On the public citation graph
Molecular Recognition in a Diverse Set of Protein–Ligand Interactions Studied with Molecular Dynamics Simulations and End-Point Free Energy Calculations
0 signed · 83 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known work and none has been retracted — and get a dated CiteStamped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.10128openalex-snapshot
Fast, efficient generation of high‐quality atomic charges. AM1‐BCC model: II. Parameterization and validation
inferredcites →https://doi.org/10.1002/jcc.10349openalex-snapshot
A point‐charge force field for molecular mechanics simulations of proteins based on condensed‐phase quantum mechanical calculations
inferredcites →https://doi.org/10.1002/pro.5560070122openalex-snapshot
Computation of electrostatic complements to proteins: A case of charge stabilized binding
inferredcites →https://doi.org/10.1002/prot.20033openalex-snapshot
Exploring protein native states and large‐scale conformational changes with a modified generalized born model
inferredcites →https://doi.org/10.1002/prot.22761openalex-snapshot
Impact of calcium on N1 influenza neuraminidase dynamics and binding free energy
inferredcites →https://doi.org/10.1002/prot.340200108openalex-snapshot
Estimation of changes in side chain configurational entropy in binding and folding: General methods and application to helix formation
inferredcites →https://doi.org/10.1006/jmbi.1998.2401openalex-snapshot
Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation 1 1Edited by J. Thornton
inferredcites →https://doi.org/10.1006/jmbi.1999.3371openalex-snapshot
Knowledge-based scoring function to predict protein-ligand interactions
inferredcites →https://doi.org/10.1007/s10822-008-9196-5openalex-snapshot
Recommendations for evaluation of computational methods
inferredcites →https://doi.org/10.1007/s10822-012-9542-5openalex-snapshot
Thermodynamic integration to predict host-guest binding affinities
inferredcites →https://doi.org/10.1016/0021-9991(77)90098-5openalex-snapshot
Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes
inferredcites →https://doi.org/10.1016/j.bmc.2012.04.019openalex-snapshot
Free energy calculations on the binding of novel thiolactomycin derivatives to E. coli fatty acid synthase I
inferredcites →https://doi.org/10.1016/j.str.2006.01.014openalex-snapshot
Flexibility and Conformational Entropy in Protein-Protein Binding
inferredcites →https://doi.org/10.1016/s0065-3233(03)66002-xopenalex-snapshot
Force Fields for Protein Simulations
inferredcites →https://doi.org/10.1021/bi8017043openalex-snapshot
Exploring the Molecular Design of Protein Interaction Sites with Molecular Dynamics Simulations and Free Energy Calculations
inferredcites →https://doi.org/10.1021/ci100490wopenalex-snapshot
Target-Specific Support Vector Machine Scoring in Structure-Based Virtual Screening: Computational Validation, In Vitro Testing in Kinases, and Effects on Lung Cancer Cell Proliferation
inferredcites →https://doi.org/10.1021/ci200078fopenalex-snapshot
Support Vector Regression Scoring of Receptor–Ligand Complexes for Rank-Ordering and Virtual Screening of Chemical Libraries
inferredcites →https://doi.org/10.1021/ci200191mopenalex-snapshot
Solvent Interaction Energy Calculations on Molecular Dynamics Trajectories: Increasing the Efficiency Using Systematic Frame Selection
inferredcites →https://doi.org/10.1021/ci3001277openalex-snapshot
ZINC: A Free Tool to Discover Chemistry for Biology
inferredcites →https://doi.org/10.1021/ct200750popenalex-snapshot
Efficient and Accurate Free Energy Calculations on Trypsin Inhibitors
inferredcites →https://doi.org/10.1021/j100058a043openalex-snapshot
Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models
inferredcites →https://doi.org/10.1021/ja00172a038openalex-snapshot
Semianalytical treatment of solvation for molecular mechanics and dynamics
inferredcites →https://doi.org/10.1021/ja003164oopenalex-snapshot
An Analysis of the Interactions between the Sem−5 SH3 Domain and Its Ligands Using Molecular Dynamics, Free Energy Calculations, and Sequence Analysis
inferredcites →https://doi.org/10.1021/ja003834qopenalex-snapshot
Use of MM-PBSA in Reproducing the Binding Free Energies to HIV-1 RT of TIBO Derivatives and Predicting the Binding Mode to HIV-1 RT of Efavirenz by Docking and MM-PBSA
inferredcites →https://doi.org/10.1021/ja060830yopenalex-snapshot
Thermodynamic Basis for Promiscuity and Selectivity in Protein−Protein Interactions: PDZ Domains, a Case Study
inferredcites →https://doi.org/10.1021/ja981844+openalex-snapshot
Continuum Solvent Studies of the Stability of DNA, RNA, and Phosphoramidate−DNA Helices
inferredcites →https://doi.org/10.1021/jm001045dopenalex-snapshot
Simulations of the Estrogen Receptor Ligand-Binding Domain: Affinity of Natural Ligands and Xenoestrogens
inferredcites →https://doi.org/10.1021/jp063479bopenalex-snapshot
How Well Does Poisson−Boltzmann Implicit Solvent Agree with Explicit Solvent? A Quantitative Analysis
inferredcites →https://doi.org/10.1021/jp994072sopenalex-snapshot
Modification of the Generalized Born Model Suitable for Macromolecules
inferredcites →https://doi.org/10.1021/ma50003a019openalex-snapshot
Method for estimating the configurational entropy of macromolecules
inferredcites →https://doi.org/10.1021/ml100031aopenalex-snapshot
Docking to Erlotinib Off-Targets Leads to Inhibitors of Lung Cancer Cell Proliferation with Suitable in Vitro Pharmacokinetics
inferredcites →https://doi.org/10.1023/a:1008763014207openalex-snapshot
Combined molecular mechanical and continuum solvent approach (MM-PBSA/GBSA) to predict ligand binding
inferredcites →https://doi.org/10.1063/1.445869openalex-snapshot
Comparison of simple potential functions for simulating liquid water
inferredcites →https://doi.org/10.1074/jbc.m313143200openalex-snapshot
The Importance of a Critical Protonation State and the Fate of the Catalytic Steps in Class A β-Lactamases and Penicillin-binding Proteins
inferredcites →https://doi.org/10.1093/protein/gzp042openalex-snapshot
Incorporating receptor flexibility in the molecular design of protein interfaces
inferredcites →https://doi.org/10.1098/rsta.2005.1627openalex-snapshot
Peptide recognition by the T cell receptor: comparison of binding free energies from thermodynamic integration, Poisson–Boltzmann and linear interaction energy approximations
inferredcites →https://doi.org/10.1107/s0021889883010985openalex-snapshot
Analytical molecular surface calculation
inferredcites →https://doi.org/10.1111/j.1747-0285.2008.00661.xopenalex-snapshot
PDBcal: A Comprehensive Dataset for Receptor–Ligand Interactions with Three‐dimensional Structures and Binding Thermodynamics from Isothermal Titration Calorimetry
inferredcites →https://doi.org/10.1126/science.7761829openalex-snapshot
Classical Electrostatics in Biology and Chemistry
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1002/asia.202400064openalex-snapshot
Synthesis of R–GABA Derivatives via Pd(II) Catalyzed Enantioselective C(sp3)−H Arylation and Virtual Validation with GABAB1 Receptor for Potential leads
inferred← citeshttps://doi.org/10.1002/cmdc.201600636openalex-snapshot
Structure‐Based Target‐Specific Screening Leads to Small‐Molecule CaMKII Inhibitors
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/10.1007/978-981-99-9462-5_19openalex-snapshot
The Potential of Systems Biology to Understand the Tenets of Host-pathogen Interaction, Toxicology, and Aging
inferred← citeshttps://doi.org/10.1007/s10822-026-00865-8openalex-snapshot
Integrated structure-based and fragment-guided design of isonicotinic acid derivatives as potential KDM4A inhibitors: an in silico study
inferred← citeshttps://doi.org/10.1007/s11172-018-2117-4openalex-snapshot
Effect of the hyaluronidase microe nvironment on the enzyme structure–function relationship and computational study of the in silico molecular docking of chondroitin sulfate and heparin short fragments to hyaluronidase
inferred← citeshttps://doi.org/10.1016/j.bbrc.2024.151003openalex-snapshot
Biophysical characterization and structural insights of leptospiral complement regulator-acquiring protein A
inferred← citeshttps://doi.org/10.1016/j.bpj.2014.11.3461openalex-snapshot
Effects of HCM cTnI Mutation R145G on Troponin Structure and Modulation by PKA Phosphorylation Elucidated by Molecular Dynamics Simulations
inferred← citeshttps://doi.org/10.1016/j.comtox.2021.100156openalex-snapshot
From genomes to molecular dynamics – A bottom up approach in extrication of SARS CoV-2 main protease inhibitors
inferred← citeshttps://doi.org/10.1016/j.csbj.2021.06.034openalex-snapshot
Structure-based in silico approaches for drug discovery against Mycobacterium tuberculosis
inferred← citeshttps://doi.org/10.1016/j.drudis.2018.11.005openalex-snapshot
Pharmacophore-based models for therapeutic drugs against phosphorylated tau in Alzheimer’s disease
inferred← citeshttps://doi.org/10.1016/j.jmgm.2015.01.005openalex-snapshot
Molecular recognition of avirulence protein (avrxa5) by eukaryotic transcription factor xa5 of rice (Oryza sativa L.): Insights from molecular dynamics simulations
inferred← citeshttps://doi.org/10.1016/j.pestbp.2017.09.009openalex-snapshot
The R81T mutation in the nicotinic acetylcholine receptor of Aphis gossypii is associated with neonicotinoid insecticide resistance with differential effects for cyano- and nitro-substituted neonicotinoids
inferred← citeshttps://doi.org/10.1016/j.prp.2023.154924openalex-snapshot
Exploring the anticancer properties of a new nicotinamide analogue: Investigations into in silico analysis, antiproliferative effects, selectivity, VEGFR-2 inhibition, apoptosis induction, and migration suppression
inferred← citeshttps://doi.org/10.1021/acs.biochem.7b00903openalex-snapshot
Effect of the Flexible Regions of the Oncoprotein Mouse Double Minute X on Inhibitor Binding Affinity
inferred← citeshttps://doi.org/10.1021/acs.chemrev.9b00055openalex-snapshot
End-Point Binding Free Energy Calculation with MM/PBSA and MM/GBSA: Strategies and Applications in Drug Design
inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00467openalex-snapshot
Interpreting Thermodynamic Profiles of Aminoadamantane Compounds Inhibiting the M2 Proton Channel of Influenza A by Free Energy Calculations
inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00709openalex-snapshot
Effect of Binding Pose and Modeled Structures on SVMGen and GlideScore Enrichment of Chemical Libraries
inferred← citeshttps://doi.org/10.1021/acs.jcim.6b00398openalex-snapshot
The Effect of Conformational Flexibility on Binding Free Energy Estimation between Kinases and Their Inhibitors
inferred← citeshttps://doi.org/10.1021/acs.jctc.2c00114openalex-snapshot
Alchemical Free Energy Estimators and Molecular Dynamics Engines: Accuracy, Precision, and Reproducibility
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.6b00979openalex-snapshot
Rapid, Accurate, Precise, and Reliable Relative Free Energy Prediction Using Ensemble Based Thermodynamic Integration
inferred← citeshttps://doi.org/10.1021/acs.jctc.7b01143openalex-snapshot
Uncertainty Quantification in Alchemical Free Energy Methods
inferred← citeshttps://doi.org/10.1021/acsomega.0c00617openalex-snapshot
Insights into the Inhibition Mechanism of Human Pancreatic α-Amylase, a Type 2 Diabetes Target, by Dehydrodieugenol B Isolated from Ocimum tenuiflorum
inferred← citeshttps://doi.org/10.1021/cb500832qopenalex-snapshot
A New Class of Orthosteric uPAR·uPA Small-Molecule Antagonists Are Allosteric Inhibitors of the uPAR·Vitronectin Interaction
inferred← citeshttps://doi.org/10.1021/ci5002026openalex-snapshot
Enrichment of Chemical Libraries Docked to Protein Conformational Ensembles and Application to Aldehyde Dehydrogenase 2
inferred← citeshttps://doi.org/10.1038/s41598-021-92785-wopenalex-snapshot
The effect of protein mutations on drug binding suggests ensuing personalised drug selection
inferred← citeshttps://doi.org/10.1039/c6sc04504aopenalex-snapshot
Metal-free O–H/C–H difunctionalization of phenols by o-hydroxyarylsulfonium salts in water
inferred← citeshttps://doi.org/10.1039/c9ra08284kopenalex-snapshot
Calculating the absolute binding free energy of the insulin dimer in an explicit solvent
inferred← citeshttps://doi.org/10.1039/d2cp00464jopenalex-snapshot
Comparative assessment of QM-based and MM-based models for prediction of protein–ligand binding affinity trends
inferred← citeshttps://doi.org/10.1063/1.4938261openalex-snapshot
Binding of ACE-inhibitors to in vitro and patient-derived amyloid-β fibril models
inferred← citeshttps://doi.org/10.1080/07391102.2020.1778530openalex-snapshot
Structure-based identification of natural compound inhibitor against M. tuberculosis thioredoxin reductase: insight from molecular docking and dynamics simulation
inferred← citeshttps://doi.org/10.1080/08927022.2022.2123917openalex-snapshot
Identification of Novel GTP Analogs as Potent and Specific Reversible Inhibitors for Transglutaminase 2
inferred← citeshttps://doi.org/10.1093/jisesa/iew008openalex-snapshot
Virtual Screening of Plant Volatile Compounds Reveals a High Affinity ofHylamorpha elegans(Coleoptera: Scarabaeidae) Odorant-Binding Proteins for Sesquiterpenes From Its Native Host
inferred← citeshttps://doi.org/10.1111/cbdd.13987openalex-snapshot
In silico design, chemical synthesis and biological screening of novel 4‐(1 H )‐pyridone‐based antimalarial agents
inferred← citeshttps://doi.org/10.1134/s1068162018020048openalex-snapshot
Conformational Transitions in 3D Model of Bovine Testicular Hyaluronidase during Molecular Docking with Glycosaminoglycan Ligands
inferred← citeshttps://doi.org/10.1186/s12915-023-01791-zopenalex-snapshot
From byte to bench to bedside: molecular dynamics simulations and drug discovery
inferred← citeshttps://doi.org/10.1371/journal.pone.0144635openalex-snapshot
Molecular Dynamics Assisted Mechanistic Study of Isoniazid-Resistance against Mycobacterium tuberculosis InhA
inferred← citeshttps://doi.org/10.1371/journal.pone.0154219openalex-snapshot
The Dynamics of the Human Leukocyte Antigen Head Domain Modulates Its Recognition by the T-Cell Receptor
inferred← citeshttps://doi.org/10.2174/0109298673354901250402143533openalex-snapshot
Boswellic Acid Derived Molecules as SARS-Cov-2 Spike Protein Inhibitors: A Comprehensive Virtual Screening, Triplicate Molecular Dynamic Simulation and Biochemical Validation
inferred← citeshttps://doi.org/10.29011/2639-4685.100011openalex-snapshot
Molecular Docking of Short-Chain Glycosaminoglycan Ligands in 3D Model of Bovine Testicular Hyaluronidase
inferred← citeshttps://doi.org/10.3103/s0027131418050073openalex-snapshot
Electrostatic Interactions in Docking a 3D Model of Bovine Testicular Hyaluronidase with a Chondroitin Sulfate Trimer and a Heparin Tetramer
inferred← citeshttps://doi.org/10.3389/fmolb.2016.00046openalex-snapshot
dMM-PBSA: A New HADDOCK Scoring Function for Protein-Peptide Docking
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.