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Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free Energy Calculations Based on Molecular Dynamics Simulations
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Outgoing claims: the papers this work cites, builds on, or argues with.
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inferred← citeshttps://doi.org/10.1002/jcc.24011openalex-snapshot
Comparison of radii sets, entropy, QM methods, and sampling on MM‐PBSA , MM‐GBSA , and QM/MM‐GBSA ligand binding energies of F . tularensis enoyl‐ ACP reductase ( F abI)
inferred← citeshttps://doi.org/10.1002/jcc.24274openalex-snapshot
Evaluating thermodynamic integration performance of the new amber molecular dynamics package and assess potential halogen bonds of enoyl-ACP reductase (FabI) benzimidazole inhibitors
inferred← citeshttps://doi.org/10.1002/jcc.24397openalex-snapshot
Reformulating the entropic contribution in molecular docking scoring functions
inferred← citeshttps://doi.org/10.1002/jcc.24467openalex-snapshot
Calculating protein–ligand binding affinities with MMPBSA: Method and error analysis
inferred← citeshttps://doi.org/10.1002/jcc.24475openalex-snapshot
Electrostatic component of binding energy: Interpreting predictions from poisson–boltzmann equation and modeling protocols
inferred← citeshttps://doi.org/10.1002/jcc.24745openalex-snapshot
Efficient gaussian density formulation of volume and surface areas of macromolecules on graphical processing units
inferred← citeshttps://doi.org/10.1002/jcc.24768openalex-snapshot
Effects from metal ion in tumor endothelial marker 8 and anthrax protective antigen: BioLayer Interferometry experiment and molecular dynamics simulation study
inferred← citeshttps://doi.org/10.1002/jcc.24839openalex-snapshot
Effect of sampling on BACE-1 ligands binding free energy predictions via MM-PBSA calculations
inferred← citeshttps://doi.org/10.1002/jcc.25072openalex-snapshot
A component analysis of the free energies of folding of 35 proteins: A consensus view on the thermodynamics of folding at the molecular level
inferred← citeshttps://doi.org/10.1002/jcc.25120openalex-snapshot
Can MM/GBSA calculations be sped up by system truncation?
inferred← citeshttps://doi.org/10.1002/jcc.25592openalex-snapshot
Calculation of hot spots for protein–protein interaction in p53/PMI‐MDM2/MDMX complexes
inferred← citeshttps://doi.org/10.1002/jcc.25715openalex-snapshot
Improving the Accuracy of Protein‐Ligand Binding Mode Prediction Using a Molecular Dynamics‐Based Pocket Generation Approach
inferred← citeshttps://doi.org/10.1002/jcc.26119openalex-snapshot
On Restraints in End‐Point Protein–Ligand Binding Free Energy Calculations
inferred← citeshttps://doi.org/10.1002/jcc.26135openalex-snapshot
Dimerization energetics of the G‐protein coupled bile acid receptor TGR5 from all‐atom simulations
inferred← citeshttps://doi.org/10.1002/jcc.26218openalex-snapshot
Accurate prediction of relative binding affinities of a series of HIV‐1 protease inhibitors using semi‐empirical quantum mechanical charge
inferred← citeshttps://doi.org/10.1002/jcc.26514openalex-snapshot
Developing a variation of 3D‐QSAR / MD method in drug design
inferred← citeshttps://doi.org/10.1002/jcc.26704openalex-snapshot
Exploring the molecular basis of UG ‐rich RNA recognition by the human splicing factor TDP ‐43 using molecular dynamics simulation and free energy calculation
inferred← citeshttps://doi.org/10.1002/jcc.26717openalex-snapshot
Identification of novel inhibitors of SARS‐CoV ‐2 main protease (Mpro) from Withania sp. by molecular docking and molecular dynamics simulation
inferred← citeshttps://doi.org/10.1002/jcc.27084openalex-snapshot
Molecular basis of RNA recognition by TBP of HIV ‐1 from multiple molecular dynamics simulations and energy predictions
inferred← citeshttps://doi.org/10.1002/jcc.27089openalex-snapshot
Development and test of highly accurate endpoint free energy methods. 1: Evaluation of ABCG2 charge model on solvation free energy prediction and optimization of atom radii suitable for more accurate solvation free energy prediction by the PBSA method
inferred← citeshttps://doi.org/10.1002/jcc.70093openalex-snapshot
Enhancing MM /P(G) BSA Methods: Integration of Formulaic Entropy for Improved Binding Free Energy Calculations
inferred← citeshttps://doi.org/10.1002/jccs.201900148openalex-snapshot
Assessing the performance of the g_mmpbsa tools to simulate the inhibition of oseltamivir to influenza virus neuraminidase by molecular mechanics Poisson–Boltzmann surface area methods
inferred← citeshttps://doi.org/10.1002/jccs.202200315openalex-snapshot
Binding free energy of several sterols to the N‐terminal domain of Niemann‐Pick C1 ‐like 1 protein due to mutation: Molecular dynamics study
inferred← citeshttps://doi.org/10.1002/jcp.30367openalex-snapshot
Higher infectivity of the SARS‐CoV‐2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data
inferred← citeshttps://doi.org/10.1002/jmr.2300openalex-snapshot
Interaction investigations of HipA binding to HipB dimer and HipB dimer + DNA complex: a molecular dynamics simulation study
inferred← citeshttps://doi.org/10.1002/jmr.2675openalex-snapshot
Molecular dynamics investigation of stereoselective inhibition mechanism of HIF‐2α/ARNT heterodimer
inferred← citeshttps://doi.org/10.1002/jmr.3008openalex-snapshot
Modeling disruption of Apis mellifera (honey bee) odorant‐binding protein function with high‐affinity binders
inferred← citeshttps://doi.org/10.1002/jnr.70035openalex-snapshot
Cannabidiol‐Rich Cannabis sativa L. Extract Alleviates LPS ‐Induced Neuroinflammation Behavioral Alterations, and Astrocytic Bioenergetic Impairment in Male Mice
inferred← citeshttps://doi.org/10.1002/jsfa.13595openalex-snapshot
Molecular recognition between volatile molecules and odorant binding proteins 7 by homology modeling, molecular docking and molecular dynamics simulation
inferred← citeshttps://doi.org/10.1002/minf.201100077openalex-snapshot
Conformational Properties and Energetic Analysis of Aliskiren in Solution and Receptor Site
inferred← citeshttps://doi.org/10.1002/minf.201100135openalex-snapshot
Free Energy Calculations by the Molecular Mechanics Poisson−Boltzmann Surface Area Method
inferred← citeshttps://doi.org/10.1002/minf.201400048openalex-snapshot
Analysis of the Resistance of Hepatitis C Virus NS5B Polymerase Inhibitors via Docking and Molecular Dynamics Simulation
inferred← citeshttps://doi.org/10.1002/minf.201600052openalex-snapshot
Computational Approaches to the Chemical Equilibrium Constant in Protein‐ligand Binding
inferred← citeshttps://doi.org/10.1002/open.202200181openalex-snapshot
Synthesis and Anti‐Inflammatory Activity of 2‐Amino‐4,5,6,7‐tetrahydrobenzo[b]thiophene‐Derived NRF2 Activators
inferred← citeshttps://doi.org/10.1002/path.6261openalex-snapshot
KAT8 / SIRT7 ‐mediated Fascin‐K41 acetylation/deacetylation regulates tumor metastasis in esophageal squamous cell carcinoma
inferred← citeshttps://doi.org/10.1002/pep2.70021openalex-snapshot
Peptide–Ligand Conjugate‐Based Immunotherapeutic Strategy Targeting Nipah Virus Glycoprotein G: A Novel Approach for Treating Virus Infection by Employing Host Innate Immune Response
inferred← citeshttps://doi.org/10.1002/pro.2168openalex-snapshot
The binding mechanism, multiple binding modes, and allosteric regulation of Staphylococcus aureus Sortase A probed by molecular dynamics simulations
inferred← citeshttps://doi.org/10.1002/pro.2829openalex-snapshot
AB ‐Bind: Antibody binding mutational database for computational affinity predictions
inferred← citeshttps://doi.org/10.1002/pro.3056openalex-snapshot
Simulation study of the ability of a computationally‐designed peptide to recognize target tRNALys3 and other decoy tRNAs
inferred← citeshttps://doi.org/10.1002/pro.4451openalex-snapshot
Host and viral proteins involved in SARS‐CoV ‐2 infection differentially bind heme
inferred← citeshttps://doi.org/10.1002/pro.4579openalex-snapshot
Engineering excitonically coupled dimers in an artificial protein for light harvesting via computational modeling
inferred← citeshttps://doi.org/10.1002/pro.70228openalex-snapshot
Exploring binding and allosteric energy landscapes for the KRAS interactions with effector proteins using Markov state modeling of conformational ensembles and allosteric network modeling
inferred← citeshttps://doi.org/10.1002/pro.70336openalex-snapshot
Calcium dissociation with carbonate ions from Pf‐ SCP , sarcoplasmic calcium‐binding protein in Pinctada fucata , contributes to calcium mineralization for shell formation
inferred← citeshttps://doi.org/10.1002/prot.23018openalex-snapshot
Virtual screening using molecular simulations
inferred← citeshttps://doi.org/10.1002/prot.23205openalex-snapshot
Allosteric regulation of PKCθ: Understanding multistep phosphorylation and priming by ligands in AGC kinases
inferred← citeshttps://doi.org/10.1002/prot.23224openalex-snapshot
Temperature‐dependent study reveals that dynamics of hydrophobic residues plays an important functional role in the mitochondrial Tim9–Tim10 complex
inferred← citeshttps://doi.org/10.1002/prot.24029openalex-snapshot
Comparison of end‐point continuum‐solvation methods for the calculation of protein–ligand binding free energies
inferred← citeshttps://doi.org/10.1002/prot.24037openalex-snapshot
Molecular modeling of hair keratin/peptide complex: Using MM‐PBSA calculations to describe experimental binding results
inferred← citeshttps://doi.org/10.1002/prot.24057openalex-snapshot
Computational investigation of the HIV‐1 Rev multimerization using molecular dynamics simulations and binding free energy calculations
inferred← citeshttps://doi.org/10.1002/prot.25030openalex-snapshot
Protein side chain conformation predictions with an MMGBSA energy function
inferred← citeshttps://doi.org/10.1002/prot.25208openalex-snapshot
A molecular dynamics study of the binary complexes of APP, JIP1, and the cargo binding domain of KLC
inferred← citeshttps://doi.org/10.1002/prot.25314openalex-snapshot
Role of N‐glycosylation in EGFR ectodomain ligand binding
inferred← citeshttps://doi.org/10.1002/prot.25322openalex-snapshot
Predicting binding modes of reversible peptide-based inhibitors of falcipain-2 consistent with structure-activity relationships
inferred← citeshttps://doi.org/10.1002/prot.25807openalex-snapshot
Effect of hydrophobic and hydrogen bonding interactions on the potency of ß‐alanine analogs of G‐protein coupled glucagon receptor inhibitors
inferred← citeshttps://doi.org/10.1002/prot.26164openalex-snapshot
Repurposing of FDA ‐approved drugs against active site and potential allosteric drug‐binding sites of COVID ‐19 main protease
inferred← citeshttps://doi.org/10.1002/prot.26196openalex-snapshot
Molecular dynamics simulations reveal the disruption mechanism of a 2,4‐thiazolidinedione derivative C30 against tau hexapeptide ( PHF6 ) oligomer
inferred← citeshttps://doi.org/10.1002/prot.26408openalex-snapshot
Engineering human JMJD2A tudor domains for an improved understanding of histone peptide recognition
inferred← citeshttps://doi.org/10.1002/prot.26470openalex-snapshot
In‐silico identification of Tyr232 in AMPKα2 as a dephosphorylation site for the protein tyrosine phosphatase PTP‐PEST
inferred← citeshttps://doi.org/10.1002/prot.26662openalex-snapshot
Dissecting the geometric and hydrophobic constraints of stapled peptides
inferred← citeshttps://doi.org/10.1002/ps.5915openalex-snapshot
Structure dynamics reveal key residues essential for the sense of 1‐dodecanol by Cydia pomonella pheromone binding protein 2 ( CpomPBP2 )
inferred← citeshttps://doi.org/10.1002/qua.24132openalex-snapshot
Quantum chemical study on molecular‐level affinity of DJ‐1 binding compounds
inferred← citeshttps://doi.org/10.1002/qua.26980openalex-snapshot
Exploring the effects of mutations on NFAT5‐DNA binding using molecular dynamics simulations and energy calculations
inferred← citeshttps://doi.org/10.1002/qua.27333openalex-snapshot
Binding interactions of EDCs to human estrogen‐related receptor gamma deciphered by multiple molecular dynamics and energy calculations
inferred← citeshttps://doi.org/10.1002/slct.202401136openalex-snapshot
Computational Insights into Enzyme‐Substrate Binding Interplay Exhibit Variable Binding Attributes: A Framework for Implementing Oxidoreductase‐Based Applications
inferred← citeshttps://doi.org/10.1002/slct.202402567openalex-snapshot
Computational Studies of Novel Aniline Pyrimidine WDR5‐MLL1 Inhibitors: QSAR, Molecular Docking, and Molecular Dynamics Simulation
inferred← citeshttps://doi.org/10.1002/slct.202500900openalex-snapshot
Investigating DNA Aptamer Binding to Domains of the SARS‐CoV‐2 Spike Protein: Insights from Molecular Dynamics and MM/PBSA Analysis
inferred← citeshttps://doi.org/10.1002/slct.202501432openalex-snapshot
A Flavonoid‐Based Approach to Mitigating Hyperglycaemia: In Silico Analysis of AMPK Activation, Membrane and Metabolic Effects of Rutin in HepG2 Cells
inferred← citeshttps://doi.org/10.1002/slct.202502689openalex-snapshot
Integrative In Silico Pipeline for Discovering Natural SHP2 Allosteric Inhibitors Against Leukaemia
inferred← citeshttps://doi.org/10.1002/slct.202507023openalex-snapshot
In Silico Identification of Potential BACE1 Inhibitors from Ruta graveolens Essential Oil Targeting Alzheimer's Disease
inferred← citeshttps://doi.org/10.1002/slct.73932openalex-snapshot
A Multiscale Computational Strategy for the Rational Design of Novel Aminoguanidine‐Based Chitinase‐h Inhibitors
inferred← citeshttps://doi.org/10.1002/slct.73996openalex-snapshot
Integrating Computational Techniques for Designing and Optimizing an mRNA Vaccine Against the Infectious Salmon Anaemia Virus
inferred← citeshttps://doi.org/10.1002/slct.74164openalex-snapshot
FtsZ‐LSTM: Generative AI Model for AntiBacterial Hits Discovery
inferred← citeshttps://doi.org/10.1002/slct.74254openalex-snapshot
Computational Intelligence Frameworks for High Throughput In Silico Mining of Antipathogenic Biomolecules for the Management of Plant Pathogens
inferred← citeshttps://doi.org/10.1002/smtd.202400006openalex-snapshot
Facile Peptide Macrocyclization and Multifunctionalization via Cyclen Installation
inferred← citeshttps://doi.org/10.1002/wcms.1306openalex-snapshot
Molecular ‘time‐machines’ to unravel key biological events for drug design
inferred← citeshttps://doi.org/10.1002/wcms.1519openalex-snapshot
Dielectric continuum methods for quantum chemistry
inferred← citeshttps://doi.org/10.1002/wcms.1581openalex-snapshot
Application advances of deep learning methods for de novo drug design and molecular dynamics simulation
inferred← citeshttps://doi.org/10.1007/698_2017_144openalex-snapshot
In Silico Mutagenesis, Docking, and Molecular Dynamics: Their Role in Biosensor Design for Environmental Analysis and Monitoring
inferred← citeshttps://doi.org/10.1007/7355_2021_130openalex-snapshot
Ligand- and Structure-Based Virtual Screening in Drug Discovery
inferred← citeshttps://doi.org/10.1007/978-1-0716-1166-1_14openalex-snapshot
Computational Design of PDZ-Peptide Binding
inferred← citeshttps://doi.org/10.1007/978-1-0716-1689-5_17openalex-snapshot
In Silico Analysis of Peptide Macrocycle–Protein Interactions
inferred← citeshttps://doi.org/10.1007/978-1-0716-2285-8_3openalex-snapshot
Site-wise Diversification of Combinatorial Libraries Using Insights from Structure-guided Stability Calculations
inferred← citeshttps://doi.org/10.1007/978-1-0716-4003-6_19openalex-snapshot
PFAS-Biomolecule Interactions: Case Study Using Asclepios Nodes and Automated Workflows in KNIME for Drug Discovery and Toxicology
inferred← citeshttps://doi.org/10.1007/978-1-0716-4591-8_15openalex-snapshot
Predicting Epitopes of Synthetic Binding Proteins Using Protein Structure Prediction and Protein-Protein Docking
inferred← citeshttps://doi.org/10.1007/978-1-0716-5041-7_4openalex-snapshot
Antibody Affinity Maturation by Computational Design
inferred← citeshttps://doi.org/10.1007/978-1-0716-5316-6_10openalex-snapshot
Computer Simulations of Multidrug Efflux Pumps of the Resistance–Nodulation–Cell Division Superfamily
inferred← citeshttps://doi.org/10.1007/978-1-4939-6798-8_17openalex-snapshot
Modeling and Design of Peptidomimetics to Modulate Protein–Protein Interactions
inferred← citeshttps://doi.org/10.1007/978-1-4939-7404-7_11openalex-snapshot
Computational Approaches to Understand Cleavage Mechanism of Amyloid Beta (Aβ) Peptide
inferred← citeshttps://doi.org/10.1007/978-1-4939-7404-7_17openalex-snapshot
Computational Approaches for Therapeutic Application of Natural Products in Alzheimer’s Disease
inferred← citeshttps://doi.org/10.1007/978-1-4939-7454-2_11openalex-snapshot
Molecular Modeling of Multidrug Properties of Resistance Nodulation Division (RND) Transporters
inferred← citeshttps://doi.org/10.1007/978-1-4939-7477-1_19openalex-snapshot
Computational Modeling of the Hsp90 Interactions with Cochaperones and Small-Molecule Inhibitors
inferred← citeshttps://doi.org/10.1007/978-1-4939-8630-9_19openalex-snapshot
The Use of Dynamic Pharmacophore in Computer-Aided Hit Discovery: A Case Study
inferred← citeshttps://doi.org/10.1007/978-1-62703-342-8_7openalex-snapshot
Molecular Dynamics Simulations in Drug Design
inferred← citeshttps://doi.org/10.1007/978-3-030-05282-9_1openalex-snapshot
Free Energy-Based Methods to Understand Drug Resistance Mutations
inferred← citeshttps://doi.org/10.1007/978-3-031-76718-0_8openalex-snapshot
Drug Design in Motion: Concepts and Applications of Classical Molecular Dynamics Simulations
inferred← citeshttps://doi.org/10.1007/978-3-031-81728-1_27openalex-snapshot
Molecular Dynamics in Predicting the Stability of Drug-Receptor Interactions
inferred← citeshttps://doi.org/10.1007/978-3-031-81728-1_34openalex-snapshot
Prioritizing Candidate Drugs Via Virtual Screening, Docking and Simulations
inferred← citeshttps://doi.org/10.1007/978-3-031-81728-1_5openalex-snapshot
Computational Approaches to Model Macromolecules
inferred← citeshttps://doi.org/10.1007/978-3-319-12211-3_14openalex-snapshot
Self-Inclusion Complexes of Monofunctionalized Beta-Cyclodextrins as Host–Guest Interaction Model Systems and Simple and Sensitive Testbeds for Implicit Solvation Methods
inferred← citeshttps://doi.org/10.1007/978-3-319-12211-3_3openalex-snapshot
A Comprehensive Exploration of Physical and Numerical Parameters in the Poisson–Boltzmann Equation for Applications to Receptor–Ligand Binding
inferred← citeshttps://doi.org/10.1007/978-3-319-16480-9_56openalex-snapshot
Molecular Dynamics Simulations of Ligand Recognition upon Binding Antithrombin: A MM/GBSA Approach
inferred← citeshttps://doi.org/10.1007/978-3-319-20040-8_3openalex-snapshot
Imaging Agent Binding to Amyloid Protofibrils
inferred← citeshttps://doi.org/10.1007/978-3-319-27282-5_31openalex-snapshot
Applications of Computational Methods to Simulations of Proteins Dynamics
inferred← citeshttps://doi.org/10.1007/978-3-319-73238-1_2openalex-snapshot
Computer-Aided Drug Discovery
inferred← citeshttps://doi.org/10.1007/978-94-007-6169-8_31-2openalex-snapshot
Applications of Computational Methods to Simulations of Protein Dynamics
inferred← citeshttps://doi.org/10.1007/978-981-13-6920-9_28openalex-snapshot
In-silico Methods of Drug Design: Molecular Simulations and Free Energy Calculations
inferred← citeshttps://doi.org/10.1007/s00011-026-02329-zopenalex-snapshot
Myeloid PKM2 deficiency alleviates allergic airway inflammation and promotes macrophage efferocytosis via SLC13A3
inferred← citeshttps://doi.org/10.1007/s00011-026-02343-1openalex-snapshot
Theaflavin attenuates atherosclerosis by targeting GSK-3β to suppress pyroptosis and Promote Autophagy in macrophages
inferred← citeshttps://doi.org/10.1007/s00018-024-05263-7openalex-snapshot
Directed-evolution mutations enhance DNA-binding affinity and protein stability of the adenine base editor ABE8e
inferred← citeshttps://doi.org/10.1007/s00044-013-0665-6openalex-snapshot
Molecular dynamics-based self-organizing molecular field analysis on 3-amino-6-arylpyrazines as the ataxia telangiectasia mutated and Rad3 related (ATR) protein kinase inhibitors
inferred← citeshttps://doi.org/10.1007/s00044-017-1901-2openalex-snapshot
Computational insights into HER3 gatekeeper T768I resistance mutation to bosutinib in HER3-related breast cancer
inferred← citeshttps://doi.org/10.1007/s00044-020-02514-7openalex-snapshot
Exploration of the selective binding mechanism of GSK3β via molecular modeling and molecular dynamics simulation studies
inferred← citeshttps://doi.org/10.1007/s00125-021-05530-3openalex-snapshot
Progressive endoplasmic reticulum stress over time due to human insulin gene mutation contributes to pancreatic beta cell dysfunction
inferred← citeshttps://doi.org/10.1007/s00203-024-04189-9openalex-snapshot
Ajoene: a natural compound with enhanced antimycobacterial and antibiofilm properties mediated by efflux pump modulation and ROS generation against M. Smegmatis
inferred← citeshttps://doi.org/10.1007/s00204-017-2011-0openalex-snapshot
Experimental and computational insights on the recognition mechanism between the estrogen receptor α with bisphenol compounds
inferred← citeshttps://doi.org/10.1007/s00204-018-2159-2openalex-snapshot
Anti-estrogenic activity of tris(2,3-dibromopropyl) isocyanurate through disruption of co-activator recruitment: experimental and computational studies
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