Published in Adv Protein Chem Struct Biol on January 01, 2011
Blind prediction of host-guest binding affinities: a new SAMPL3 challenge. J Comput Aided Mol Des (2012) 1.23
Perspective: Alchemical free energy calculations for drug discovery. J Chem Phys (2012) 1.10
Theory of binless multi-state free energy estimation with applications to protein-ligand binding. J Chem Phys (2012) 1.10
Prediction of SAMPL3 host-guest affinities with the binding energy distribution analysis method (BEDAM). J Comput Aided Mol Des (2012) 1.09
Conformational Transitions and Convergence of Absolute Binding Free Energy Calculations. J Chem Theory Comput (2012) 0.99
Virtual screening of integrase inhibitors by large scale binding free energy calculations: the SAMPL4 challenge. J Comput Aided Mol Des (2014) 0.96
Large scale affinity calculations of cyclodextrin host-guest complexes: Understanding the role of reorganization in the molecular recognition process. J Chem Theory Comput (2013) 0.96
Large-scale asynchronous and distributed multidimensional replica exchange molecular simulations and efficiency analysis. J Comput Chem (2015) 0.92
Hybrid Steered Molecular Dynamics Approach to Computing Absolute Binding Free Energy of Ligand-Protein Complexes: A Brute Force Approach That Is Fast and Accurate. J Chem Theory Comput (2015) 0.89
Computing Protein-Protein Association Affinity with Hybrid Steered Molecular Dynamics. J Chem Theory Comput (2015) 0.85
Role of Ligand Reorganization and Conformational Restraints on the Binding Free Energies of DAPY Non-Nucleoside Inhibitors to HIV Reverse Transcriptase. Comput Mol Biosci (2012) 0.84
BEDAM binding free energy predictions for the SAMPL4 octa-acid host challenge. J Comput Aided Mol Des (2015) 0.83
Distinguishing binders from false positives by free energy calculations: fragment screening against the flap site of HIV protease. J Phys Chem B (2014) 0.81
Recent Progress in Treating Protein-Ligand Interactions with Quantum-Mechanical Methods. Int J Mol Sci (2016) 0.80
Asynchronous Replica Exchange Software for Grid and Heterogeneous Computing. Comput Phys Commun (2015) 0.79
Protein-Ligand Electrostatic Binding Free Energies from Explicit and Implicit Solvation. J Chem Theory Comput (2015) 0.79
Implicit solvent methods for free energy estimation. Eur J Med Chem (2014) 0.78
A unique binding mode of the eukaryotic translation initiation factor 4E for guiding the design of novel peptide inhibitors. Protein Sci (2015) 0.77
Agonist and antagonist binding to the nuclear vitamin D receptor: dynamics, mutation effects and functional implications. In Silico Pharmacol (2013) 0.77
A combined treatment of hydration and dynamical effects for the modeling of host-guest binding thermodynamics: the SAMPL5 blinded challenge. J Comput Aided Mol Des (2016) 0.76
Computing the binding affinity of a ligand buried deep inside a protein with the hybrid steered molecular dynamics. Biochem Biophys Res Commun (2016) 0.75
Optimized CGenFF force-field parameters for acylphosphate and N-phosphonosulfonimidoyl functional groups. J Mol Model (2013) 0.75
Free Energy-Based Virtual Screening and Optimization of RNase H Inhibitors of HIV-1 Reverse Transcriptase. ACS Omega (2016) 0.75
Binding affinities controlled by shifting conformational equilibria: opportunities and limitations. Biophys J (2015) 0.75
Ligand binding and dynamics of the monomeric epidermal growth factor receptor ectodomain. Proteins (2013) 0.75
A Simple PB/LIE Free Energy Function Accurately Predicts the Peptide Binding Specificity of the Tiam1 PDZ Domain. Front Mol Biosci (2017) 0.75
All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B (1998) 54.00
Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc Chem Res (2000) 10.78
Effective energy function for proteins in solution. Proteins (1999) 9.44
The statistical-thermodynamic basis for computation of binding affinities: a critical review. Biophys J (1997) 7.64
Optimized Monte Carlo data analysis. Phys Rev Lett (1989) 7.03
Implicit solvent models. Biophys Chem (1999) 6.79
Generalized born models of macromolecular solvation effects. Annu Rev Phys Chem (2000) 6.55
Calculation of protein-ligand binding affinities. Annu Rev Biophys Biomol Struct (2007) 6.12
The many roles of computation in drug discovery. Science (2004) 5.66
Virtual screening of chemical libraries. Nature (2004) 4.84
Ligand configurational entropy and protein binding. Proc Natl Acad Sci U S A (2007) 4.33
Statistically optimal analysis of samples from multiple equilibrium states. J Chem Phys (2008) 3.87
Molecular recognition and docking algorithms. Annu Rev Biophys Biomol Struct (2003) 3.40
Improving implicit solvent simulations: a Poisson-centric view. Curr Opin Struct Biol (2005) 3.38
Calculation of absolute protein-ligand binding free energy from computer simulations. Proc Natl Acad Sci U S A (2005) 3.21
A model binding site for testing scoring functions in molecular docking. J Mol Biol (2002) 2.94
Efficient drug lead discovery and optimization. Acc Chem Res (2009) 2.90
Absolute binding free energy calculations using molecular dynamics simulations with restraining potentials. Biophys J (2006) 2.88
Replica exchange with solute tempering: a method for sampling biological systems in explicit water. Proc Natl Acad Sci U S A (2005) 2.88
Binding of small-molecule ligands to proteins: "what you see" is not always "what you get". Structure (2009) 2.83
Computations of standard binding free energies with molecular dynamics simulations. J Phys Chem B (2009) 2.80
Revisiting free energy calculations: a theoretical connection to MM/PBSA and direct calculation of the association free energy. Biophys J (2004) 2.69
Assessing implicit models for nonpolar mean solvation forces: the importance of dispersion and volume terms. Proc Natl Acad Sci U S A (2006) 2.56
Free energy, entropy, and induced fit in host-guest recognition: calculations with the second-generation mining minima algorithm. J Am Chem Soc (2004) 2.36
Alchemical free energy methods for drug discovery: progress and challenges. Curr Opin Struct Biol (2011) 2.31
Temperature weighted histogram analysis method, replica exchange, and transition paths. J Phys Chem B (2005) 2.30
Recent advances in implicit solvent-based methods for biomolecular simulations. Curr Opin Struct Biol (2008) 2.20
Predicting absolute ligand binding free energies to a simple model site. J Mol Biol (2007) 2.19
Computer simulations with explicit solvent: recent progress in the thermodynamic decomposition of free energies and in modeling electrostatic effects. Annu Rev Phys Chem (1998) 2.18
On the calculation of absolute macromolecular binding free energies. Proc Natl Acad Sci U S A (2002) 2.17
Absolute and relative binding free energy calculations of the interaction of biotin and its analogs with streptavidin using molecular dynamics/free energy perturbation approaches. Proteins (1993) 2.13
A cavity-containing mutant of T4 lysozyme is stabilized by buried benzene. Nature (1992) 2.10
On the use of orientational restraints and symmetry corrections in alchemical free energy calculations. J Chem Phys (2006) 2.10
Conformational analysis of drug-like molecules bound to proteins: an extensive study of ligand reorganization upon binding. J Med Chem (2004) 2.04
Theory of free energy and entropy in noncovalent binding. Chem Rev (2009) 1.96
Nonlinear scaling schemes for Lennard-Jones interactions in free energy calculations. J Chem Phys (2007) 1.94
Good practices in free-energy calculations. J Phys Chem B (2010) 1.90
Predicting ligand binding affinity with alchemical free energy methods in a polar model binding site. J Mol Biol (2009) 1.90
Direct calculation of the binding free energies of FKBP ligands. J Chem Phys (2005) 1.88
A synthetic host-guest system achieves avidin-biotin affinity by overcoming enthalpy-entropy compensation. Proc Natl Acad Sci U S A (2007) 1.87
Perspective on Free-Energy Perturbation Calculations for Chemical Equilibria. J Chem Theory Comput (2008) 1.80
Calculation of Standard Binding Free Energies: Aromatic Molecules in the T4 Lysozyme L99A Mutant. J Chem Theory Comput (2006) 1.77
Calculation of protein-ligand binding free energy by using a polarizable potential. Proc Natl Acad Sci U S A (2008) 1.75
Energetic origins of specificity of ligand binding in an interior nonpolar cavity of T4 lysozyme. Biochemistry (1995) 1.75
The Confine-and-Release Method: Obtaining Correct Binding Free Energies in the Presence of Protein Conformational Change. J Chem Theory Comput (2007) 1.73
A bias-exchange approach to protein folding. J Phys Chem B (2007) 1.72
Cavities in molecular liquids and the theory of hydrophobic solubilities. J Am Chem Soc (1990) 1.72
Virtual screening strategies in drug discovery. Curr Opin Chem Biol (2007) 1.67
Calculation of absolute protein-ligand binding affinity using path and endpoint approaches. Biophys J (2005) 1.65
Free-energy landscape for beta hairpin folding from combined parallel tempering and metadynamics. J Am Chem Soc (2006) 1.56
The Binding Energy Distribution Analysis Method (BEDAM) for the Estimation of Protein-Ligand Binding Affinities. J Chem Theory Comput (2010) 1.52
Trypsin-ligand binding free energies from explicit and implicit solvent simulations with polarizable potential. J Comput Chem (2009) 1.46
The AGBNP2 Implicit Solvation Model. J Chem Theory Comput (2009) 1.43
Decoys for docking. J Med Chem (2005) 1.43
Prediction of protein-ligand binding affinity by free energy simulations: assumptions, pitfalls and expectations. J Comput Aided Mol Des (2010) 1.41
Host-guest complexes with protein-ligand-like affinities: computational analysis and design. J Am Chem Soc (2009) 1.38
Thermodynamic and structural effects of conformational constraints in protein-ligand interactions. Entropic paradoxy associated with ligand preorganization. J Am Chem Soc (2009) 1.37
Tork: Conformational analysis method for molecules and complexes. J Comput Chem (2003) 1.35
Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations. J Chem Theory Comput (2010) 1.35
Computation of Absolute Hydration and Binding Free Energy with Free Energy Perturbation Distributed Replica-Exchange Molecular Dynamics (FEP/REMD). J Chem Theory Comput (2009) 1.30
Comparative performance of several flexible docking programs and scoring functions: enrichment studies for a diverse set of pharmaceutically relevant targets. J Chem Inf Model (2007) 1.29
Towards predictive ligand design with free-energy based computational methods? Curr Med Chem (2006) 1.28
Computational evaluation of protein-small molecule binding. Curr Opin Struct Biol (2009) 1.27
Parallelized-over-parts computation of absolute binding free energy with docking and molecular dynamics. J Chem Phys (2006) 1.27
Lambda-dynamics free energy simulation methods. J Comput Chem (2009) 1.25
Evaluating the Accuracy of the Quasiharmonic Approximation. J Chem Theory Comput (2005) 1.22
Free energy calculations for theophylline binding to an RNA aptamer: Comparison of MM-PBSA and thermodynamic integration methods. Biopolymers (2003) 1.21
Hydrophobic aided replica exchange: an efficient algorithm for protein folding in explicit solvent. J Phys Chem B (2006) 1.20
Constant pH replica exchange molecular dynamics in biomolecules using a discrete protonation model. J Chem Theory Comput (2010) 1.16
Coupling of replica exchange simulations to a non-Boltzmann structure reservoir. J Phys Chem B (2007) 1.12
Hamiltonian replica exchange molecular dynamics using soft-core interactions. J Chem Phys (2008) 1.10
Free energies of ligand binding for structurally diverse compounds. Proc Natl Acad Sci U S A (2005) 1.10
High-throughput calculation of protein-ligand binding affinities: modification and adaptation of the MM-PBSA protocol to enterprise grid computing. J Chem Inf Model (2006) 1.09
Absolute binding free energy calculations of sparsomycin analogs to the bacterial ribosome. J Phys Chem B (2010) 1.03
On the theory of noncovalent binding. Biophys J (2004) 1.01
Use of 2-aminopurine as a fluorescent tool for characterizing antibiotic recognition of the bacterial rRNA A-site. Tetrahedron (2007) 1.00
Drug-like bioactive structures and conformational coverage with the LigPrep/ConfGen suite: comparison to programs MOE and catalyst. J Chem Inf Model (2010) 0.99
Importance of ligand reorganization free energy in protein-ligand binding-affinity prediction. J Am Chem Soc (2009) 0.96
In silico vaccine design based on molecular simulations of rhinovirus chimeras presenting HIV-1 gp41 epitopes. J Mol Biol (2008) 0.91
Conformational populations of ligand-sized molecules by replica exchange molecular dynamics and temperature reweighting. J Comput Chem (2010) 0.90
Accounting for ligand conformational restriction in calculations of protein-ligand binding affinities. Biophys J (2010) 0.87
Computing Relative Free Energies of Solvation using Single Reference Thermodynamic Integration Augmented with Hamiltonian Replica Exchange. J Chem Theory Comput (2010) 0.85
Antigenic characteristics of rhinovirus chimeras designed in silico for enhanced presentation of HIV-1 gp41 epitopes [corrected]. J Mol Biol (2010) 0.85
Rapid estimation of relative protein-ligand binding affinities using a high-throughput version of MM-PBSA. J Chem Inf Model (2007) 0.83
Comparison of computational approaches for predicting the effects of missense mutations on p53 function. J Mol Graph Model (2008) 0.80
Free-energy profiles of membrane insertion of the M2 transmembrane peptide from influenza A virus. Biophys J (2008) 0.76
Integrated Modeling Program, Applied Chemical Theory (IMPACT). J Comput Chem (2005) 3.71
AGBNP: an analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling. J Comput Chem (2004) 3.39
The SGB/NP hydration free energy model based on the surface generalized born solvent reaction field and novel nonpolar hydration free energy estimators. J Comput Chem (2002) 2.52
Temperature weighted histogram analysis method, replica exchange, and transition paths. J Phys Chem B (2005) 2.30
Direct Determination of Kinetic Rates from Single-Molecule Photon Arrival Trajectories Using Hidden Markov Models. J Phys Chem A (2003) 1.85
HIV-1 reverse transcriptase structure with RNase H inhibitor dihydroxy benzoyl naphthyl hydrazone bound at a novel site. ACS Chem Biol (2006) 1.83
Antibacterial peptide microcin J25 inhibits transcription by binding within and obstructing the RNA polymerase secondary channel. Mol Cell (2004) 1.80
Protein folding pathways from replica exchange simulations and a kinetic network model. Proc Natl Acad Sci U S A (2005) 1.72
Prediction of Protein Loop Conformations using the AGBNP Implicit Solvent Model and Torsion Angle Sampling. J Chem Theory Comput (2008) 1.72
Free energy surfaces of beta-hairpin and alpha-helical peptides generated by replica exchange molecular dynamics with the AGBNP implicit solvent model. Proteins (2004) 1.67
Simulating replica exchange simulations of protein folding with a kinetic network model. Proc Natl Acad Sci U S A (2007) 1.65
Biliary cast syndrome following liver transplantation: Predictive factors and clinical outcomes. Liver Transpl (2008) 1.57
The Binding Energy Distribution Analysis Method (BEDAM) for the Estimation of Protein-Ligand Binding Affinities. J Chem Theory Comput (2010) 1.52
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 (2002) 1.45
A large data set comparison of protein structures determined by crystallography and NMR: statistical test for structural differences and the effect of crystal packing. Proteins (2007) 1.44
The AGBNP2 Implicit Solvation Model. J Chem Theory Comput (2009) 1.43
Structural reorganization of alpha-synuclein at low pH observed by NMR and REMD simulations. J Mol Biol (2009) 1.39
Comparative performance of several flexible docking programs and scoring functions: enrichment studies for a diverse set of pharmaceutically relevant targets. J Chem Inf Model (2007) 1.29
Advances in all atom sampling methods for modeling protein-ligand binding affinities. Curr Opin Struct Biol (2011) 1.25
Conformational equilibria and free energy profiles for the allosteric transition of the ribose-binding protein. J Mol Biol (2005) 1.20
Have we seen all structures corresponding to short protein fragments in the Protein Data Bank? An update. Protein Eng (2003) 1.10
Theory of binless multi-state free energy estimation with applications to protein-ligand binding. J Chem Phys (2012) 1.10
Prediction of SAMPL3 host-guest affinities with the binding energy distribution analysis method (BEDAM). J Comput Aided Mol Des (2012) 1.09
Conformational equilibrium of cytochrome P450 BM-3 complexed with N-palmitoylglycine: a replica exchange molecular dynamics study. J Am Chem Soc (2006) 1.05
Distance-restrained docking of rifampicin and rifamycin SV to RNA polymerase using systematic FRET measurements: developing benchmarks of model quality and reliability. Biophys J (2004) 1.03
Pairwise and higher-order correlations among drug-resistance mutations in HIV-1 subtype B protease. BMC Bioinformatics (2009) 1.02
Insights into the dynamics of HIV-1 protease: a kinetic network model constructed from atomistic simulations. J Am Chem Soc (2011) 1.02
Simple continuous and discrete models for simulating replica exchange simulations of protein folding. J Phys Chem B (2008) 1.01
Conformational Transitions and Convergence of Absolute Binding Free Energy Calculations. J Chem Theory Comput (2012) 0.99
How kinetics within the unfolded state affects protein folding: an analysis based on markov state models and an ultra-long MD trajectory. J Phys Chem B (2013) 0.98
Kinetic network study of the diversity and temperature dependence of Trp-Cage folding pathways: combining transition path theory with stochastic simulations. J Phys Chem B (2011) 0.98
Asynchronous replica exchange for molecular simulations. J Comput Chem (2008) 0.97
Virtual screening of integrase inhibitors by large scale binding free energy calculations: the SAMPL4 challenge. J Comput Aided Mol Des (2014) 0.96
Recovering kinetics from a simplified protein folding model using replica exchange simulations: a kinetic network and effective stochastic dynamics. J Phys Chem B (2009) 0.96
Inference of signaling and gene regulatory networks by steady-state perturbation experiments: structure and accuracy. J Theor Biol (2005) 0.95
Complete protein structure determination using backbone residual dipolar couplings and sidechain rotamer prediction. J Struct Funct Genomics (2002) 0.93
Identification of alternative binding sites for inhibitors of HIV-1 ribonuclease H through comparative analysis of virtual enrichment studies. J Chem Inf Model (2011) 0.93
In silico vaccine design based on molecular simulations of rhinovirus chimeras presenting HIV-1 gp41 epitopes. J Mol Biol (2008) 0.91
Exploring structural variability in X-ray crystallographic models using protein local optimization by torsion-angle sampling. Acta Crystallogr D Biol Crystallogr (2008) 0.91
Conformational populations of ligand-sized molecules by replica exchange molecular dynamics and temperature reweighting. J Comput Chem (2010) 0.90
Correlated electrostatic mutations provide a reservoir of stability in HIV protease. PLoS Comput Biol (2012) 0.90
NMR relaxation in proteins with fast internal motions and slow conformational exchange: model-free framework and Markov state simulations. J Phys Chem B (2013) 0.87
Conformational dynamics of substrate in the active site of cytochrome P450 BM-3/NPG complex: insights from NMR order parameters. J Am Chem Soc (2007) 0.85
Antigenic characteristics of rhinovirus chimeras designed in silico for enhanced presentation of HIV-1 gp41 epitopes [corrected]. J Mol Biol (2010) 0.85
Chimeric rhinoviruses displaying MPER epitopes elicit anti-HIV neutralizing responses. PLoS One (2013) 0.84
Fatal lactic acidosis associated with the use of combination oral medications to treat reactivation of hepatitis B. J Clin Gastroenterol (2009) 0.84
Correlation between 13Calpha chemical shifts and helix content of peptide ensembles. Protein Sci (2008) 0.83
BEDAM binding free energy predictions for the SAMPL4 octa-acid host challenge. J Comput Aided Mol Des (2015) 0.83
Protein sequential resonance assignments by combinatorial enumeration using 13C alpha chemical shifts and their (i, i-1) sequential connectivities. J Biomol NMR (2002) 0.82
Investigation of the Polymeric Properties of α-Synuclein and Comparison with NMR Experiments: A Replica Exchange Molecular Dynamics Study. J Chem Theory Comput (2012) 0.82
Distinguishing binders from false positives by free energy calculations: fragment screening against the flap site of HIV protease. J Phys Chem B (2014) 0.81
Distinguishing among structural ensembles of the GB1 peptide: REMD simulations and NMR experiments. J Am Chem Soc (2007) 0.80
The linear interaction energy method for the prediction of protein stability changes upon mutation. Proteins (2011) 0.79
Conformational analysis of the DFG-out kinase motif and biochemical profiling of structurally validated type II inhibitors. J Med Chem (2014) 0.78
Binding Energy Distribution Analysis Method: Hamiltonian Replica Exchange with Torsional Flattening for Binding Mode Prediction and Binding Free Energy Estimation. J Chem Theory Comput (2016) 0.78
Connecting free energy surfaces in implicit and explicit solvent: an efficient method to compute conformational and solvation free energies. J Chem Theory Comput (2015) 0.76
Molecular dynamics of the proline switch and its role in Crk signaling. J Phys Chem B (2014) 0.75
Large-Scale Asynchronous and Distributed Multidimensional Replica Exchange Molecular Simulations and Efficiency Analysis. J Comput Chem (2016) 0.75