| review article | Q7318358 |
| scholarly article | Q13442814 |
| P8978 | DBLP publication ID | journals/jcc/KnightB09 |
| P356 | DOI | 10.1002/JCC.21295 |
| P8608 | Fatcat ID | release_xh2ykva7xbbm7jypl7nis4434m |
| P932 | PMC publication ID | 2730455 |
| P698 | PubMed publication ID | 19421993 |
| P5875 | ResearchGate publication ID | 24408019 |
| P2093 | author name string | Charles L Brooks | |
| Jennifer L Knight | |||
| P2860 | cites work | Prevalence of HIV-1 resistant to antiretroviral drugs in 81 individuals newly infected by sexual contact or injecting drug use. Investigators of the Quebec Primary Infection Study. | Q54059737 |
| Aqueous Solvation Free Energies of Ions and Ion−Water Clusters Based on an Accurate Value for the Absolute Aqueous Solvation Free Energy of the Proton | Q57250536 | ||
| Constant-pH molecular dynamics using continuous titration coordinates | Q62764040 | ||
| Multiple copy simultaneous search and construction of ligands in binding sites: application to inhibitors of HIV-1 aspartic proteinase | Q72856007 | ||
| Efficient and precise solvation free energies via alchemical adiabatic molecular dynamics | Q80190150 | ||
| Computer-aided design of non-nucleoside inhibitors of HIV-1 reverse transcriptase | Q81428499 | ||
| Towards predictive ligand design with free-energy based computational methods? | Q28278909 | ||
| Toward the accurate first-principles prediction of ionization equilibria in proteins. | Q30355994 | ||
| Patterns of resistance mutations to antiretroviral drugs in extensively treated HIV-1-infected patients with failure of highly active antiretroviral therapy | Q31930788 | ||
| Resistance against reverse transcriptase inhibitors | Q33946937 | ||
| The many roles of computation in drug discovery | Q34307063 | ||
| Constant pH molecular dynamics with proton tautomerism | Q34350350 | ||
| Protein and peptide folding explored with molecular simulations | Q34691193 | ||
| Exploring atomistic details of pH-dependent peptide folding | Q35214651 | ||
| Linking folding with aggregation in Alzheimer's beta-amyloid peptides | Q36089177 | ||
| Calculation of protein-ligand binding affinities. | Q36698596 | ||
| Folding intermediate in the villin headpiece domain arises from disruption of a N-terminal hydrogen-bonded network | Q36897575 | ||
| Free energy via molecular simulation: applications to chemical and biomolecular systems | Q38648060 | ||
| Prediction of the binding free energies of new TIBO-like HIV-1 reverse transcriptase inhibitors using a combination of PROFEC, PB/SA, CMC/MD, and free energy calculations | Q41612429 | ||
| Application of the lambda-dynamics method to evaluate the relative binding free energies of inhibitors to HCV protease. | Q42981559 | ||
| Evidence for a catalytic dyad in the active site of homocitrate synthase from Saccharomyces cerevisiae | Q44281030 | ||
| Exhaustive mutagenesis in silico: multicoordinate free energy calculations on proteins and peptides | Q46149002 | ||
| Single ion hydration free energies: a consistent comparison between experiment and classical molecular simulation | Q47205235 | ||
| Conformational sampling via a self-regulating effective energy surface. | Q51941909 | ||
| New Monte Carlo algorithm: Entropic sampling. | Q52393347 | ||
| P433 | issue | 11 | |
| P304 | page(s) | 1692-700 | |
| P577 | publication date | 2009-08-01 | |
| P1433 | published in | Journal of Computational Chemistry | Q3186908 |
| P1476 | title | λ-Dynamics free energy simulation methods | |
| P478 | volume | 30 |
| Q48193566 | A GPU-Accelerated Parameter Interpolation Thermodynamic Integration Free Energy Method |
| Q51609290 | A molecular dynamics study of a miRNA:mRNA interaction. |
| Q51673438 | Accurate calculations of the hydration free energies of druglike molecules using the reference interaction site model. |
| Q48002173 | Adaptive Landscape Flattening Accelerates Sampling of Alchemical Space in Multisite λ Dynamics. |
| Q54685571 | Adaptive lambda square dynamics simulation: an efficient conformational sampling method for biomolecules. |
| Q34762201 | Advances in all atom sampling methods for modeling protein-ligand binding affinities |
| Q41973094 | Anomalous surface diffusion of protons on lipid membranes |
| Q35382222 | Applying efficient implicit nongeometric constraints in alchemical free energy simulations |
| Q57831745 | Avoiding the van der Waals endpoint problem using serial atomic insertion |
| Q43063613 | Biasing Potential Replica Exchange Multisite λ-Dynamics for Efficient Free Energy Calculations |
| Q90295745 | Blinded prediction of protein-ligand binding affinity using Amber thermodynamic integration for the 2018 D3R grand challenge 4 |
| Q38890648 | Computational functional group mapping for drug discovery |
| Q35069159 | Computational ligand-based rational design: Role of conformational sampling and force fields in model development. |
| Q35773629 | Conformational Transitions and Convergence of Absolute Binding Free Energy Calculations |
| Q35751959 | Constant pH Molecular Dynamics Simulations of Nucleic Acids in Explicit Solvent |
| Q35382958 | Constant pH molecular dynamics of proteins in explicit solvent with proton tautomerism |
| Q34449500 | Correlating protein hot spot surface analysis using ProBiS with simulated free energies of protein-protein interfacial residues |
| Q41989179 | Distinguishing binders from false positives by free energy calculations: fragment screening against the flap site of HIV protease |
| Q51035374 | Efficient hybrid non-equilibrium molecular dynamics--Monte Carlo simulations with symmetric momentum reversal. |
| Q36625958 | Evaluating thermodynamic integration performance of the new amber molecular dynamics package and assess potential halogen bonds of enoyl-ACP reductase (FabI) benzimidazole inhibitors |
| Q28386158 | Extending fragment-based free energy calculations with library Monte Carlo simulation: annealing in interaction space |
| Q90348968 | Fast, Accurate, and Reliable Protocols for Routine Calculations of Protein-Ligand Binding Affinities in Drug Design Projects Using AMBER GPU-TI with ff14SB/GAFF |
| Q47842925 | Gibbs Sampler-Based λ-Dynamics and Rao-Blackwell Estimator for Alchemical Free Energy Calculation |
| Q48288437 | Identification of simple reaction coordinates from complex dynamics. |
| Q110950183 | Implementation of adaptive integration method for free energy calculations in molecular systems |
| Q34065083 | Large scale affinity calculations of cyclodextrin host-guest complexes: Understanding the role of reorganization in the molecular recognition process. |
| Q40420002 | Limits of Free Energy Computation for Protein-Ligand Interactions |
| Q35887173 | Locating binding poses in protein-ligand systems using reconnaissance metadynamics |
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| Q26772040 | Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms |
| Q35572848 | Multi-Site λ-dynamics for simulated Structure-Activity Relationship studies |
| Q45307247 | On-the-fly reconstruction of free-energy profiles using logarithmic mean-force dynamics. |
| Q53435617 | Orthogonal sampling in free-energy calculations of residue mutations in a tripeptide: TI versus λ-LEUS. |
| Q88918619 | Predicting Binding Free Energies in a Large Combinatorial Chemical Space Using Multisite λ Dynamics |
| Q35541836 | Predicting extreme pKa shifts in staphylococcal nuclease mutants with constant pH molecular dynamics |
| Q37761334 | Prediction of protein-ligand binding affinity by free energy simulations: assumptions, pitfalls and expectations |
| Q33581606 | Protein thermostability calculations using alchemical free energy simulations |
| Q36243073 | Recent theoretical and computational advances for modeling protein-ligand binding affinities |
| Q35746730 | Revealing the Mechanisms of Protein Disorder and N-Glycosylation in CD44-Hyaluronan Binding Using Molecular Simulation |
| Q39013150 | Rigidity and flexibility in the tetrasaccharide linker of proteoglycans from atomic-resolution molecular simulation |
| Q55690504 | Role of Pseudoisocytidine Tautomerization in Triplex-Forming Oligonucleotides: In Silico and in Vitro Studies. |
| Q41081254 | Sensitivity in Binding Free Energies Due to Protein Reorganization |
| Q35794917 | Statistical mechanics and molecular dynamics in evaluating thermodynamic properties of biomolecular recognition |
| Q90445530 | Structural characterization and molecular dynamics simulations of the caprine and bovine solute carrier family 11 A1 (SLC11A1) |
| Q48319349 | The Surprising Importance of Peptide Bond Contacts in Drug-Protein Interactions. |
| Q37943378 | Theoretical prediction of drug-receptor interactions |
| Q30400985 | Trends in template/fragment-free protein structure prediction |
| Q49118107 | Umbrella integration with higher-order correction terms. |
| Q37114199 | Unconstrained Enhanced Sampling for Free Energy Calculations of Biomolecules: A Review |
| Q42216392 | Uncovering pH-dependent transient states of proteins with buried ionizable residues |
| Q36697118 | pH-dependent dynamics of complex RNA macromolecules |
| Q30153235 | pH-dependent transient conformational states control optical properties in cyan fluorescent protein |
| Q37701600 | pH-induced stability switching of the bacteriophage HK97 maturation pathway |
| Q40563969 | pH-sensitive residues in the p19 RNA silencing suppressor protein from carnation Italian ringspot virus affect siRNA binding stability |
| Q36839169 | λ-Meta Dynamics Approach To Compute Absolute Solvation Free Energy |
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