| 1 | Elucidating the Molecular Determinants of the Binding Modes of a Third-Generation HIV-1 Integrase Strand Transfer Inhibitor: The Importance of Side Chain and Solvent Reorganization | 3.2 | 5 | Citations (PDF) |
| 2 | Potts Hamiltonian Models and Molecular Dynamics Free Energy Simulations for Predicting the Impact of Mutations on Protein Kinase Stability | 2.7 | 14 | Citations (PDF) |
| 3 | Kinetic coevolutionary models predict the temporal emergence of HIV-1 resistance mutations under drug selection pressure | 7.5 | 16 | Citations (PDF) |
| 4 | Evolutionary sequence and structural basis for the distinct conformational landscapes of Tyr and Ser/Thr kinases | 13.7 | 21 | Citations (PDF) |
| 5 | Mechanisms of HIV-1 integrase resistance to dolutegravir and potent inhibition of drug-resistant variants | 10.9 | 36 | Citations (PDF) |
| 6 | Unique features of different classes of
G‐protein‐coupled
receptors revealed from sequence coevolutionary and structural analysis | 2.6 | 11 | Citations (PDF) |
| 7 | Limits to detecting epistasis in the fitness landscape of HIV | 2.3 | 11 | Citations (PDF) |
| 8 | Structure-based virtual screening workflow to identify antivirals targeting HIV-1 capsid | 2.4 | 8 | Citations (PDF) |
| 9 | Contingency and Entrenchment of Drug-Resistance Mutations in HIV Viral Proteins | 2.7 | 12 | Citations (PDF) |
| 10 | Mi3-GPU: MCMC-based inverse Ising inference on GPUs for protein covariation analysis | 7.5 | 31 | Citations (PDF) |
| 11 | Computational design of small molecular modulators of protein–protein interactions with a novel thermodynamic cycle: Allosteric inhibitors of HIV‐1 integrase | 5.9 | 8 | Citations (PDF) |
| 12 | Molecular Dynamics Free Energy Simulations Reveal the Mechanism for the Antiviral Resistance of the M66I HIV-1 Capsid Mutation | 3.2 | 18 | Citations (PDF) |
| 13 | Protein Loop Conformational Free Energy Changes via an Alchemical Path without Reaction Coordinates | 4.2 | 8 | Citations (PDF) |
| 14 | The generative capacity of probabilistic protein sequence models | 13.7 | 41 | Citations (PDF) |
| 15 | Absolute Protein Binding Free Energy Simulations for Ligands with Multiple Poses, a Thermodynamic Path That Avoids Exhaustive Enumeration of the Poses | 4.8 | 18 | Citations (PDF) |
| 16 | Ligand Binding Thermodynamic Cycles: Hysteresis, the Locally Weighted Histogram Analysis Method, and the Overlapping States Matrix | 5.1 | 9 | Citations (PDF) |
| 17 | Exploring the Free-Energy Landscape and Thermodynamics of Protein-Protein Association | 2.2 | 28 | Citations (PDF) |
| 18 | Cavity Particle in Aqueous Solution with a Hydrophobic Solute: Structure, Energetics, and Functionals | 2.7 | 2 | Citations (PDF) |
| 19 | Spatially-Decomposed Free Energy of Solvation Based on the Endpoint Density-Functional Method | 5.1 | 14 | Citations (PDF) |
| 20 | Influence of multiple-sequence-alignment depth on Potts statistical models of protein covariation | 2.1 | 30 | Citations (PDF) |
| 21 | The UWHAM and SWHAM Software Package | 3.4 | 10 | Citations (PDF) |
| 22 | Massive-Scale Binding Free Energy Simulations of HIV Integrase Complexes Using Asynchronous Replica Exchange Framework Implemented on the IBM WCG Distributed Network | 4.5 | 6 | Citations (PDF) |
| 23 | The Excess Chemical Potential of Water at the Interface with a Protein from End Point Simulations | 2.7 | 12 | Citations (PDF) |
| 24 | Coevolutionary Landscape of Kinase Family Proteins: Sequence Probabilities and Functional Motifs | 2.2 | 28 | Citations (PDF) |
| 25 | The Role of Interfacial Water in Protein–Ligand Binding: Insights from the Indirect Solvent Mediated Potential of Mean Force | 5.1 | 33 | Citations (PDF) |
| 26 | Comparing alchemical and physical pathway methods for computing the absolute binding free energy of charged ligands | 2.7 | 38 | Citations (PDF) |
| 27 | Improving Prediction Accuracy of Binding Free Energies and Poses of HIV Integrase Complexes Using the Binding Energy Distribution Analysis Method with Flattening Potentials | 4.5 | 7 | Citations (PDF) |
| 28 | Conformational Free Energy Changes via an Alchemical Path without Reaction Coordinates | 4.2 | 14 | Citations (PDF) |
| 29 | Relationship between Solvation Thermodynamics from IST and DFT Perspectives | 2.7 | 19 | Citations (PDF) |
| 30 | Inference of Epistatic Effects Leading to Entrenchment and Drug Resistance in HIV-1 Protease | 4.7 | 59 | Citations (PDF) |
| 31 | Computing conformational free energy differences in explicit solvent: An efficient thermodynamic cycle using an auxiliary potential and a free energy functional constructed from the end points | 4.8 | 16 | Citations (PDF) |
| 32 | Stratified UWHAM and Its Stochastic Approximation for Multicanonical Simulations Which Are Far from Equilibrium | 5.1 | 10 | Citations (PDF) |
| 33 | Potts Hamiltonian models of protein co-variation, free energy landscapes, and evolutionary fitness | 6.4 | 117 | Citations (PDF) |
| 34 | Structural propensities of kinase family proteins from a Potts model of residue co‐variation | 5.9 | 62 | Citations (PDF) |
| 35 | Locally weighted histogram analysis and stochastic solution for large-scale multi-state free energy estimation | 2.8 | 17 | Citations (PDF) |
| 36 | Large‐Scale Asynchronous and Distributed Multidimensional Replica Exchange Molecular Simulations and Efficiency Analysis | 4.8 | 0 | Citations (PDF) |
| 37 | Binding Energy Distribution Analysis Method: Hamiltonian Replica Exchange with Torsional Flattening for Binding Mode Prediction and Binding Free Energy Estimation | 5.1 | 15 | Citations (PDF) |
| 38 | Simulating Replica Exchange: Markov State Models, Proposal Schemes, and the Infinite Swapping Limit | 2.7 | 51 | Citations (PDF) |
| 39 | A New Class of Allosteric HIV-1 Integrase Inhibitors Identified by Crystallographic Fragment Screening of the Catalytic Core Domain | 2.2 | 26 | Citations (PDF) |
| 40 | Parameterization of an effective potential for protein–ligand binding from host–guest affinity data | 3.0 | 32 | Citations (PDF) |
| 41 | Large scale free energy calculations for blind predictions of protein–ligand binding: the D3R Grand Challenge 2015 | 2.4 | 18 | Citations (PDF) |
| 42 | Allosteric HIV‐1 integrase inhibitors promote aberrant protein multimerization by directly mediating inter‐subunit interactions: Structural and thermodynamic modeling studies | 5.9 | 35 | Citations (PDF) |
| 43 | A combined treatment of hydration and dynamical effects for the modeling of host–guest binding thermodynamics: the SAMPL5 blinded challenge | 2.4 | 19 | Citations (PDF) |
| 44 | Large‐scale asynchronous and distributed multidimensional replica exchange molecular simulations and efficiency analysis | 4.8 | 21 | Citations (PDF) |
| 45 | Distinguishing Binders from False Positives by Free Energy Calculations: Fragment Screening Against the Flap Site of HIV Protease | 2.7 | 67 | Citations (PDF) |
| 46 | BEDAM binding free energy predictions for the SAMPL4 octa-acid host challenge | 2.4 | 17 | Citations (PDF) |
| 47 | Asynchronous replica exchange software for grid and heterogeneous computing | 7.5 | 40 | Citations (PDF) |
| 48 | Deep Sequencing of Protease Inhibitor Resistant HIV Patient Isolates Reveals Patterns of Correlated Mutations in Gag and Protease | 3.1 | 43 | Citations (PDF) |
| 49 | Connecting Free Energy Surfaces in Implicit and Explicit Solvent: An Efficient Method To Compute Conformational and Solvation Free Energies | 5.1 | 11 | Citations (PDF) |
| 50 | A Stochastic Solution to the Unbinned WHAM Equations | 4.2 | 33 | Citations (PDF) |
| 51 | First Passage Times, Lifetimes, and Relaxation Times of Unfolded Proteins | 8.2 | 15 | Citations (PDF) |
| 52 | Conformational Analysis of the DFG-Out Kinase Motif and Biochemical Profiling of Structurally Validated Type II Inhibitors | 5.6 | 236 | Citations (PDF) |
| 53 | The mechanism of H171T resistance reveals the importance of Nδ-protonated His171 for the binding of allosteric inhibitor BI-D to HIV-1 integrase | 3.5 | 41 | Citations (PDF) |
| 54 | Virtual screening of integrase inhibitors by large scale binding free energy calculations: the SAMPL4 challenge | 2.4 | 57 | Citations (PDF) |
| 55 | Molecular Dynamics of the Proline Switch and Its Role in Crk Signaling | 2.7 | 23 | Citations (PDF) |
| 56 | How long does it take to equilibrate the unfolded state of a protein? | 5.9 | 24 | Citations (PDF) |
| 57 | How Kinetics within the Unfolded State Affects Protein Folding: An Analysis Based on Markov State Models and an Ultra-Long MD Trajectory | 2.7 | 60 | Citations (PDF) |
| 58 | NMR Relaxation in Proteins with Fast Internal Motions and Slow Conformational Exchange: Model-Free Framework and Markov State Simulations | 2.7 | 29 | Citations (PDF) |
| 59 | Large Scale Affinity Calculations of Cyclodextrin Host–Guest Complexes: Understanding the Role of Reorganization in the Molecular Recognition Process | 5.1 | 88 | Citations (PDF) |
| 60 | Correlated Electrostatic Mutations Provide a Reservoir of Stability in HIV Protease | 3.1 | 34 | Citations (PDF) |
| 61 | Theory of binless multi-state free energy estimation with applications to protein-ligand binding | 2.8 | 170 | Citations (PDF) |
| 62 | Investigation of the Polymeric Properties of α-Synuclein and Comparison with NMR Experiments: A Replica Exchange Molecular Dynamics Study | 5.1 | 33 | Citations (PDF) |
| 63 | The linear interaction energy method for the prediction of protein stability changes upon mutation | 2.6 | 32 | Citations (PDF) |
| 64 | Conformational Transitions and Convergence of Absolute Binding Free Energy Calculations | 5.1 | 60 | Citations (PDF) |
| 65 | Prediction of SAMPL3 host-guest affinities with the binding energy distribution analysis method (BEDAM) | 2.4 | 43 | Citations (PDF) |
| 66 | Kinetic Network Study of the Diversity and Temperature Dependence of Trp-Cage Folding Pathways: Combining Transition Path Theory with Stochastic Simulations | 2.7 | 46 | Citations (PDF) |
| 67 | Identification of Alternative Binding Sites for Inhibitors of HIV-1 Ribonuclease H Through Comparative Analysis of Virtual Enrichment Studies | 4.5 | 36 | Citations (PDF) |
| 68 | Advances in all atom sampling methods for modeling protein–ligand binding affinities | 6.4 | 100 | Citations (PDF) |
| 69 | Insights into the Dynamics of HIV-1 Protease: A Kinetic Network Model Constructed from Atomistic Simulations | 15.0 | 57 | Citations (PDF) |
| 70 | Conformational populations of ligand‐sized molecules by replica exchange molecular dynamics and temperature reweighting | 4.8 | 22 | Citations (PDF) |
| 71 | Binding Energy Distribution Analysis Method (BEDAM) for Estimation of Protein−Ligand Binding Affinities | 5.1 | 154 | Citations (PDF) |
| 72 | Antigenic Characteristics of Rhinovirus Chimeras Designed in silico for En5hanced Presentation of HIV-1 gp41 Epitopes | 4.1 | 15 | Citations (PDF) |
| 73 | Pairwise and higher-order correlations among drug-resistance mutations in HIV-1 subtype B protease | 3.0 | 27 | Citations (PDF) |
| 74 | Recovering Kinetics from a Simplified Protein Folding Model Using Replica Exchange Simulations: A Kinetic Network and Effective Stochastic Dynamics | 2.7 | 28 | Citations (PDF) |
| 75 | In Silico Vaccine Design Based on Molecular Simulations of Rhinovirus Chimeras Presenting HIV-1 gp41 Epitopes | 4.1 | 50 | Citations (PDF) |
| 76 | Structural Reorganization of α-Synuclein at Low pH Observed by NMR and REMD Simulations | 4.1 | 189 | Citations (PDF) |
| 77 | Molecular Dynamics Study of Non-nucleoside Reverse Transcriptase Inhibitor 4-[[4-[[4-[(E)-2-Cyanoethenyl]-2,6-dimethylphenyl]amino]-2-pyrimidinyl]amino]benzonitrile (TMC278/Rilpivirine) Aggregates: Correlation between Amphiphilic Properties of the Drug and Oral Bioavailability | 5.6 | 17 | Citations (PDF) |
| 78 | The AGBNP2 Implicit Solvation Model | 5.1 | 114 | Citations (PDF) |
| 79 | Conformational Landscape of the Human Immunodeficiency Virus Type 1 Reverse Transcriptase Non-Nucleoside Inhibitor Binding Pocket: Lessons for Inhibitor Design from a Cluster Analysis of Many Crystal Structures | 5.6 | 34 | Citations (PDF) |
| 80 | Exploring structural variability in X-ray crystallographic models using protein local optimization by torsion-angle sampling | 3.1 | 15 | Citations (PDF) |
| 81 | Asynchronous replica exchange for molecular simulations | 4.8 | 40 | Citations (PDF) |
| 82 | Correlation between 13Cα chemical shifts and helix content of peptide ensembles | 5.9 | 13 | Citations (PDF) |
| 83 | Prediction of Protein Loop Conformations Using the AGBNP Implicit Solvent Model and Torsion Angle Sampling | 5.1 | 62 | Citations (PDF) |
| 84 | Simple Continuous and Discrete Models for Simulating Replica Exchange Simulations of Protein Folding | 2.7 | 35 | Citations (PDF) |
| 85 | Simulating replica exchange simulations of protein folding with a kinetic network model | 7.5 | 102 | Citations (PDF) |
| 86 | Linear Interaction Energy (LIE) Models for Ligand Binding in Implicit Solvent: Theory and Application to the Binding of NNRTIs to HIV-1 Reverse Transcriptase | 5.1 | 50 | Citations (PDF) |
| 87 | Comparative Performance of Several Flexible Docking Programs and Scoring Functions: Enrichment Studies for a Diverse Set of Pharmaceutically Relevant Targets | 4.5 | 160 | Citations (PDF) |
| 88 | Conformational Dynamics of Substrate in the Active Site of Cytochrome P450 BM-3/NPG Complex: Insights from NMR Order Parameters | 15.0 | 18 | Citations (PDF) |
| 89 | Distinguishing among Structural Ensembles of the GB1 Peptide: REMD Simulations and NMR Experiments | 15.0 | 24 | Citations (PDF) |
| 90 | A large data set comparison of protein structures determined by crystallography and NMR: Statistical test for structural differences and the effect of crystal packing | 2.6 | 117 | Citations (PDF) |
| 91 | Conformational Equilibrium of Cytochrome P450 BM-3 Complexed withN-Palmitoylglycine: A Replica Exchange Molecular Dynamics Study | 15.0 | 60 | Citations (PDF) |
| 92 | Integrated Modeling Program, Applied Chemical Theory (IMPACT) | 4.8 | 1,456 | Citations (PDF) |
| 93 | Inference of signaling and gene regulatory networks by steady-state perturbation experiments: structure and accuracy | 1.6 | 78 | Citations (PDF) |
| 94 | Protein folding pathways from replica exchange simulations and a kinetic network model | 7.5 | 136 | Citations (PDF) |
| 95 | Temperature Weighted Histogram Analysis Method, Replica Exchange, and Transition Paths† | 2.7 | 186 | Citations (PDF) |
| 96 | Conformational Equilibria and Free Energy Profiles for the Allosteric Transition of the Ribose-binding Protein | 4.1 | 72 | Citations (PDF) |
| 97 | Distance-Restrained Docking of Rifampicin and Rifamycin SV to RNA Polymerase Using Systematic FRET Measurements: Developing Benchmarks of Model Quality and Reliability | 2.2 | 46 | Citations (PDF) |
| 98 | Free energy surfaces of β-hairpin and α-helical peptides generated by replica exchange molecular dynamics with the AGBNP implicit solvent model | 2.6 | 124 | Citations (PDF) |
| 99 | AGBNP: An analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling | 4.8 | 320 | Citations (PDF) |
| 100 | Antibacterial Peptide Microcin J25 Inhibits Transcription by Binding within and Obstructing the RNA Polymerase Secondary Channel | 13.3 | 219 | Citations (PDF) |
| 101 | Long-Time Conformational Transitions of Alanine Dipeptide in Aqueous Solution: Continuous and Discrete-State Kinetic Models | 2.7 | 82 | Citations (PDF) |
| 102 | On the Nonpolar Hydration Free Energy of Proteins: Surface Area and Continuum Solvent Models for the Solute−Solvent Interaction Energy | 15.0 | 271 | Citations (PDF) |
| 103 | Direct Determination of Kinetic Rates from Single-Molecule Photon Arrival Trajectories Using Hidden Markov Models | 2.5 | 131 | Citations (PDF) |
| 104 | Have we seen all structures corresponding to short protein fragments in the Protein Data Bank? An update | 2.6 | 47 | Citations (PDF) |
| 105 | Chloride Ion Hydration and Diffusion in Supercritical Water Using a Polarizable Water Model | 2.7 | 24 | Citations (PDF) |
| 106 | Structural Organization of Bacterial RNA Polymerase Holoenzyme and the RNA Polymerase-Promoter Open Complex | 33.6 | 293 | Citations (PDF) |
| 107 | The SGB/NP hydration free energy model based on the surface generalized born solvent reaction field and novel nonpolar hydration free energy estimators | 4.8 | 237 | Citations (PDF) |
| 108 | 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 | 2.6 | 123 | Citations (PDF) |
| 109 | Title is missing! | 1.5 | 20 | Citations (PDF) |
| 110 | Title is missing! | 0.0 | 37 | Citations (PDF) |
| 111 | Protein Structural Motif Recognition via NMR Residual Dipolar Couplings | 15.0 | 37 | Citations (PDF) |
| 112 | New Linear Interaction Method for Binding Affinity Calculations Using a Continuum Solvent Model | 2.7 | 128 | Citations (PDF) |
| 113 | A Model for Studying Drying at Hydrophobic Interfaces: Structural and Thermodynamic Properties† | 2.7 | 98 | Citations (PDF) |
| 114 | Solvent models for protein-ligand binding: Comparison of implicit solvent poisson and surface generalized born models with explicit solvent simulations | 4.8 | 118 | Citations (PDF) |
| 115 | Title is missing! | 1.5 | 69 | Citations (PDF) |
| 116 | A Bayesian Statistical Method for the Detection and Quantification of Rotational Diffusion Anisotropy from NMR Relaxation Data | 1.6 | 17 | Citations (PDF) |
| 117 | Title is missing! | 1.5 | 20 | Citations (PDF) |
| 118 | Enthalpy−Entropy and Cavity Decomposition of Alkane Hydration Free Energies: Numerical Results and Implications for Theories of Hydrophobic Solvation | 2.7 | 333 | Citations (PDF) |
| 119 | Simplified amino acid alphabets for protein fold recognition and implications for folding | 2.6 | 224 | Citations (PDF) |
| 120 | Iterative sequence/secondary structure search for protein homologs: comparison with amino acid sequence alignments and application to fold recognition in genome databases | 4.7 | 50 | Citations (PDF) |
| 121 | Functional Group Contributions to Partial Molar Compressibilities of Alcohols in Water | 2.7 | 18 | Citations (PDF) |
| 122 | Estimation of Dynamic Parameters from NMR Relaxation Data using the Lipari–Szabo Model-Free Approach and Bayesian Statistical Methods | 1.6 | 52 | Citations (PDF) |
| 123 | Title is missing! | 1.5 | 35 | Citations (PDF) |
| 124 | Protein hydration and unfolding – insights from experimental partial specific volumes and unfolded protein models | 4.2 | 100 | Citations (PDF) |
| 125 | Entropy−Enthalpy Compensation in Solvation and Ligand Binding Revisited | 15.0 | 133 | Citations (PDF) |
| 126 | On the local and nonlocal components of solvation thermodynamics and their relation to solvation shell models | 2.8 | 48 | Citations (PDF) |
| 127 | Tertiary Contacts in αa-Lactalbumin at pH 7 and pH 2: A Molecular Dynamics Study | 2.6 | 3 | Citations (PDF) |
| 128 | COMPUTER SIMULATIONS WITH EXPLICIT SOLVENT: Recent Progress in the Thermodynamic Decomposition of Free Energies and in Modeling Electrostatic Effects | 11.0 | 259 | Citations (PDF) |
| 129 | Large scale simulation of macromolecules in solution: Combining the periodic fast multipole method with multiple time step integrators | 2.8 | 111 | Citations (PDF) |
| 130 | Thermodynamic Decomposition of Hydration Free Energies by Computer Simulation: Application to Amines, Oxides, and Sulfides | 2.7 | 64 | Citations (PDF) |
| 131 | Impact of the Precision in NMR Relaxation Measurements on the Interpretation of Protein Dynamics | 15.0 | 17 | Citations (PDF) |
| 132 | On Finite-Size Corrections to the Free Energy of Ionic Hydration | 2.7 | 97 | Citations (PDF) |
| 133 | Monte Carlo Study of the Effect of Pressure on Hydrophobic Association | 2.7 | 71 | Citations (PDF) |
| 134 | Thermodynamics of the Hydration Shell. 2. Excess Volume and Compressibility of a Hydrophobic Solute | 3.1 | 103 | Citations (PDF) |
| 135 | Dielectric response of solvent surrounding an ion pair: Ewald potential versus spherical truncation | 2.7 | 29 | Citations (PDF) |
| 136 | Prediction of pKaShifts without Truncation of Electrostatic Interactions: An Explicit Solvent Calculation for Succinic Acid | 3.1 | 35 | Citations (PDF) |
| 137 | Evaluating polarizable potentials on distributed memory parallel computers: Program development and applications | 4.8 | 10 | Citations (PDF) |
| 138 | Crankshaft motions of the polypeptide backbone in molecular dynamics simulations of human type-α transforming growth factor | 1.5 | 72 | Citations (PDF) |
| 139 | On finite‐size effects in computer simulations using the Ewald potential | 2.8 | 166 | Citations (PDF) |
| 140 | Solvation Free Energies of Small Amides and Amines from Molecular Dynamics/Free Energy Perturbation Simulations Using Pairwise Additive and Many-Body Polarizable Potentials | 3.1 | 105 | Citations (PDF) |
| 141 | An Anisotropic Polarizable Water Model: Incorporation of All-Atom Polarizabilities into Molecular Mechanics Force Fields | 3.1 | 206 | Citations (PDF) |
| 142 | Thermodynamics of the Hydration Shell. 1. Excess Energy of a Hydrophobic Solute | 3.1 | 116 | Citations (PDF) |
| 143 | Molecular mechanics and electrostatic effects | 2.1 | 24 | Citations (PDF) |
| 144 | Three-dimensional structure of echistatin and dynamics of the active site | 1.5 | 19 | Citations (PDF) |
| 145 | Intrinsic pKas of ionizable residues in proteins: An explicit solvent calculation for lysozyme | 2.6 | 97 | Citations (PDF) |
| 146 | Solvent effects on the torsional dynamics of a twisted intramolecular charge transfer (TICT) molecule: bianthryl in acetonitrile | 2.2 | 15 | Citations (PDF) |
| 147 | Global folding of proteins using a limited number of distance constraints | 2.6 | 35 | Citations (PDF) |
| 148 | Dielectric and thermodynamic response of a generalized reaction field model for liquid state simulations | 2.8 | 72 | Citations (PDF) |
| 149 | Vibrational relaxation and Bloch–Redfield theory | 2.8 | 86 | Citations (PDF) |
| 150 | Molecular dynamics simulation of solvated protein at high pressure | 2.4 | 149 | Citations (PDF) |
| 151 | Simulating the effect of the two-spin approximation on the generation of protein structures from NOE data | 0.7 | 2 | Citations (PDF) |
| 152 | Molecular electrostatic potentials and partial atomic charges from correlated wave functions: Applications to the electronic ground and excited states of 3-methylindole | 4.8 | 19 | Citations (PDF) |
| 153 | A molecular dynamics study of pressure effects on solvation and optical spectra: the ground and excited states of formaldehyde in water | 3.1 | 31 | Citations (PDF) |
| 154 | Solvent effects on the adiabatic free energy difference between the ground and excited states of methylindole in water | 3.1 | 21 | Citations (PDF) |
| 155 | Molecular dynamics simulations of water with Ewald summation for the long range electrostatic interactions | 2.7 | 91 | Citations (PDF) |
| 156 | Stabilization of α-helical secondary structure during high-temperature molecular-dynamics simulations of α-lactalbumin | 2.2 | 15 | Citations (PDF) |
| 157 | Gaussian fluctuation formula for electrostatic free‐energy changes in solution | 2.8 | 180 | Citations (PDF) |
| 158 | Analysis of side-chain conformational distributions in neutrophil peptide-5 nmr structures | 2.9 | 10 | Citations (PDF) |
| 159 | Conserving energy during molecular dynamics simulations of water, proteins, and proteins in water | 4.8 | 90 | Citations (PDF) |
| 160 | Molecular mechanics parameters for electronically excited states: The (n, π*) singlet state of formaldehyde | 2.7 | 12 | Citations (PDF) |
| 161 | Field strength dependence of dielectric saturation in liquid water | 3.1 | 51 | Citations (PDF) |
| 162 | Molecular dynamics simulation of time-resolved fluorescence and nonequilibrium solvation of formaldehyde in water | 3.1 | 100 | Citations (PDF) |
| 163 | Determining local conformational variations in DNA | 4.1 | 77 | Citations (PDF) |
| 164 | Salt-induced conformational changes in DNA: analysis using the polymer RISM theory | 3.1 | 34 | Citations (PDF) |
| 165 | Simple models for solvation effects on electronic transition energies: Formaldehyde and water | 2.7 | 34 | Citations (PDF) |
| 166 | Solution structures of proteins from NMR data and modeling: alternative folds for neutrophil peptide 5 | 2.4 | 47 | Citations (PDF) |
| 167 | Solvent effects on optical absorption spectra: the 1A1 .fwdarw. 1A2 transition of formaldehyde in water | 15.0 | 136 | Citations (PDF) |
| 168 | Computer simulations of the dielectric properties of water: Studies of the simple point charge and transferrable intermolecular potential models | 2.8 | 188 | Citations (PDF) |
| 169 | Variable quadratic propagator for quantum Monte Carlo simulations | 2.7 | 30 | Citations (PDF) |
| 170 | Determination of Protein Structures in Solution Using Nmr Data and Impact | 0.3 | 33 | Citations (PDF) |
| 171 | Ionic association in methanol and related solvents: an extended RISM analysis | 3.1 | 34 | Citations (PDF) |
| 172 | A new RISM integral equation for solvated polymers | 2.7 | 25 | Citations (PDF) |
| 173 | Computer Simulations of Macromolecular Dynamics: Models for Vibrational Spectroscopy and X-Ray Refinement | 4.0 | 7 | Citations (PDF) |
| 174 | Temperature-dependent molecular dynamics and restrained X-ray refinement simulations of a Z-DNA hexamer | 4.1 | 29 | Citations (PDF) |
| 175 | Effect of anisotropy and anharmonicity on protein crystallographic refinement | 4.1 | 188 | Citations (PDF) |
| 176 | Using Macromolecular Dynamics Simulations to Interpret Experiments | 2.0 | 2 | Citations (PDF) |
| 177 | Implementation of a macromolecular mechanics program on a cyber 205 supercomputer | 1.4 | 8 | Citations (PDF) |
| 178 | Visualization of energetics and conformations from molecular computer simulations | 2.7 | 6 | Citations (PDF) |
| 179 | Corrections to the quasiharmonic approximation for evaluating molecular entropies | 2.8 | 38 | Citations (PDF) |
| 180 | An optimized harmonic reference system for the evaluation of discretized path integrals | 2.8 | 58 | Citations (PDF) |
| 181 | Motional averaging of proton nuclear Overhauser effects in proteins. Predictions from a molecular dynamics simulation of lysozyme | 15.0 | 122 | Citations (PDF) |
| 182 | Evaluation of the configurational entropy for proteins: application to molecular dynamics simulations of an α-helix | 5.0 | 257 | Citations (PDF) |
| 183 | Quasi-harmonic method for calculating vibrational spectra from classical simulations on multi-dimensional anharmonic potential surfaces | 3.1 | 60 | Citations (PDF) |
| 184 | Normal mode paths for hydrogen exchange in the peptide ferrichrome | 7.5 | 10 | Citations (PDF) |
| 185 | Molecular dynamics of an -helical polypeptide: Temperature dependence and deviation from harmonic behavior | 7.5 | 132 | Citations (PDF) |
| 186 | alpha-Helix dipole model and electrostatic stabilization of 4-alpha-helical proteins. | 7.5 | 132 | Citations (PDF) |
| 187 | Initial fluorescence depolarization of tyrosines in proteins | 15.0 | 55 | Citations (PDF) |
| 188 | Protein dynamics and NMR relaxation: comparison of simulations with experiment | 37.9 | 108 | Citations (PDF) |
| 189 | Increase of carbon-13 NMR relaxation times in proteins due to picosecond motional averaging | 15.0 | 72 | Citations (PDF) |
| 190 | NMR relaxation parameters in molecules with internal motion: exact Langevin trajectory results compared with simplified relaxation models | 15.0 | 114 | Citations (PDF) |
| 191 | Correlated helix-coil transitions in polypeptides | 2.9 | 25 | Citations (PDF) |
| 192 | Molecular dynamics studies of nmr relaxation in proteins | 2.2 | 13 | Citations (PDF) |
| 193 | Vibrational approach to the dynamics of an ?-helix | 2.9 | 92 | Citations (PDF) |
| 194 | Diffusive langevin dynamics of model alkanes | 2.7 | 128 | Citations (PDF) |
| 195 | HIV-1 integrase tetramers are the antiviral target of pyridine-based allosteric integrase inhibitors | 0.7 | 49 | Citations (PDF) |
| 196 | Epistasis and entrenchment of drug resistance in HIV-1 subtype B | 0.7 | 45 | Citations (PDF) |
| 197 | Evolutionary divergence in the conformational landscapes of tyrosine vs serine/threonine kinases | 0.7 | 34 | Citations (PDF) |
| 198 | Predicting side chain conformations in folded proteins by AlphaFold: Perspective and challenges | 2.2 | 2 | Citations (PDF) |
| 199 | Phylogenetic corrections and higher-order sequence statistics in protein families: Potts vs multiple sequence alignment transformer machine learning models | 4.0 | 3 | Citations (PDF) |
| 200 | Predicting water at the protein interface in cryo-EM structures from MD-excess chemical potential | 2.2 | 0 | Citations (PDF) |
| 201 | Toward Reconciling the Standard Binding Free Energy of Lenacapavir to HIV-1 Capsid with Experiment: Thermodynamic Effects of Solvent Buffer and Ligand Reorganization | 2.7 | 0 | Citations (PDF) |
| 202 | BPS2026 – Potts model analysis of mutation effects on protein stability, cooperativity, and drug resistance | 2.2 | 0 | Citations (PDF) |
| 203 | Benchmarking free energy calculations: Analysis of single and double mutations across two simulation software platforms for two protein systems | 2.3 | 0 | Citations (PDF) |
| 204 | Results of a Large-Scale Study of the Binding of 50 Type II Inhibitors to 348 Kinases: The Role of Protein Reorganization | 5.6 | 0 | Citations (PDF) |
| 205 | Temporal Evolution of Drug Resistance to HIV Integrase Inhibitors | 3.2 | 0 | Citations (PDF) |
