| scholarly article | Q13442814 |
| P50 | author | Ken A. Dill | Q6387211 |
| David L. Mobley | Q55143475 | ||
| P2093 | author name string | Brian K Shoichet | |
| Alan P Graves | |||
| John D Chodera | |||
| Andrea C McReynolds | |||
| P2860 | cites work | Processing of X-ray diffraction data collected in oscillation mode | Q26778468 |
| A model binding site for testing scoring functions in molecular docking | Q27639604 | ||
| Specificity of ligand binding in a buried nonpolar cavity of T4 lysozyme: linkage of dynamics and structural plasticity | Q27729769 | ||
| Similar hydrophobic replacements of Leu99 and Phe153 within the core of T4 lysozyme have different structural and thermodynamic consequences | Q27732090 | ||
| Coot: model-building tools for molecular graphics | Q27860505 | ||
| GROMACS: fast, flexible, and free | Q27860998 | ||
| Refinement of macromolecular structures by the maximum-likelihood method | Q27861011 | ||
| Principles of docking: An overview of search algorithms and a guide to scoring functions | Q28217048 | ||
| Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect | Q28292427 | ||
| Development and testing of a general amber force field | Q29547642 | ||
| A multistep approach to structure-based drug design: studying ligand binding at the human neutrophil elastase | Q82836079 | ||
| Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models | Q29616389 | ||
| Automatic atom type and bond type perception in molecular mechanical calculations | Q29616744 | ||
| Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation | Q29617869 | ||
| Decoys for docking | Q30350781 | ||
| The Confine-and-Release Method: Obtaining Correct Binding Free Energies in the Presence of Protein Conformational Change | Q30372513 | ||
| Binding of a diverse set of ligands to avidin and streptavidin: an accurate quantitative prediction of their relative affinities by a combination of molecular mechanics and continuum solvent models | Q31446320 | ||
| Calculation of absolute protein-ligand binding free energy from computer simulations | Q33784404 | ||
| The statistical-thermodynamic basis for computation of binding affinities: a critical review | Q33915676 | ||
| Exploring the helix-coil transition via all-atom equilibrium ensemble simulations | Q34189691 | ||
| Testing a flexible-receptor docking algorithm in a model binding site | Q34309041 | ||
| Absolute binding free energy calculations using molecular dynamics simulations with restraining potentials | Q35051978 | ||
| Enhancing the accuracy, the efficiency and the scope of free energy simulations | Q36101094 | ||
| Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integration | Q36104911 | ||
| On the importance of atomic fluctuations, protein flexibility, and solvent in ion permeation | Q36445767 | ||
| Molecular mechanics methods for predicting protein-ligand binding. | Q36699089 | ||
| Potentials of mean force for acetylcholine unbinding from the alpha7 nicotinic acetylcholine receptor ligand-binding domain | Q36897559 | ||
| Accurate and efficient corrections for missing dispersion interactions in molecular simulations | Q36975952 | ||
| Second-site revertants of an inactive T4 lysozyme mutant restore activity by restructuring the active site cleft | Q38336671 | ||
| Direct calculation of the binding free energies of FKBP ligands | Q39131231 | ||
| On the use of orientational restraints and symmetry corrections in alchemical free energy calculations | Q42106721 | ||
| Calculation of absolute protein-ligand binding affinity using path and endpoint approaches | Q42132116 | ||
| Thermodynamic stability of water molecules in the bacteriorhodopsin proton channel: a molecular dynamics free energy perturbation study | Q42536182 | ||
| Comparison of charge models for fixed-charge force fields: small-molecule hydration free energies in explicit solvent. | Q46136993 | ||
| On the value of c: can low affinity systems be studied by isothermal titration calorimetry? | Q47357121 | ||
| Modeling protein-small molecule interactions: structure and thermodynamics of noble gases binding in a cavity in mutant phage T4 lysozyme L99A. | Q51380052 | ||
| A new ultrasensitive scanning calorimeter. | Q52042000 | ||
| Ligand solvation in molecular docking. | Q52214239 | ||
| Calculation of Standard Binding Free Energies: Aromatic Molecules in the T4 Lysozyme L99A Mutant. | Q53190267 | ||
| THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method | Q56157177 | ||
| Calculation of the Redox Potential of the Protein Azurin and Some Mutants | Q56880712 | ||
| GROMACS 3.0: a package for molecular simulation and trajectory analysis | Q57082068 | ||
| New Class IV Charge Model for Extracting Accurate Partial Charges from Wave Functions | Q57402373 | ||
| Model for Aqueous Solvation Based on Class IV Atomic Charges and First Solvation Shell Effects | Q57402397 | ||
| Molecular dynamics with coupling to an external bath | Q57569060 | ||
| Principles of docking: An overview of search algorithms and a guide to scoring functions | Q57808017 | ||
| Computational study of ground-state chiral induction in small peptides: Comparison of the relative stability of selected amino acid dimers and oligomers in homochiral and heterochiral combinations | Q58005542 | ||
| Absolute Binding Free Energies: A Quantitative Approach for Their Calculation | Q62589247 | ||
| Energetic origins of specificity of ligand binding in an interior nonpolar cavity of T4 lysozyme | Q71881818 | ||
| Evaluating the molecular mechanics poisson-boltzmann surface area free energy method using a congeneric series of ligands to p38 MAP kinase | Q81514871 | ||
| P433 | issue | 4 | |
| P407 | language of work or name | English | Q1860 |
| P921 | main subject | ligand binding | Q61659151 |
| P1104 | number of pages | 17 | |
| P304 | page(s) | 1118-1134 | |
| P577 | publication date | 2007-06-08 | |
| P1433 | published in | Journal of Molecular Biology | Q925779 |
| P1476 | title | Predicting absolute ligand binding free energies to a simple model site | |
| P478 | volume | 371 |
| Q40276857 | 3D-RISM-Dock: A New Fragment-Based Drug Design Protocol |
| Q28304560 | A machine learning-based method to improve docking scoring functions and its application to drug repurposing |
| Q28474233 | AMMOS: Automated Molecular Mechanics Optimization tool for in silico Screening |
| Q48063202 | Absolute Binding Free Energies between T4 Lysozyme and 141 Small Molecules: Calculations Based on Multiple Rigid Receptor Configurations. |
| Q47567527 | Absolute binding free energies for octa-acids and guests in SAMPL5 : Evaluating binding free energies for octa-acid and guest complexes in the SAMPL5 blind challenge. |
| Q28385662 | Absolute free energy of binding of avidin/biotin, revisited |
| Q39343604 | Accounting for ligand conformational restriction in calculations of protein-ligand binding affinities |
| Q37063817 | Accurate calculation of mutational effects on the thermodynamics of inhibitor binding to p38α MAP kinase: a combined computational and experimental study |
| Q36427764 | Accurate calculation of the absolute free energy of binding for drug molecules |
| Q38698407 | Advances in free-energy-based simulations of protein folding and ligand binding. |
| Q30427576 | Alchemical free energy methods for drug discovery: progress and challenges |
| Q30419602 | Alchemical prediction of hydration free energies for SAMPL. |
| Q36802557 | Application of a polarizable force field to calculations of relative protein-ligand binding affinities |
| Q27702054 | Application of the PM6 semi-empirical method to modeling proteins enhances docking accuracy of AutoDock |
| Q34285601 | Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements |
| Q55093077 | Atomic resolution mechanism of ligand binding to a solvent inaccessible cavity in T4 lysozyme. |
| Q57831745 | Avoiding the van der Waals endpoint problem using serial atomic insertion |
| Q50783639 | Bayesian estimation of free energies from equilibrium simulations. |
| Q30392142 | Beyond Membrane Protein Structure: Drug Discovery, Dynamics and Difficulties |
| Q55476262 | Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes via Nonequilibrium Candidate Monte Carlo. |
| Q37372747 | Binding of small-molecule ligands to proteins: "what you see" is not always "what you get". |
| Q35983363 | Biomolecular Force Field Parameterization via Atoms-in-Molecule Electron Density Partitioning |
| Q36191972 | Biophysical limits of protein-ligand binding |
| Q27679245 | Blind Prediction of Charged Ligand Binding Affinities in a Model Binding Site |
| Q30362300 | Bringing Clarity to the Prediction of Protein-Ligand Binding Free Energies via "Blurring" |
| Q37149321 | Calculating the sensitivity and robustness of binding free energy calculations to force field parameters |
| Q28396455 | Calculation of the Absolute Free Energy of Binding and Related Entropies with the HSMD-TI Method: The FKBP12-L8 Complex |
| Q37626128 | Classical electrostatics for biomolecular simulations |
| Q57463686 | Comparison of the umbrella sampling and the double decoupling method in binding free energy predictions for SAMPL6 octa-acid host-guest challenges |
| Q44694277 | Computation of binding free energy with molecular dynamics and grand canonical Monte Carlo simulations |
| Q92485740 | Computation of protein-ligand binding free energies using quantum mechanical bespoke force fields |
| Q39551290 | Computation of relative binding free energy for an inhibitor and its analogs binding with Erk kinase using thermodynamic integration MD simulation. |
| Q28475699 | Computational fragment-based binding site identification by ligand competitive saturation |
| Q35728158 | Computational investigation of glycosylation effects on a family 1 carbohydrate-binding module |
| Q47979119 | Computationally-guided optimization of small-molecule inhibitors of the Aurora A kinase-TPX2 protein-protein interaction |
| Q37335295 | Computations of standard binding free energies with molecular dynamics simulations |
| Q92613345 | Computing Relative Binding Affinity of Ligands to Receptor: An Effective Hybrid Single-Dual-Topology Free-Energy Perturbation Approach in NAMD |
| Q34385618 | Computing Relative Free Energies of Solvation using Single Reference Thermodynamic Integration Augmented with Hamiltonian Replica Exchange |
| Q35773629 | Conformational Transitions and Convergence of Absolute Binding Free Energy Calculations |
| Q89543575 | Convolutional neural network scoring and minimization in the D3R 2017 community challenge |
| Q34449500 | Correlating protein hot spot surface analysis using ProBiS with simulated free energies of protein-protein interfacial residues |
| Q35748554 | DOCK 6: Impact of new features and current docking performance |
| Q42189457 | Density functional theory calculations on entire proteins for free energies of binding: application to a model polar binding site |
| Q57905894 | Dependency of ligand free energy landscapes on charge parameters and solvent models |
| Q24651388 | Design of protein-ligand binding based on the molecular-mechanics energy model |
| Q30489011 | Docking Screens for Novel Ligands Conferring New Biology |
| Q39317819 | Docking-undocking combination applied to the D3R Grand Challenge 2015. |
| Q28477930 | Drug discovery using chemical systems biology: weak inhibition of multiple kinases may contribute to the anti-cancer effect of nelfinavir |
| Q24633124 | Druggability Assessment of Allosteric Proteins by Dynamics Simulations in the Presence of Probe Molecules |
| Q35137099 | Effects of Biomolecular Flexibility on Alchemical Calculations of Absolute Binding Free Energies |
| Q51608662 | Efficiency of alchemical free energy simulations. I. A practical comparison of the exponential formula, thermodynamic integration, and Bennett's acceptance ratio method. |
| Q99589369 | Efficient consideration of coordinated water molecules improves computational protein-protein and protein-ligand docking discrimination |
| Q42780060 | Elucidating the energetics of entropically driven protein-ligand association: calculations of absolute binding free energy and entropy |
| Q41379884 | Enantiomeric discrimination of chiral organic salts by chiral aza-15-crown-5 ether with C 1 symmetry: experimental and theoretical approaches |
| Q90737957 | Energetic Fingerprinting of Ligand Binding to Paralogous Proteins: The Case of the Apoptotic Pathway |
| Q59349138 | Enhanced Monte Carlo Methods for Modeling Proteins Including Computation of Absolute Free Energies of Binding |
| Q56989498 | Enhanced Sampling in Free Energy Calculations: Combining SGLD with the Bennett’s Acceptance Ratio and Enveloping Distribution Sampling Methods |
| Q34011410 | Entropy-enthalpy compensation: role and ramifications in biomolecular ligand recognition and design |
| Q88055732 | Escape of a Small Molecule from Inside T4 Lysozyme by Multiple Pathways |
| Q57815938 | Escaping atom types in force fields using direct chemical perception |
| Q35169555 | Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations |
| Q51550370 | Free energy calculations offer insights into the influence of receptor flexibility on ligand-receptor binding affinities. |
| Q39645443 | Free energy calculations on snake venom metalloproteinase BaP1. |
| Q41998223 | Hybrid Steered Molecular Dynamics-Docking: An Efficient Solution to the Problem of Ranking Inhibitor Affinities Against a Flexible Drug Target |
| Q46546512 | II. Dissociation free energies in drug-receptor systems via nonequilibrium alchemical simulations: application to the FK506-related immunophilin ligands. |
| Q30409188 | Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics |
| Q37644156 | Implementation of the Hungarian algorithm to account for ligand symmetry and similarity in structure-based design |
| Q35435838 | Improved Binding Free Energy Predictions from Single-Reference Thermodynamic Integration Augmented with Hamiltonian Replica Exchange |
| Q98471323 | Influence of ligand's directional configuration, chrysenes as model compounds, on the binding activity with aryl hydrocarbon receptor |
| Q36105308 | Insights from free-energy calculations: protein conformational equilibrium, driving forces, and ligand-binding modes |
| Q38684570 | Insights into Ligand-Protein Binding from Local Mechanical Response. |
| Q51501779 | Large-scale symmetry-adapted perturbation theory computations via density fitting and Laplace transformation techniques: investigating the fundamental forces of DNA-intercalator interactions. |
| Q30410587 | Lead optimization mapper: automating free energy calculations for lead optimization |
| Q51604998 | Let's get honest about sampling. |
| Q42633034 | Ligand binding to the voltage-gated Kv1.5 potassium channel in the open state--docking and computer simulations of a homology model |
| Q40420002 | Limits of Free Energy Computation for Protein-Ligand Interactions |
| Q51334109 | Modeling loop backbone flexibility in receptor-ligand docking simulations. |
| Q46221653 | Modeling molecular and ionic absolute solvation free energies with quasichemical theory bounds |
| Q36277660 | Molecular binding: Under water's influence |
| Q35356510 | Molecular insights of protein contour recognition with ligand pharmacophoric sites through combinatorial library design and MD simulation in validating HTLV-1 PR inhibitors |
| Q37701502 | Multiscale Free Energy Simulations: An Efficient Method for Connecting Classical MD Simulations to QM or QM/MM Free Energies Using Non-Boltzmann Bennett Reweighting Schemes |
| Q43214837 | Multiscale Monte Carlo Sampling of Protein Sidechains: Application to Binding Pocket Flexibility |
| Q41912526 | New method for calculating the absolute free energy of binding: the effect of a mobile loop on the avidin/biotin complex |
| Q34699411 | No free energy lunch |
| Q51608927 | Non-Boltzmann sampling and Bennett's acceptance ratio method: how to profit from bending the rules. |
| Q46037009 | Nonlinear scaling schemes for Lennard-Jones interactions in free energy calculations. |
| Q90715209 | Optimal Measurement Network of Pairwise Differences |
| Q50562075 | Optimal allosteric stabilization sites using contact stabilization analysis. |
| Q37166094 | Path-integral method for predicting relative binding affinities of protein-ligand complexes. |
| Q30422862 | Perspective: Alchemical free energy calculations for drug discovery |
| Q39235195 | Predicting Binding Free Energies: Frontiers and Benchmarks |
| Q27657572 | Predicting Ligand Binding Affinity with Alchemical Free Energy Methods in a Polar Model Binding Site |
| Q36645023 | Predicting binding affinities of host-guest systems in the SAMPL3 blind challenge: the performance of relative free energy calculations |
| Q84014403 | Predicting hydration free energies using all-atom molecular dynamics simulations and multiple starting conformations |
| Q37761334 | Prediction of protein-ligand binding affinity by free energy simulations: assumptions, pitfalls and expectations |
| Q28818600 | Predictions of Ligand Selectivity from Absolute Binding Free Energy Calculations |
| Q28817868 | Protein-Ligand Electrostatic Binding Free Energies from Explicit and Implicit Solvation |
| Q97692526 | Protein-ligand binding with the coarse-grained Martini model |
| Q39865277 | QM/MM refinement and analysis of protein bound retinoic acid |
| Q42739559 | Quantifying water-mediated protein-ligand interactions in a glutamate receptor: a DFT study |
| Q47302876 | Quantitative Assessment of the Energetics of Dopamine Translocation by Human Dopamine Transporter |
| Q36243073 | Recent theoretical and computational advances for modeling protein-ligand binding affinities |
| Q57038883 | Reduced Free Energy Perturbation/Hamiltonian Replica Exchange Molecular Dynamics Method with Unbiased Alchemical Thermodynamic Axis |
| Q48050957 | Relative Binding Free Energy Calculations Applied to Protein Homology Models |
| Q47291097 | Relative Binding Free Energy Calculations in Drug Discovery: Recent Advances and Practical Considerations |
| Q27649874 | Rescoring Docking Hit Lists for Model Cavity Sites: Predictions and Experimental Testing |
| Q46096236 | Resolving the Ligand-Binding Specificity in c-MYC G-Quadruplex DNA: Absolute Binding Free Energy Calculations and SPR Experiment |
| Q48030331 | Role of structural water for prediction of cation binding sites in apoproteins |
| Q41081254 | Sensitivity in Binding Free Energies Due to Protein Reorganization |
| Q36688022 | Separated topologies--a method for relative binding free energy calculations using orientational restraints |
| Q35566613 | Site Identification by Ligand Competitive Saturation (SILCS) simulations for fragment-based drug design |
| Q38112629 | Small-molecule ligand docking into comparative models with Rosetta |
| Q30540733 | Standard binding free energies from computer simulations: What is the best strategy? |
| Q35794917 | Statistical mechanics and molecular dynamics in evaluating thermodynamic properties of biomolecular recognition |
| Q34761978 | Structure-based systems biology for analyzing off-target binding |
| Q34352706 | The Binding Energy Distribution Analysis Method (BEDAM) for the Estimation of Protein-Ligand Binding Affinities |
| Q39664353 | The errors of our ways: taking account of error in computer-aided drug design to build confidence intervals for our next 25 years |
| Q27333830 | The free energy landscape of small molecule unbinding |
| Q42155548 | The measured and calculated affinity of methyl- and methoxy-substituted benzoquinones for the Q(A) site of bacterial reaction centers |
| Q37776040 | The tuberculosis structural genomics consortium: a structural genomics approach to drug discovery |
| Q50214049 | Thermodynamics of DNA: sensitizer recognition. Characterizing binding motifs with all-atom simulations. |
| Q33376019 | Toward a molecular understanding of the interaction of dual specificity phosphatases with substrates: insights from structure-based modeling and high throughput screening |
| Q88424164 | Uncertainty Quantification in Alchemical Free Energy Methods |
| Q40608421 | Using docking and alchemical free energy approach to determine the binding mechanism of eEF2K inhibitors and prioritizing the compound synthesis |
| Q33940014 | Using free energy of binding calculations to improve the accuracy of virtual screening predictions |
| Q47261847 | Using the fast fourier transform in binding free energy calculations |
Search more.