On the public citation graph
Including Explicit Water Molecules as Part of the Protein Structure in MM/PBSA Calculations
0 signed · 62 inferred · view as graph
Inferred edges come from two machine sources: sweeps of open repository metadata (mostly SSRN and Zenodo), and a bulk OpenAlex citation snapshot. Every row below is labelled with the one it came from. Neither is a complete citation index — absence here is not evidence of absence.
Is this your work? Sign in with ORCID and put your name on the
claims that are yours.
Reference health. See whether every reference in this work resolves to a
known work and none has been retracted — and get a dated CiteStamped
badge you can embed.
What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1002/jcc.10120openalex-snapshot
Accelerated Poisson–Boltzmann calculations for static and dynamic systems
inferredcites →https://doi.org/10.1002/jcc.21456openalex-snapshot
Assessment of linear finite‐difference Poisson–Boltzmann solvers
inferredcites →https://doi.org/10.1002/pro.5560071002openalex-snapshot
Cluster analysis of consensus water sites in thrombin and trypsin shows conservation between serine proteases and contributions to ligand specificity
inferredcites →https://doi.org/10.1002/pro.61openalex-snapshot
A review about nothing: Are apolar cavities in proteins really empty?
inferredcites →https://doi.org/10.1016/0969-2126(93)90005-2openalex-snapshot
Influenza B virus neuraminidase can synthesize its own inhibitor
inferredcites →https://doi.org/10.1016/j.bmc.2007.08.019openalex-snapshot
Validation of an automated procedure for the prediction of relative free energies of binding on a set of aldose reductase inhibitors
inferredcites →https://doi.org/10.1016/j.bmcl.2009.08.082openalex-snapshot
Discovery of N-substituted pyridinones as potent and selective inhibitors of p38 kinase
inferredcites →https://doi.org/10.1016/j.bmcl.2011.01.046openalex-snapshot
Design and synthesis of a novel, orally active, brain penetrant, tri-substituted thiophene based JNK inhibitor
inferredcites →https://doi.org/10.1016/j.jmgm.2009.02.007openalex-snapshot
Bridge water mediates nevirapine binding to wild type and Y181C HIV-1 reverse transcriptase—Evidence from molecular dynamics simulations and MM-PBSA calculations
inferredcites →https://doi.org/10.1016/s0969-2126(98)00075-6openalex-snapshot
Drug design against a shifting target: a structural basis for resistance to inhibitors in a variant of influenza virus neuraminidase
inferredcites →https://doi.org/10.1021/ar000033jopenalex-snapshot
Calculating Structures and Free Energies of Complex Molecules: Combining Molecular Mechanics and Continuum Models
inferredcites →https://doi.org/10.1021/ci100275aopenalex-snapshot
Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free Energy Calculations Based on Molecular Dynamics Simulations
inferredcites →https://doi.org/10.1021/ci400285zopenalex-snapshot
Improved Ligand Binding Energies Derived from Molecular Dynamics: Replicate Sampling Enhances the Search of Conformational Space
inferredcites →https://doi.org/10.1021/ct100504hopenalex-snapshot
Effects of Water Placement on Predictions of Binding Affinities for p38α MAP Kinase Inhibitors
inferredcites →https://doi.org/10.1021/ct200163copenalex-snapshot
Comparison of the Efficiency of the LIE and MM/GBSA Methods to Calculate Ligand-Binding Energies
inferredcites →https://doi.org/10.1021/ct8003707openalex-snapshot
MM-PBSA Captures Key Role of Intercalating Water Molecules at a Protein−Protein Interface
inferredcites →https://doi.org/10.1021/jm000241hopenalex-snapshot
Binding of a Diverse Set of Ligands to Avidin and Streptavidin: An Accurate Quantitative Prediction of Their Relative Affinities by a Combination of Molecular Mechanics and Continuum Solvent Models
inferredcites →https://doi.org/10.1021/jm049081qopenalex-snapshot
Validation and Use of the MM-PBSA Approach for Drug Discovery
inferredcites →https://doi.org/10.1021/jm050306mopenalex-snapshot
Evaluating the Molecular Mechanics Poisson−Boltzmann Surface Area Free Energy Method Using a Congeneric Series of Ligands to p38 MAP Kinase
inferredcites →https://doi.org/10.1021/jm0608210openalex-snapshot
Ligand Affinities Predicted with the MM/PBSA Method: Dependence on the Simulation Method and the Force Field
inferredcites →https://doi.org/10.1186/1472-6807-7-1openalex-snapshot
Sequence and structural features of carbohydrate binding in proteins and assessment of predictability using a neural network.
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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/s00344-019-10030-1openalex-snapshot
Computational-Aided Discovery of Novel 1,3-Benzodioxole Plant Growth Retardants
inferred← citeshttps://doi.org/10.1007/s10822-019-00201-3openalex-snapshot
Evaluating the performance of MM/PBSA for binding affinity prediction using class A GPCR crystal structures
inferred← citeshttps://doi.org/10.1016/j.bmc.2019.06.032openalex-snapshot
Design, synthesis, biological activities, and dynamic simulation study of novel thiourea derivatives with gibberellin activity towards Arabidopsis thaliana
inferred← citeshttps://doi.org/10.1016/j.bmcl.2017.11.003openalex-snapshot
Design, synthesis and biological evaluation of novel oseltamivir derivatives as potent neuraminidase inhibitors
inferred← citeshttps://doi.org/10.1016/j.bmcl.2018.10.040openalex-snapshot
Design, synthesis and biological evaluation of novel zanamivir derivatives as potent neuraminidase inhibitors
inferred← citeshttps://doi.org/10.1016/j.jmgm.2015.02.005openalex-snapshot
Interactions between Bcl-xl and its inhibitors: Insights into ligand design from molecular dynamics simulation
inferred← citeshttps://doi.org/10.1016/j.jmgm.2017.02.015openalex-snapshot
Computational investigation of fullerene-DNA interactions: Implications of fullerene’s size and functionalization on DNA structure and binding energetics
inferred← citeshttps://doi.org/10.1016/j.jmgm.2017.03.010openalex-snapshot
Conformational and energy evaluations of novel peptides binding to dengue virus envelope protein
inferred← citeshttps://doi.org/10.1016/j.jmgm.2019.03.022openalex-snapshot
Insights into the structure-affinity relationships and solvation effects between OfHex1 and inhibitors using molecular dynamics simulations
inferred← citeshttps://doi.org/10.1016/j.molstruc.2023.135257openalex-snapshot
Design and structure optimization of novel butenolide derivatives as low bee-toxicity candidates
inferred← citeshttps://doi.org/10.1016/j.nexres.2026.102468openalex-snapshot
Integrated molecular docking, molecular dynamics, and MM/PBSA studies of Azadirachta indica Phytochemicals as potential DNA gyrase inhibitors against methicillin-resistant Staphylococcus aureus (MRSA)
inferred← citeshttps://doi.org/10.1021/acs.biochem.5b00853openalex-snapshot
Dynamic and Static Water Molecules Complement the TN16 Conformational Heterogeneity inside the Tubulin Cavity
inferred← citeshttps://doi.org/10.1021/acs.jcim.1c00765openalex-snapshot
Reliable In Silico Ranking of Engineered Therapeutic TCR Binding Affinities with MMPB/GBSA
inferred← citeshttps://doi.org/10.1021/acs.jcim.3c00776openalex-snapshot
DOX_BDW: Incorporating Solvation and Desolvation Effects of Cavity Water into Nonfitting Protein–Ligand Binding Affinity Prediction
inferred← citeshttps://doi.org/10.1021/acs.jcim.6b00196openalex-snapshot
Improved Computation of Protein–Protein Relative Binding Energies with the Nwat-MMGBSA Method
inferred← citeshttps://doi.org/10.1021/acs.jcim.6b00378openalex-snapshot
New Parameters for Higher Accuracy in the Computation of Binding Free Energy Differences upon Alanine Scanning Mutagenesis on Protein–Protein Interfaces
inferred← citeshttps://doi.org/10.1021/acs.jctc.3c01225openalex-snapshot
Computational Mutagenesis of Antibody Fragments: Disentangling Side Chains from ΔΔG Predictions
inferred← citeshttps://doi.org/10.1021/acs.jctc.5b00179openalex-snapshot
Rapid, Precise, and Reproducible Prediction of Peptide–MHC Binding Affinities from Molecular Dynamics That Correlate Well with Experiment
inferred← citeshttps://doi.org/10.1021/acs.jctc.5b00684openalex-snapshot
Examining the Assumptions Underlying Continuum-Solvent Models
inferred← citeshttps://doi.org/10.1021/acs.jctc.6b00794openalex-snapshot
Rapid and Reliable Binding Affinity Prediction of Bromodomain Inhibitors: A Computational Study
inferred← citeshttps://doi.org/10.1021/acs.jpcb.2c07079openalex-snapshot
Assessment of Different Parameters on the Accuracy of Computational Alanine Scanning of Protein–Protein Complexes with the Molecular Mechanics/Generalized Born Surface Area Method
inferred← citeshttps://doi.org/10.1021/acs.jpcb.4c02255openalex-snapshot
Multilayered Computational Framework for Designing Peptide Inhibitors of HVEM-LIGHT Interaction
inferred← citeshttps://doi.org/10.1021/acs.jpcb.8b05135openalex-snapshot
Dynamic Description of the Catalytic Cycle of Malate Enzyme: Stereoselective Recognition of Substrate, Chemical Reaction, and Ligand Release
inferred← citeshttps://doi.org/10.1021/acsomega.7b01403openalex-snapshot
Small Molecules Targeting the Inactive Form of the Mnk1/2 Kinases
inferred← citeshttps://doi.org/10.1021/ct5005017openalex-snapshot
Problems of Robustness in Poisson–Boltzmann Binding Free Energies
inferred← citeshttps://doi.org/10.1038/s41597-022-01631-9openalex-snapshot
PLAS-5k: Dataset of Protein-Ligand Affinities from Molecular Dynamics for Machine Learning Applications
inferred← citeshttps://doi.org/10.1038/s41598-019-41758-1openalex-snapshot
Application of ESMACS binding free energy protocols to diverse datasets: Bromodomain-containing protein 4
inferred← citeshttps://doi.org/10.1039/c6mb00139dopenalex-snapshot
Interactions of omeprazole-based analogues with cytochrome P450 2C19: a computational study
inferred← citeshttps://doi.org/10.1039/c7cp08241jopenalex-snapshot
Importance of protein flexibility in molecular recognition: a case study on Type-I1/2 inhibitors of ALK
inferred← citeshttps://doi.org/10.1039/d2cp03705jopenalex-snapshot
BRD4: quantum mechanical protein–ligand binding free energies using the full-protein DFT-based QM-PBSA method
inferred← citeshttps://doi.org/10.1080/07391102.2023.2229449openalex-snapshot
Building polarization into protein-inhibitor binding dynamics in rational drug design for rheumatoid arthritis
inferred← citeshttps://doi.org/10.1080/17460441.2021.1942836openalex-snapshot
What is the current value of MM/PBSA and MM/GBSA methods in drug discovery?
inferred← citeshttps://doi.org/10.1111/cbdd.13347openalex-snapshot
An attempt to incorporate effect of direct interaction between a ligand and explicit water molecules into MM /3D‐ RISM
inferred← citeshttps://doi.org/10.1111/cbdd.13733openalex-snapshot
The effect of multiple simulation parameters on MM/PBSA performance for binding affinity prediction of CB1 cannabinoid receptor agonists and antagonists
inferred← citeshttps://doi.org/10.1142/s0219633619500081openalex-snapshot
Characterizing the interaction modes of PAR4 receptor with agonist and antagonist by molecular simulation approach
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1004693openalex-snapshot
Molecular Mechanisms of Glutamine Synthetase Mutations that Lead to Clinically Relevant Pathologies
inferred← citeshttps://doi.org/10.3389/fchem.2018.00043openalex-snapshot
An Efficient Implementation of the Nwat-MMGBSA Method to Rescore Docking Results in Medium-Throughput Virtual Screenings
inferred← citeshttps://doi.org/10.3389/fmolb.2017.00087openalex-snapshot
Recent Developments and Applications of the MMPBSA Method
inferred← citeshttps://doi.org/10.3390/ijms160714786openalex-snapshot
Characterization of the Interaction between Gallic Acid and Lysozyme by Molecular Dynamics Simulation and Optical Spectroscopy
inferred← citeshttps://doi.org/10.3390/ijms22179354openalex-snapshot
Design and Characterization of a Cell-Penetrating Peptide Derived from the SOX2 Transcription Factor
Editorial review for independent work. ICSAC — the Institute for Complexity
Science and Advanced Computing — runs a structured editorial panel for researchers
publishing outside journals, and publishes on CiteStamp rails. Submission is free
and goes through ORCID: icsacinstitute.org/submit.