Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models

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3. Comprehensive Insights into the Catalytic Mechanism of Middle East Respiratory Syndrome 3C-Like Protease and Severe Acute Respiratory Syndrome 3C-Like Protease
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4. Drug Design: Free-energy calculations in structure-based drug design
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5. Probing the Structure of Lysozyme–Carbon‐Nanotube Hybrids with Molecular Dynamics
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7. Application of a post-docking procedure based on MM-PBSA and MM-GBSA on single and multiple protein conformations
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8. Determination of the α-Conotoxin Vc1.1 Binding Site on the α9α10 Nicotinic Acetylcholine Receptor
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9. Structure-Based Design of Novel Chk1 Inhibitors: Insights into Hydrogen Bonding and Protein−Ligand Affinity
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10. CHARMM-GUI Ligand Binder for Absolute Binding Free Energy Calculations and Its Application
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13. High spin cobalt(II) as a probe for the investigation of metalloproteins.
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14. Different positron emission tomography tau tracers bind to multiple binding sites on the tau fibril: insight from computational modeling
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15. Large Scale Affinity Calculations of Cyclodextrin Host–Guest Complexes: Understanding the Role of Reorganization in the Molecular Recognition Process
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16. Removal of bisphenol A and 17α-ethinyl estradiol by combined coagulation and adsorption using carbon nanomaterials and powdered activated carbon
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17. Insight into Crizotinib Resistance Mechanisms Caused by Three Mutations in ALK Tyrosine Kinase using Free Energy Calculation Approaches
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18. The Semiempirical Quantum Mechanical Scoring Function for In Silico Drug Design
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19. Curcumin Binds to Aβ1–40Peptides and Fibrils Stronger Than Ibuprofen and Naproxen
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20. α-Glucosidase and α-Amylase Inhibitors from Arcytophyllum thymifolium
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21. Elucidating biophysical basis of binding of inhibitors to SARS-CoV-2 main protease by using molecular dynamics simulations and free energy calculations
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22. Old drug new use - Amoxapine and its metabolites as potent bacterial β-glucuronidase inhibitors for alleviating cancer drug toxicity
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23. Discovery of SARS-CoV-2 M pro peptide inhibitors from modelling substrate and ligand binding
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24. How Dopamine Transporter Interacts with Dopamine: Insights from Molecular Modeling and Simulation
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25. Complexity and simplicity of ligand–macromolecule interactions: the energy landscape perspective
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26. Isaindigotone Derivatives: A New Class of Highly Selective Ligands for Telomeric G-Quadruplex DNA
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27. Predicting folding free energy changes upon single point mutations
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28. Direct Observation of Protein Folding, Aggregation, and a Prion-like Conformational Conversion
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29. Small Molecule Inhibitors of ERCC1-XPF Protein-Protein Interaction Synergize Alkylating Agents in Cancer Cells
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30. Fast and accurate computation schemes for evaluating vibrational entropy of proteins
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31. Aminoacyl β-naphthylamides as substrates and modulators of AcrB multidrug efflux pump
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32. Toward Fully Automated High Performance Computing Drug Discovery: A Massively Parallel Virtual Screening Pipeline for Docking and Molecular Mechanics/Generalized Born Surface Area Rescoring to Improve Enrichment
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33. High-Throughput Calculation of Protein−Ligand Binding Affinities: Modification and Adaptation of the MM-PBSA Protocol to Enterprise Grid Computing
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34. Hydrophobic Interactions Are a Key to MDM2 Inhibition by Polyphenols as Revealed by Molecular Dynamics Simulations and MM/PBSA Free Energy Calculations
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35. Homology modeling of DFG-in FMS-like tyrosine kinase 3 (FLT3) and structure-based virtual screening for inhibitor identification
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36. Limits of Free Energy Computation for Protein−Ligand Interactions
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37. Treatment of geometric singularities in implicit solvent models
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38. Molecular modeling study on the resistance mechanism of HCV NS3/4A serine protease mutants R155K, A156V and D168A to TMC435
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39. Understanding the Effect of Polylysine Architecture on DNA Binding Using Molecular Dynamics Simulations
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40. Characterization of PDZ domain–peptide interactions using an integrated protocol of QM/MM, PB/SA, and CFEA analyses
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41. Polydopamine-induced growth of mineralized γ-FeOOH nanorods for construction of silk fabric with excellent superhydrophobicity, flame retardancy and UV resistance
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42. Structural Basis of TLR2/TLR1 Activation by the Synthetic Agonist Diprovocim
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43. Molecular Analysis of the HIV-1 Resistance Development: Enzymatic Activities, Crystal Structures, and Thermodynamics of Nelfinavir-resistant HIV Protease Mutants
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44. Characterization of a rituximab variant with potent antitumor activity against rituximab-resistant B-cell lymphoma
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45. Inhibition of Leishmania infantum Trypanothione Reductase by Azole‐Based Compounds: a Comparative Analysis with Its Physiological Substrate by X‐ray Crystallography
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46. Identification of a novel binding mechanism of Quinoline based molecules with lactate dehydrogenase of Plasmodium falciparum
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47. Understanding Hydrophobic Effects: Insights from Water Density Fluctuations
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48. Structure and Dynamics of Zymogen Human Blood Coagulation Factor X
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49. Carbohydrate–Protein Interactions
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50. A Coarse-Grained Model of DNA with Explicit Solvation by Water and Ions
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51. Drug Affinity Responsive Target Stability (DARTS) Identifies Laurifolioside as a New Clathrin Heavy Chain Modulator
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52. Structural and Dynamic Characterizations Highlight the Deleterious Role of SULT1A1 R213H Polymorphism in Substrate Binding
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53. Vitamin D and lumisterol derivatives can act on liver X receptors (LXRs)
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54. Improving ligand‐ranking of AutoDock Vina by changing the empirical parameters
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55. Advances and applications of binding affinity prediction methods in drug discovery
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56. Molecular features of interaction between VEGFA and anti-angiogenic drugs used in retinal diseases: a computational approach
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57. Revealing the favorable dissociation pathway of type II kinase inhibitors via enhanced sampling simulations and two-end-state calculations
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58. Ligand Affinities Estimated by Quantum Chemical Calculations
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59. Molecular modeling studies to characterize N -phenylpyrimidin-2-amine selectivity for CDK2 and CDK4 through 3D-QSAR and molecular dynamics simulations
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60. Enhancing the catalytic activity of a novel GH5 cellulase GtCel5 from Gloeophyllum trabeum CBS 900.73 by site-directed mutagenesis on loop 6
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61. Recurrent activating mutations of PPARγ associated with luminal bladder tumors
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63. A Multistep Approach to Structure-Based Drug Design: Studying Ligand Binding at the Human Neutrophil Elastase
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64. Conformational entropy changes upon lactose binding to the carbohydrate recognition domain of galectin-3
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68. Exploration of chlorinated thienyl chalcones: A new class of monoamine oxidase-B inhibitors
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69. Stabilization of G-quadruplex DNA by C-5-methyl-cytosine in bcl-2 promoter: Implications for epigenetic regulation
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70. Simple, Intuitive Calculations of Free Energy of Binding for Protein−Ligand Complexes. 2. Computational Titration and pH Effects in Molecular Models of Neuraminidase−Inhibitor Complexes
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72. Comparing experimental and computational alanine scanning techniques for probing a prototypical protein–protein interaction
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74. Prediction of Binding Free Energy of Protein–Ligand Complexes with a Hybrid Molecular Mechanics/Generalized Born Surface Area and Machine Learning Method
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75. Mixed Quantum Mechanics/Molecular Mechanics Scoring Function To Predict Protein−Ligand Binding Affinity
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76. Molecular Basis of the Interaction for an Essential Subunit PA−PB1 in Influenza Virus RNA Polymerase: Insights from Molecular Dynamics Simulation and Free Energy Calculation
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77. Direct Binding of Fas-associated Death Domain (FADD) to the Tumor Necrosis Factor-related Apoptosis-inducing Ligand Receptor DR5 Is Regulated by the Death Effector Domain of FADD
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78. Computational and Experimental Insight into the Molecular Mechanism of Carboxamide Inhibitors of Succinate‐Ubquinone Oxidoreductase
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79. On the Use of Interaction Entropy and Related Methods to Estimate Binding Entropies
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80. Dynamics of Recognition between tRNA and Elongation Factor Tu
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81. Performance of the MM/GBSA scoring using a binding site hydrogen bond network-based frame selection: the protein kinase case
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82. Design, Synthesis, and Biophysical and Biological Evaluation of a Series of Pyrrolobenzodiazepine−Poly(N-methylpyrrole) Conjugates
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83. Computational Methods for Biomolecular Electrostatics
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84. Explicit Ligand Hydration Shells Improve the Correlation between MM-PB/GBSA Binding Energies and Experimental Activities
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85. Comparison of the Efficiency of the LIE and MM/GBSA Methods to Calculate Ligand-Binding Energies
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86. Molecular Dynamics Simulations Show That Conformational Selection Governs the Binding Preferences of Imatinib for Several Tyrosine Kinases
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87. A challenging system: Free energy prediction for factor Xa
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88. Top Leads for Swine Influenza A/H1N1 Virus Revealed by Steered Molecular Dynamics Approach
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89. Bindungsaffinitäten von Wirt‐Gast‐, Protein‐Ligand‐ und Protein‐Übergangszustands‐Komplexen
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92. Identification of Amino Acids in the Human Tetherin Transmembrane Domain Responsible for HIV-1 Vpu Interaction and Susceptibility
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93. Bioinformatics-Aided Venomics
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94. Structures of the E46K Mutant-Type α-Synuclein Protein and Impact of E46K Mutation on the Structures of the Wild-Type α-Synuclein Protein
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95. Computational studies of protegrin antimicrobial peptides: A review
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96. Combining Structural Modeling with Ensemble Machine Learning to Accurately Predict Protein Fold Stability and Binding Affinity Effects upon Mutation
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97. Binding Affinities of Factor Xa Inhibitors Estimated by Thermodynamic Integration and MM/GBSA
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98. Mutation D816V Alters the Internal Structure and Dynamics of c-KIT Receptor Cytoplasmic Region: Implications for Dimerization and Activation Mechanisms
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99. Computational Insights into the Interactions between DNA and siRNA with “Rigid” and “Flexible” Triazine Dendrimers
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100. MM-ISMSA: An Ultrafast and Accurate Scoring Function for Protein–Protein Docking
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