| Q41442805 | A Comparative Insight into Amprenavir Resistance of Mutations V32I, G48V, I50V, I54V, and I84V in HIV-1 Protease Based on Thermodynamic Integration and MM-PBSA Methods |
| Q47225555 | A Coupled Ionization-Conformational Equilibrium Is Required To Understand The Properties of Ionizable Residues in the Hydrophobic Interior of Staphylococcal Nuclease. |
| Q99412764 | A Double-Well Ultra-Coarse-Grained Model to Describe Protein Conformational Transitions |
| Q55384421 | A Force Balanced Fragmentation Method for ab Initio Molecular Dynamic Simulation of Protein. |
| Q61655288 | A Fragment Quantum Mechanical Method for Metalloproteins |
| Q35846942 | A New Quantum Calibrated Force Field for Zinc-Protein Complex |
| Q36104925 | A Semiautomated Structure-Based Method To Predict Substrates of Enzymes via Molecular Docking: A Case Study with Candida antarctica Lipase B. |
| Q34771965 | A coupled two-dimensional main chain torsional potential for protein dynamics: generation and implementation. |
| Q93156518 | A force consistent method for electrostatic energy calculation in fluctuating charge model |
| Q27658175 | A new activity of anti-HIV and anti-tumor protein GAP31: DNA adenosine glycosidase--structural and modeling insight into its functions |
| Q50755403 | A new algorithm for construction of coarse-grained sites of large biomolecules |
| Q81458834 | A new method for direct calculation of total energy of protein |
| Q51134805 | A new quantum method for electrostatic solvation energy of protein |
| Q34529293 | A numerically stable restrained electrostatic potential charge fitting method |
| Q84940226 | Ab Initio QM/MM Free Energy Simulations of Peptide Bond Formation in the Ribosome Support an Eight-Membered Ring Reaction Mechanism |
| Q92860154 | Accelerated Molecular Dynamics Simulation for Helical Proteins Folding in Explicit Water |
| Q51754470 | Accessing the applicability of polarized protein-specific charge in linear interaction energy analysis |
| Q93091152 | Accurate and Efficient Calculation of Protein-Protein Binding Free Energy-Interaction Entropy with Residue Type-Specific Dielectric Constants |
| Q57402591 | Accurate quantum mechanical reaction probabilities for the reaction O+H2→OH+H |
| Q45039065 | Acidic pH retards the fibrillization of human islet amyloid polypeptide due to electrostatic repulsion of histidines |
| Q89889295 | Alanine scanning combined with interaction entropy studying the differences of binding mechanism on HIV-1 and HIV-2 proteases with inhibitor |
| Q99561021 | An Approach to Computing Solvent Reorganization Energy |
| Q46345693 | An Electrochemical Biosensor with Dual Signal Outputs: Toward Simultaneous Quantification of pH and O2 in the Brain upon Ischemia and in a Tumor during Cancer Starvation Therapy |
| Q91981240 | An Energy Optimization Strategy Based on the Perfect Conformation of Prolyl Endopeptidase for Improving Catalytic Efficiency |
| Q46511954 | An efficient approach for ab initio energy calculation of biopolymers |
| Q51247213 | An implementation of hydrophobic force in implicit solvent molecular dynamics simulation for packed proteins |
| Q43865467 | An improved fragment-based quantum mechanical method for calculation of electrostatic solvation energy of proteins |
| Q30427012 | Assessing the accuracy of the general AMBER force field for 2,2,2-trifluoroethanol as solvent |
| Q57121075 | Assessing the performance of MM/PBSA and MM/GBSA methods. 7. Entropy effects on the performance of end-point binding free energy calculation approaches |
| Q40304247 | Automated Fragmentation QM/MM Calculation of Amide Proton Chemical Shifts in Proteins with Explicit Solvent Model |
| Q55033746 | Automated Fragmentation QM/MM Calculation of NMR Chemical Shifts for Protein-Ligand Complexes. |
| Q93852260 | BAR-based Optimum Adaptive Steered MD for Configurational Sampling |
| Q48788986 | BAR-based optimum adaptive sampling regime for variance minimization in alchemical transformation |
| Q47201765 | BAR-based optimum adaptive sampling regime for variance minimization in alchemical transformation: the nonequilibrium stratification |
| Q91575119 | BAR-based optimum adaptive steered MD for configurational sampling |
| Q85315286 | Beyond QM/MM: fragment quantum mechanical methods |
| Q91802045 | Binding Modes of Small-Molecule Inhibitors to the EED Pocket of PRC2 |
| Q92739545 | Binding modes and conformational changes of FK506-binding protein 51 induced by inhibitor bindings: insight into molecular mechanisms based on multiple simulation technologies |
| Q90482786 | Calculation of hot spots for protein-protein interaction in p53/PMI-MDM2/MDMX complexes |
| Q46595732 | Calculations of Solvation Free Energy through Energy Reweighting from Molecular Mechanics to Quantum Mechanics |
| Q43238017 | Class I phospho-inositide-3-kinases (PI3Ks) isoform-specific inhibition study by the combination of docking and molecular dynamics simulation |
| Q83386978 | Combined Theoretical and Experimental Study on High Diastereoselective Chirality Transfer Based on [2.2]Paracyclophane Derivative Chiral Reagent |
| Q46809277 | Combined effect of confinement and affinity of crowded environment on conformation switching of adenylate kinase |
| Q85222044 | Combustion Driven by Fragment-based Ab Initio Molecular Dynamics Simulation |
| Q51705033 | Communications: Electron polarization critically stabilizes the Mg2+ complex in the catalytic core domain of HIV-1 integrase |
| Q61655291 | Comparison of the unfolding and oligomerization of human prion protein under acidic and neutral environments by molecular dynamics simulations |
| Q50181749 | Computational Alanine Scanning with Interaction Entropy for Protein-ligand Binding Free Energies |
| Q52573365 | Computational Protein Design with Deep Learning Neural Networks |
| Q49165041 | Computational Study of PCSK9-EGFA Complex with Effective Polarizable Bond Force Field |
| Q89989303 | Computational approaches to studying methylated H4K20 recognition by DNA repair factor 53BP1 |
| Q30844023 | Correct folding of an α-helix and a β-hairpin using a polarized 2D torsional potential |
| Q44824304 | Correction of erroneously packed protein's side chains in the NMR structure based on ab initio chemical shift calculations |
| Q87160153 | Correction: Fragment density functional theory calculation of NMR chemical shifts for proteins with implicit solvation |
| Q35568038 | Coupled two-dimensional main-chain torsional potential for protein dynamics II: performance and validation |
| Q56341573 | Crius: A novel fragment-based algorithm of de novo substrate prediction for enzymes |
| Q92187469 | Decoding molecular mechanism of inhibitor bindings to CDK2 using molecular dynamics simulations and binding free energy calculations |
| Q91552457 | DeepDDG: Predicting the Stability Change of Protein Point Mutations Using Neural Networks |
| Q89998627 | DenseCPD: Improving the Accuracy of Neural-Network-Based Computational Protein Sequence Design with DenseNet |
| Q90375540 | Determining Optimal Coarse-Grained Representation for Biomolecules Using Internal Cluster Validation Indexes |
| Q36783764 | Developing polarized protein-specific charges for protein dynamics: MD free energy calculation of pKa shifts for Asp26/Asp20 in thioredoxin |
| Q100536187 | Development of a New Scoring Function for Virtual Screening: APBScore |
| Q54572470 | Development of an effective polarizable bond method for biomolecular simulation. |
| Q50965967 | Direct folding simulation of helical proteins using an effective polarizable bond force field |
| Q87406327 | Discovery and characterization of novel, potent, and selective cytochrome P450 2J2 inhibitors |
| Q24644512 | Discovery of small-molecule HIV-1 fusion and integrase inhibitors oleuropein and hydroxytyrosol: Part I. fusion [corrected] inhibition |
| Q42214034 | Discovery of small-molecule HIV-1 fusion and integrase inhibitors oleuropein and hydroxytyrosol: part II. integrase inhibition |
| Q79212676 | Dissociation of heme from gaseous myoglobin ions studied by infrared multiphoton dissociation spectroscopy and Fourier-transform ion cyclotron resonance mass spectrometry |
| Q90122153 | Drug-resistance mechanisms of three mutations in anaplastic lymphoma kinase against two inhibitors based on MM/PBSA combined with interaction entropy |
| Q54596685 | Dynamical Stability and Assembly Cooperativity of β-Sheet Amyloid Oligomers – Effect of Polarization |
| Q41853051 | Dynamical binding of hydrogen-bond surrogate derived Bak helices to antiapoptotic protein Bcl-xL. |
| Q61655290 | Effect of Substituents in Different Positions of Aminothiazole Hinge-Binding Scaffolds on Inhibitor–CDK2 Association Probed by Interaction Entropy Method |
| Q83865765 | Effect of interprotein polarization on protein–protein binding energy |
| Q51817747 | Effect of mismatch on binding of ADAR2/GluR-2 pre-mRNA complex |
| Q92581710 | Effect of mutations on binding of ligands to guanine riboswitch probed by free energy perturbation and molecular dynamics simulations |
| Q37622781 | Effect of polarization on HIV-1protease and fluoro-substituted inhibitors binding energies by large scale molecular dynamics simulations |
| Q35035243 | Effect of self-assembly of fullerene nano-particles on lipid membrane |
| Q52649964 | Effect of strong electric field on the conformational integrity of insulin |
| Q50980101 | Efficient bond function basis set for pi-pi interaction energies |
| Q84971413 | Electronic polarization is important in stabilizing the native structures of proteins |
| Q30361195 | Electronic polarization stabilizes tertiary structure prediction of HP-36. |
| Q90686632 | Electrostatic Polarization Effect on Cooperative Aggregation of Full Length Human Islet Amyloid |
| Q83786332 | Electrostatic polarization is critical for the strong binding in streptavidin-biotin system |
| Q43123818 | Electrostatic polarization makes a substantial contribution to the free energy of avidin-biotin binding |
| Q46788655 | Electrostatically embedded generalized molecular fractionation with conjugate caps method for full quantum mechanical calculation of protein energy |
| Q68686427 | End-Point Binding Free Energy Calculation with MM/PBSA and MM/GBSA: Strategies and Applications in Drug Design |
| Q79946200 | Energy and electron transfer in beta-alkynyl-linked porphyrin-[60]fullerene dyads |
| Q90459382 | Entropic effect and residue specific entropic contribution to the cooperativity in streptavidin-biotin binding |
| Q62022309 | Erratum to “Discovery of small-molecule HIV-1 fusion and integrase inhibitors oleuropein and hydroxytyrosol: Part I. Integrase inhibition” [Biochem. Biophys. Res. Commun. 354 (2007) 872–878] |
| Q31155071 | Evaluation of the Coupled Two-Dimensional Main Chain Torsional Potential in Modeling Intrinsically Disordered Proteins |
| Q51654036 | Examination of the quality of various force fields and solvation models for the equilibrium simulations of GA88 and GB88. |
| Q84931703 | Exploring the Molecular Mechanism of Stabilization of the Adhesion Domains of Human CD2 by N-Glycosylation |
| Q57167603 | Exploring the Reasons for Decrease in Binding Affinity of HIV-2 Against HIV-1 Protease Complex Using Interaction Entropy Under Polarized Force Field |
| Q84629463 | Folding dynamics of a small protein at room temperature via simulated coherent two-dimensional infrared spectroscopy |
| Q84711537 | Folding of a helix at room temperature is critically aided by electrostatic polarization of intraprotein hydrogen bonds |
| Q83522034 | Folding of a helix is critically stabilized by polarization of backbone hydrogen bonds: study in explicit water |
| Q90627190 | Formation mechanism and spectroscopy of C6H radicals in extreme environments: a theoretical study |
| Q48042572 | Fragment Quantum Mechanical Method for Large-Sized Ion-Water Clusters |
| Q61655295 | Fragment density functional theory calculation of NMR chemical shifts for proteins with implicit solvation |
| Q51599700 | Fragment quantum chemical approach to geometry optimization and vibrational spectrum calculation of proteins |
| Q46891373 | Fragment quantum mechanical calculation of proteins and its applications |
| Q48045719 | Full QM Calculation of RNA Energy Using Electrostatically Embedded Generalized Molecular Fractionation with Conjugate Caps Method |
| Q44957119 | Fully quantum mechanical energy optimization for protein-ligand structure |
| Q28652087 | Functional loop dynamics of the streptavidin-biotin complex |
| Q37211933 | Global dynamics and transition state theories: Comparative study of reaction rate constants for gas-phase chemical reactions. |
| Q40928611 | Glycosylation Modulates Human CD2-CD58 Adhesion via Conformational Adjustment |
| Q89829431 | How CuCl and CuCl2 Insert into C-N Bonds of Diazo Compounds: An Electronic Structure and Mechanistic Study |
| Q36323666 | Hybrid QM/MM study of FMO complex with polarized protein-specific charge |
| Q52575882 | Hydrogen-bond structure dynamics in bulk water: insights from ab initio simulations with coupled cluster theory. |
| Q98307170 | Identification of three new compounds that directly target human serine hydroxymethyltransferase SHMT2 |
| Q35132447 | Implementing electrostatic polarization cannot fill the gap between experimental and theoretical measurements for the ultrafast fluorescence decay of myoglobin. |
| Q51013950 | Improving the scoring of protein-ligand binding affinity by including the effects of structural water and electronic polarization |
| Q45342240 | Insights on Na+ binding and conformational dynamics in multidrug and toxic compound extrusion transporter NorM |
| Q38838777 | Interaction Entropy for Computational Alanine Scanning |
| Q51383023 | Interaction Entropy: A New Paradigm for Highly Efficient and Reliable Computation of Protein-Ligand Binding Free Energy |
| Q50926285 | Interaction entropy for protein-protein binding |
| Q30375748 | Intra-protein hydrogen bonding is dynamically stabilized by electronic polarization. |
| Q57402571 | L2 amplitude density method for multichannel inelastic and rearrangement collisions |
| Q90267293 | Mechanistic Studies of CO2 Cycloaddition Reaction Catalyzed by Amine-Functionalized Ionic Liquids |
| Q46326598 | Molecular Dynamics Simulation Study on the Molecular Structures of the Amylin Fibril Models |
| Q51021433 | Molecular Dynamics Simulation and Computational Two-Dimensional Infrared Spectroscopic Study of Model Amyloid β-Peptide Oligomers |
| Q91790788 | Molecular Dynamics Simulation of Zinc Ion in Water with an ab Initio Based Neural Network Potential |
| Q94564580 | Molecular Mechanism of Selective Binding of NMS-P118 to PARP-1 and PARP-2: A Computational Perspective |
| Q92500476 | Molecular basis of SMAC-XIAP binding and the effect of electrostatic polarization |
| Q83021848 | Molecular dynamic simulation of the Kv1.2 voltage-gated potassium channel in open and closed state conformations |
| Q85686022 | Molecular dynamics simulation of protein crystal with polarized protein-specific force field |
| Q86070535 | Molecular dynamics study of DNA binding by INT‐DBD under a polarized force field |
| Q44249137 | NMR scalar coupling constant reveals that intraprotein hydrogen bonds are dynamically stabilized by electronic polarization |
| Q84726505 | Neural Network Based in Silico Simulation of Combustion Reactions |
| Q47687041 | New Advance in Computational Chemistry: Full Quantum Mechanical ab Initio Computation of Streptavidin-Biotin Interaction Energy |
| Q57966512 | Nonadiabatic effects in the H+D2 reaction |
| Q83152955 | Nonadiabatic reactant-product decoupling calculation for the F(2P(1/2)) + H2 reaction |
| Q42186848 | Novel theoretically designed HIV-1 non-nucleoside reverse transcriptase inhibitors derived from nevirapine |
| Q47870628 | Origins of Protons in C-H Bond Insertion Products of Phenols: Proton-Self-Sufficient Function via Water Molecules. |
| Q39843459 | PBSA_E: A PBSA-Based Free Energy Estimator for Protein-Ligand Binding Affinity |
| Q82725316 | Polarization of intraprotein hydrogen bond is critical to thermal stability of short helix |
| Q30428568 | Predicting mutation-induced Stark shifts in the active site of a protein with a polarized force field |
| Q57814434 | Probing the Ion-Specific Effects at the Water/Air Interface and Water-Mediated Ion Pairing in Sodium Halide Solution with Ab initio Molecular Dynamics |
| Q48047200 | Protein simulation using coarse-grained two-bead multipole force field with polarizable water models |
| Q84269969 | Protein's electronic polarization contributes significantly to its catalytic function |
| Q38693023 | Protein-Ligand Empirical Interaction Components for Virtual Screening |
| Q84942209 | Quantifying the Stabilizing Energy of the Intraprotein Hydrogen Bond Due to Local Mutation |
| Q30382258 | Quantum Fragment Based ab Initio Molecular Dynamics for Proteins. |
| Q35812336 | Quantum and molecular dynamics study for binding of macrocyclic inhibitors to human alpha-thrombin. |
| Q30868814 | Quantum calculation of protein NMR chemical shifts based on the automated fragmentation method |
| Q46661986 | Quantum computational analysis for drug resistance of HIV-1 reverse transcriptase to nevirapine through point mutations |
| Q80545864 | Quantum dynamics study of H+NH3-->H2+NH2 reaction |
| Q57402563 | Quantum mechanical algebraic variational methods for inelastic and reactive molecular collisions |
| Q40322069 | Quantum mechanical calculation of electric fields and vibrational Stark shifts at active site of human aldose reductase |
| Q44988987 | Quantum mechanical map for protein-ligand binding with application to beta-trypsin/benzamidine complex |
| Q47396879 | Quantum mechanical studies of residue-specific hydrophobic interactions in p53-MDM2 binding. |
| Q80368031 | Quantum scattering calculation of the O(1D)+HBr reaction |
| Q51903747 | Quantum study of HIV-1 protease-bridge water interaction |
| Q61655161 | ReacNetGen: an Automatic Reaction Network Generator for Reactive Molecular Dynamic Simulations |
| Q76649977 | ReacNetGenerator: an Automatic Reaction Network Generator for Reactive Molecular Dynamic Simulations |
| Q42879958 | Selective Binding of Antiinfluenza Drugs and Their Analogues to ‘Open’ and ‘Closed’ Conformations of H5N1 Neuraminidase |
| Q81742305 | Selectivity of neutral/weakly basic P1 group inhibitors of thrombin and trypsin by a molecular dynamics study |
| Q33457442 | Simulation of NMR data reveals that proteins' local structures are stabilized by electronic polarization |
| Q46358655 | Single Biosensor for Simultaneous Quantification of Glucose and pH in a Rat Brain of Diabetic Model Using Both Current and Potential Outputs |
| Q57402578 | Storage management strategies in large-scale quantum dynamics calculations |
| Q84568836 | Structure and dynamics of a dizinc metalloprotein: effect of charge transfer and polarization |
| Q50903074 | Structure of liquid water - a dynamical mixture of tetrahedral and 'ring-and-chain' like structures |
| Q45422738 | Structure, mechanism, and enantioselectivity shifting of lipase LipK107 with a simple way. |
| Q92814326 | Study of SHMT2 Inhibitors and Their Binding Mechanism by Computational Alanine Scanning |
| Q86761903 | Studying the Effect of Site-Specific Hydrophobicity and Polarization on Hydrogen Bond Energy of Protein Using a Polarizable Method |
| Q92980999 | Sulfur-substitution-induced base flipping in the DNA duplex |
| Q51123164 | TMFF-A Two-Bead Multipole Force Field for Coarse-Grained Molecular Dynamics Simulation of Protein |
| Q45393755 | The F130L mutation in streptavidin reduces its binding affinity to biotin through electronic polarization effect. |
| Q46966849 | The critical effect of polarization on the dynamical structure of guanine quadruplex DNA |
| Q51941481 | The generalized molecular fractionation with conjugate caps/molecular mechanics method for direct calculation of protein energy |
| Q64987688 | The impact of interior dielectric constant and entropic change on HIV-1 complex binding free energy prediction. |
| Q34991330 | The intrinsic helical propensities of the helical fragments in prion protein under neutral and low pH conditions: a replica exchange molecular dynamics study |
| Q80367514 | The investigation of spin-orbit effect for the F((2)P)+HD reaction |
| Q36955733 | The origin of the cooperativity in the streptavidin-biotin system: A computational investigation through molecular dynamics simulations |
| Q93851690 | Theoretical Understanding of the Thermodynamics and Interactions in Transcriptional Regulator TtgR-Ligand Binding |
| Q38338648 | Theoretical method for full ab initio calculation of DNA/RNA-ligand interaction energy |
| Q92227372 | Theoretical understanding of the thermodynamics and interactions in transcriptional regulator TtgR-ligand binding |
| Q93853463 | Thermodynamic Insights of Base Flipping in TNA Duplex: Force Fields, Salt Concentrations, and Free Energy Simulation Methods |
| Q48046239 | Two-bead polarizable water models combined with a two-bead multipole force field (TMFF) for coarse-grained simulation of proteins |
| Q84977139 | Understanding the Molecular Mechanism of Enzyme Dynamics of Ribonuclease A through Protonation/Deprotonation of HIS48 |
| Q69398578 | Understanding the selectivity of inhibitors toward PI4KIIIα and PI4KIIIβ based molecular modeling |
| Q28661028 | Unveiling the gating mechanism of ECF transporter RibU |
| Q57402607 | Variational basis-set calculations of accurate quantum mechanical reaction probabilities |
| Q113977355 | neural network MD simulation of thermal decomposition of a high energy material CL-20/TNT |
| Q43660394 | pH-Dependent Conformational Ensemble and Polymorphism of Amyloid-β Core Fragment |
| Q57402608 | ℒ2Calculations of accurate quantal-dynamical reactive scattering transition probabilities and their use to test semiclassical applications |