| scholarly article | Q13442814 |
| P50 | author | Huiyong Sun | Q43371037 |
| John Z. H. Zhang | Q68686424 | ||
| Guoqiang Feng | Q87729741 | ||
| P2093 | author name string | Lili Duan | |
| Yuchen Li | |||
| Susu Zhong | |||
| Yalong Cong | |||
| P2860 | cites work | Structure of HIV-1 protease with KNI-272, a tight-binding transition-state analog containing allophenylnorstatine | Q27732560 |
| dMM-PBSA: A New HADDOCK Scoring Function for Protein-Peptide Docking | Q28596516 | ||
| Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models | Q29616389 | ||
| Reduced surface: an efficient way to compute molecular surfaces | Q29617526 | ||
| An analysis of the interactions between the Sem-5 SH3 domain and its ligands using molecular dynamics, free energy calculations, and sequence analysis. | Q30168058 | ||
| Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes. | Q30333153 | ||
| Some practical approaches to treating electrostatic polarization of proteins. | Q30363095 | ||
| Intra-protein hydrogen bonding is dynamically stabilized by electronic polarization. | Q30375748 | ||
| Contribution of the surface free energy perturbation to protein-solvent interactions | Q30420323 | ||
| Assessing the performance of MM/PBSA and MM/GBSA methods. 4. Accuracies of MM/PBSA and MM/GBSA methodologies evaluated by various simulation protocols using PDBbind data set. | Q30835329 | ||
| Simulation of NMR data reveals that proteins' local structures are stabilized by electronic polarization | Q33457442 | ||
| Detecting and understanding combinatorial mutation patterns responsible for HIV drug resistance | Q33667350 | ||
| Computational alanine scanning of the 1:1 human growth hormone-receptor complex | Q34120440 | ||
| Revisiting free energy calculations: a theoretical connection to MM/PBSA and direct calculation of the association free energy | Q34184435 | ||
| Polarizable force fields | Q34215898 | ||
| Comparative assessment of scoring functions on an updated benchmark: 2. Evaluation methods and general results | Q34414010 | ||
| A numerically stable restrained electrostatic potential charge fitting method | Q34529293 | ||
| Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations | Q34531578 | ||
| Predicting drug resistance of the HIV-1 protease using molecular interaction energy components | Q35534782 | ||
| Improving MM-GB/SA Scoring through the Application of the Variable Dielectric Model | Q35955749 | ||
| Developing polarized protein-specific charges for protein dynamics: MD free energy calculation of pKa shifts for Asp26/Asp20 in thioredoxin | Q36783764 | ||
| Large-scale molecular dynamics simulation: Effect of polarization on thrombin-ligand binding energy | Q37163377 | ||
| Perspective on Free-Energy Perturbation Calculations for Chemical Equilibria | Q37426275 | ||
| Effect of polarization on HIV-1protease and fluoro-substituted inhibitors binding energies by large scale molecular dynamics simulations | Q37622781 | ||
| Development of a polarizable force field for proteins via ab initio quantum chemistry: first generation model and gas phase tests | Q37658323 | ||
| Computing Clinically Relevant Binding Free Energies of HIV-1 Protease Inhibitors. | Q37665027 | ||
| Protocol for fast screening of multi-target drug candidates: Application to Alzheimer's disease | Q38603615 | ||
| Free energy via molecular simulation: applications to chemical and biomolecular systems | Q38648060 | ||
| Interaction Entropy for Computational Alanine Scanning | Q38838777 | ||
| Efficient Approximation of Ligand Rotational and Translational Entropy Changes upon Binding for Use in MM-PBSA Calculations | Q39084371 | ||
| New Parameters for Higher Accuracy in the Computation of Binding Free Energy Differences upon Alanine Scanning Mutagenesis on Protein-Protein Interfaces | Q39114456 | ||
| Calculating protein-ligand binding affinities with MMPBSA: Method and error analysis | Q39502838 | ||
| Assessing the performance of the MM/PBSA and MM/GBSA methods. 6. Capability to predict protein-protein binding free energies and re-rank binding poses generated by protein-protein docking | Q39574481 | ||
| Computational Alanine Scanning Mutagenesis: MM-PBSA vs TI. | Q40298343 | ||
| Statistical Analysis on the Performance of Molecular Mechanics Poisson-Boltzmann Surface Area versus Absolute Binding Free Energy Calculations: Bromodomains as a Case Study | Q41674692 | ||
| Accurate ensemble molecular dynamics binding free energy ranking of multidrug-resistant HIV-1 proteases | Q43103118 | ||
| Electrostatic polarization makes a substantial contribution to the free energy of avidin-biotin binding | Q43123818 | ||
| Evaluating the potency of HIV-1 protease drugs to combat resistance | Q43196448 | ||
| Effect of atomic charge, solvation, entropy, and ligand protonation state on MM-PB(GB)SA binding energies of HIV protease. | Q44238646 | ||
| Addressing limitations with the MM-GB/SA scoring procedure using the WaterMap method and free energy perturbation calculations | Q44628698 | ||
| Assessing the performance of MM/PBSA and MM/GBSA methods. 3. The impact of force fields and ligand charge models | Q45179427 | ||
| Free energy calculations on dimer stability of the HIV protease using molecular dynamics and a continuum solvent model | Q46045309 | ||
| Protein polarization is critical to stabilizing AF-2 and helix-2' domains in ligand binding to PPAR-gamma | Q46248596 | ||
| Molecular dynamics and free energy studies on the wild-type and double mutant HIV-1 protease complexed with amprenavir and two amprenavir-related inhibitors: mechanism for binding and drug resistance | Q46523471 | ||
| Accelerated Poisson-Boltzmann calculations for static and dynamic systems | Q46543722 | ||
| Trypsin-Ligand binding affinities calculated using an effective interaction entropy method under polarized force field. | Q47129892 | ||
| Inhibition of Mammalian 15-Lipoxygenase by Three Ebselen-like Drugs. A QM/MM and MM/PBSA Comparative Study. | Q47356260 | ||
| Orcein-Related Small Molecule O4 Destabilizes hIAPP Protofibrils by Interacting Mostly with the Amyloidogenic Core Region | Q48054810 | ||
| Computational Alanine Scanning with Interaction Entropy for Protein-ligand Binding Free Energies | Q50181749 | ||
| Interaction entropy for protein-protein binding. | Q50926285 | ||
| Effect of electrostatic polarization and bridging water on CDK2-ligand binding affinities calculated using a highly efficient interaction entropy method. | Q51075716 | ||
| Interaction Entropy: A New Paradigm for Highly Efficient and Reliable Computation of Protein-Ligand Binding Free Energy. | Q51383023 | ||
| Fast and accurate computation schemes for evaluating vibrational entropy of proteins. | Q51605931 | ||
| Assessing the performance of MM/PBSA and MM/GBSA methods. 5. Improved docking performance using high solute dielectric constant MM/GBSA and MM/PBSA rescoring. | Q54323649 | ||
| Assessing the performance of MM/PBSA and MM/GBSA methods. 7. Entropy effects on the performance of end-point binding free energy calculation approaches | Q57121075 | ||
| Free energy perturbation calculations on binding and catalysis after mutating Asn 155 in subtilisin | Q59071554 | ||
| Conformational flexibility of the catalytic Asp dyad in HIV-1 protease: An ab initio study on the free enzyme | Q73594370 | ||
| Binding free energy contributions of interfacial waters in HIV-1 protease/inhibitor complexes | Q80214872 | ||
| Validation and use of the MM-PBSA approach for drug discovery | Q81826120 | ||
| Origin of decrease in potency of darunavir and two related antiviral inhibitors against HIV-2 compared to HIV-1 protease | Q83331103 | ||
| Folding of a helix is critically stabilized by polarization of backbone hydrogen bonds: study in explicit water | Q83522034 | ||
| Folding of a helix at room temperature is critically aided by electrostatic polarization of intraprotein hydrogen bonds | Q84711537 | ||
| Quantifying the stabilizing energy of the intraprotein hydrogen bond due to local mutation | Q84942209 | ||
| A Direct Comparison of the MM-GB/SA Scoring Procedure and Free-Energy Perturbation Calculations Using Carbonic Anhydrase as a Test Case: Strengths and Pitfalls of Each Approach | Q86804384 | ||
| Determination of absolute configuration and binding efficacy of benzimidazole-based FabI inhibitors through the support of electronic circular dichroism and MM-GBSA techniques | Q88578538 | ||
| The Flavonoid Apigenin Is a Progesterone Receptor Modulator with In Vivo Activity in the Uterus | Q88598561 | ||
| P433 | issue | 6 | |
| P304 | page(s) | 064101 | |
| P577 | publication date | 2018-11-01 | |
| P1433 | published in | Structural dynamics (Melville, N.Y.) | Q27726914 |
| P1476 | title | The impact of interior dielectric constant and entropic change on HIV-1 complex binding free energy prediction | |
| P478 | volume | 5 |
| Q112616362 | Could graph neural networks learn better molecular representation for drug discovery? A comparison study of descriptor-based and graph-based models |
| Q97086757 | Virtual screening of approved drugs as potential SARS-CoV-2 main protease inhibitors |
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