of the umbrella potential and application to peptide folding

1999 • 16 citations

Structural diversity of sequentially identical subsequences of proteins

1996 • 5 citations