On the public citation graph
Investigation on the Effect of Key Water Molecules on Docking Performance in CSARdock Exercise
0 signed · 107 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known work and none has been retracted — and get a dated CiteStamped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/(sici)1097-0134(19991001)37:1<88::aid-prot9>3.0.co;2-oopenalex-snapshot
Exhaustive docking of molecular fragments with electrostatic solvation
inferredcites →https://doi.org/10.1002/anie.200200539openalex-snapshot
Application and Limitations of X‐ray Crystallographic Data in Structure‐Based Ligand and Drug Design
inferredcites →https://doi.org/10.1002/cmdc.201000533openalex-snapshot
Contribution of Explicit Solvent Effects to the Binding Affinity of Small‐Molecule Inhibitors in Blood Coagulation Factor Serine Proteases
inferredcites →https://doi.org/10.1002/jcc.10074openalex-snapshot
Extracting hydration sites around proteins from explicit water simulations
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.1032openalex-snapshot
A smooth permittivity function for Poisson–Boltzmann solvation methods
inferredcites →https://doi.org/10.1002/jcc.21334openalex-snapshot
AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
inferredcites →https://doi.org/10.1002/jcc.21775openalex-snapshot
Role of bridging water molecules in GSK3β‐inhibitor complexes: Insights from QM/MM, MD, and molecular docking studies
inferredcites →https://doi.org/10.1002/jmr.1077openalex-snapshot
Challenges and advances in computational docking: 2009 in review
inferredcites →https://doi.org/10.1002/pro.192openalex-snapshot
Blind docking of pharmaceutically relevant compounds using RosettaLigand
inferredcites →https://doi.org/10.1002/prot.21086openalex-snapshot
ROSETTALIGAND: Protein–small molecule docking with full side‐chain flexibility
inferredcites →https://doi.org/10.1002/prot.21311openalex-snapshot
Locating missing water molecules in protein cavities by the three‐dimensional reference interaction site model theory of molecular solvation
inferredcites →https://doi.org/10.1002/prot.23244openalex-snapshot
Thermodynamic analysis of water molecules at the surface of proteins and applications to binding site prediction and characterization
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/10.1016/j.bmc.2007.01.012openalex-snapshot
Discovery of 1,4-dihydroindeno[1,2-c]pyrazoles as a novel class of potent and selective checkpoint kinase 1 inhibitors
inferredcites →https://doi.org/10.1016/j.chembiol.2010.11.011openalex-snapshot
Species-Specific and Inhibitor-Dependent Conformations of LpxC: Implications for Antibiotic Design
inferredcites →https://doi.org/10.1016/j.jmb.2008.11.010openalex-snapshot
RosettaLigand Docking with Full Ligand and Receptor Flexibility
inferredcites →https://doi.org/10.1016/j.jmb.2012.01.054openalex-snapshot
Impact of Ligand and Protein Desolvation on Ligand Binding to the S1 Pocket of Thrombin
inferredcites →https://doi.org/10.1021/ci100510mopenalex-snapshot
Molecular Docking with Ligand Attached Water Molecules
inferredcites →https://doi.org/10.1021/ci6003527openalex-snapshot
Analysis of Ligand-Bound Water Molecules in High-Resolution Crystal Structures of Protein−Ligand Complexes
inferredcites →https://doi.org/10.1021/ci700285eopenalex-snapshot
Ligand−Protein Docking with Water Molecules
inferredcites →https://doi.org/10.1021/ci8004176openalex-snapshot
Docking Ligands into Flexible and Solvated Macromolecules. 3. Impact of Input Ligand Conformation, Protein Flexibility, and Water Molecules on the Accuracy of Docking Programs
inferredcites →https://doi.org/10.1021/ci900293eopenalex-snapshot
Role of Water in Molecular Docking Simulations of Cytochrome P450 2D6
inferredcites →https://doi.org/10.1021/ci900345hopenalex-snapshot
Ligand−Protein Cross-Docking with Water Molecules
inferredcites →https://doi.org/10.1021/j100058a043openalex-snapshot
Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models
inferredcites →https://doi.org/10.1021/j100161a002openalex-snapshot
Continuum based calculations of hydration entropies and the hydrophobic effect
inferredcites →https://doi.org/10.1021/j100349a053openalex-snapshot
Calculation of the thermodynamic properties of aqueous electrolytes to 1000.degree.C and 5000 bar from a semicontinuum model for ion hydration
inferredcites →https://doi.org/10.1021/ja00172a038openalex-snapshot
Semianalytical treatment of solvation for molecular mechanics and dynamics
inferredcites →https://doi.org/10.1021/ja004315qopenalex-snapshot
Involvement of Water in Carbohydrate−Protein Binding
inferredcites →https://doi.org/10.1021/ja905029topenalex-snapshot
Ligand Mapping on Protein Surfaces by the 3D-RISM Theory: Toward Computational Fragment-Based Drug Design
inferredcites →https://doi.org/10.1021/ja984102popenalex-snapshot
Inclusion of Solvation in Ligand Binding Free Energy Calculations Using the Generalized-Born Model
inferredcites →https://doi.org/10.1021/jm000206aopenalex-snapshot
4-Anilino-6,7-dialkoxyquinoline-3-carbonitrile Inhibitors of Epidermal Growth Factor Receptor Kinase and Their Bioisosteric Relationship to the 4-Anilino-6,7-dialkoxyquinazoline Inhibitors
inferredcites →https://doi.org/10.1021/jm00053a018openalex-snapshot
Further development of hydrogen bond functions for use in determining energetically favorable binding sites on molecules of known structure. 1. Ligand probe groups with the ability to form two hydrogen bonds
inferredcites →https://doi.org/10.1021/jm00145a002openalex-snapshot
A computational procedure for determining energetically favorable binding sites on biologically important macromolecules
inferredcites →https://doi.org/10.1021/jm0300072openalex-snapshot
Identification of Novel Binding Interactions in the Development of Potent, Selective 2-Naphthamidine Inhibitors of Urokinase. Synthesis, Structural Analysis, and SAR of N -Phenyl Amide 6-Substitution
inferredcites →https://doi.org/10.1021/jm049650uopenalex-snapshot
Binding Mode Prediction of Cytochrome P450 and Thymidine Kinase Protein−Ligand Complexes by Consideration of Water and Rescoring in Automated Docking
inferredcites →https://doi.org/10.1021/jm051197eopenalex-snapshot
MolDock: A New Technique for High-Accuracy Molecular Docking
inferredcites →https://doi.org/10.1021/jm061277yopenalex-snapshot
Diverse, High-Quality Test Set for the Validation of Protein−Ligand Docking Performance
inferredcites →https://doi.org/10.1021/jm2005145openalex-snapshot
A Force Field with Discrete Displaceable Waters and Desolvation Entropy for Hydrated Ligand Docking
inferredcites →https://doi.org/10.1021/jm8006239openalex-snapshot
Exploiting Ordered Waters in Molecular Docking
inferredcites →https://doi.org/10.1021/jm900630qopenalex-snapshot
Structure-Guided Design of Potent and Selective Pyrimidylpyrrole Inhibitors of Extracellular Signal-Regulated Kinase (ERK) Using Conformational Control
inferredcites →https://doi.org/10.1021/jp9047456openalex-snapshot
Prediction of the Water Content in Protein Binding Sites
inferredcites →https://doi.org/10.1021/ml100008sopenalex-snapshot
Hydration Site Thermodynamics Explain SARs for Triazolylpurines Analogues Binding to the A2A Receptor
inferredcites →https://doi.org/10.1073/pnas.1114107108openalex-snapshot
Mechanism of the hydrophobic effect in the biomolecular recognition of arylsulfonamides by carbonic anhydrase
inferredcites →https://doi.org/10.1073/pnas.96.1.103openalex-snapshot
Disordered water within a hydrophobic protein cavity visualized by x-ray crystallography
inferredcites →https://doi.org/10.1107/s0907444998012086openalex-snapshot
How many water molecules can be detected by protein crystallography?
inferredcites →https://doi.org/10.1126/science.8278812openalex-snapshot
Rational Design of Potent, Bioavailable, Nonpeptide Cyclic Ureas as HIV Protease Inhibitors
inferredcites →https://doi.org/10.1186/1471-2105-12-77openalex-snapshot
pROC: an open-source package for R and S+ to analyze and compare ROC curves
inferredcites →https://doi.org/10.1371/journal.pone.0032036openalex-snapshot
Rapid and Accurate Prediction and Scoring of Water Molecules in Protein Binding Sites
inferredcites →https://doi.org/10.1517/17460441.2011.534452openalex-snapshot
Accounting for water molecules in drug design
inferredcites →https://doi.org/10.2174/156802610790232288openalex-snapshot
The Role of Water Molecules in Computational Drug Design
inferredcites →https://doi.org/10.2174/157340911795677602openalex-snapshot
Molecular Docking: A Powerful Approach for Structure-Based Drug Discovery
inferredcites →https://doi.org/10.32614/r.manualsopenalex-snapshot
R: A Language and Environment for Statistical Computing
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1002/jmr.2471openalex-snapshot
Improvements, trends, and new ideas in molecular docking: 2012–2013 in review
inferred← citeshttps://doi.org/10.1002/prot.24530openalex-snapshot
Incorporating replacement free energy of binding-site waters in molecular docking
inferred← citeshttps://doi.org/10.1002/qua.25644openalex-snapshot
Does the presence of water clusters induce the binding affinity of CK2 halogen ligands?: A quantum chemical perspective study
inferred← citeshttps://doi.org/10.1007/7355_2016_24openalex-snapshot
Integration on Ligand and Structure Based Approaches in GPCRs
inferred← citeshttps://doi.org/10.1007/s00894-015-2834-7openalex-snapshot
Improving protein-ligand docking with flexible interfacial water molecules using SWRosettaLigand
inferred← citeshttps://doi.org/10.1007/s10822-015-9834-7openalex-snapshot
Covalent docking of selected boron-based serine beta-lactamase inhibitors
inferred← citeshttps://doi.org/10.1007/s10822-016-9931-2openalex-snapshot
Prospective evaluation of shape similarity based pose prediction method in D3R Grand Challenge 2015
inferred← citeshttps://doi.org/10.1007/s10822-019-00239-3openalex-snapshot
The role of hydration effects in 5-fluorouridine binding to SOD1: insight from a new 3D-RISM-KH based protocol for including structural water in docking simulations
inferred← citeshttps://doi.org/10.1007/s11356-018-3048-1openalex-snapshot
Interaction of metals from group 10 (Ni, Pd, and Pt) and 11 (Cu, Ag, and Au) with human blood δ-ALA-D: in vitro and in silico studies
inferred← citeshttps://doi.org/10.1007/s12539-019-00327-wopenalex-snapshot
An Overview of Scoring Functions Used for Protein–Ligand Interactions in Molecular Docking
inferred← citeshttps://doi.org/10.1007/s13721-020-0219-zopenalex-snapshot
Targeting galectin-3 by natural glycosides: a computational approach
inferred← citeshttps://doi.org/10.1016/b978-0-12-409547-2.12352-2openalex-snapshot
Molecular Docking—A Solved Problem?
inferred← citeshttps://doi.org/10.1016/b978-0-323-90608-1.00005-8openalex-snapshot
Fundamental considerations in drug design
inferred← citeshttps://doi.org/10.1016/b978-0-323-90608-1.00006-xopenalex-snapshot
Limitations and future challenges of computer-aided drug design methods
inferred← citeshttps://doi.org/10.1016/b978-0-443-29808-0.00016-9openalex-snapshot
Molecular docking—A solved problem?
inferred← citeshttps://doi.org/10.1016/b978-0-443-30042-4.00015-8openalex-snapshot
Conserved waters in protein structure and function with applications to drug design
inferred← citeshttps://doi.org/10.1016/bs.apha.2025.02.004openalex-snapshot
Molecular and structure-based drug design: From theory to practice
inferred← citeshttps://doi.org/10.1016/j.cbi.2015.02.006openalex-snapshot
Effects of tanshinones from Salvia miltiorrhiza on CYP2C19 activity in human liver microsomes: Enzyme kinetic and molecular docking studies
inferred← citeshttps://doi.org/10.1016/j.cclet.2018.06.003openalex-snapshot
Selective recognition of HIV RNA by dinuclear metallic ligands
inferred← citeshttps://doi.org/10.1016/j.ejmech.2015.11.045openalex-snapshot
Modification of the anabaseine pyridine nucleus allows achieving binding and functional selectivity for the α3β4 nicotinic acetylcholine receptor subtype
inferred← citeshttps://doi.org/10.1016/j.jmgm.2019.107510openalex-snapshot
A computational study on the role of water and conformational fluctuations in Hsp90 in response to inhibitors
inferred← citeshttps://doi.org/10.1021/acs.chemrev.4c00807openalex-snapshot
A Computational Perspective to Intermolecular Interactions and the Role of the Solvent on Regulating Protein Properties
inferred← citeshttps://doi.org/10.1021/acs.jcim.0c00542openalex-snapshot
Guiding Conventional Protein–Ligand Docking Software with Convolutional Neural Networks
inferred← citeshttps://doi.org/10.1021/acs.jcim.2c00127openalex-snapshot
Predicting Protein–Ligand Docking Structure with Graph Neural Network
inferred← citeshttps://doi.org/10.1021/acs.jcim.5c02352openalex-snapshot
Solvent-Site Prediction for Fragment Docking and Its Implication on Fragment-Based Drug Discovery
inferred← citeshttps://doi.org/10.1021/acs.jcim.6c00498openalex-snapshot
Comparative Evaluation of Explicit Solvent Models for RNA-Ligand Docking
inferred← citeshttps://doi.org/10.1021/acs.jpcb.6b00789openalex-snapshot
Relative Binding Affinities of Monolignols to Horseradish Peroxidase
inferred← citeshttps://doi.org/10.1021/acschemneuro.0c00407openalex-snapshot
Comparison of Pharmacological Properties between the Kappa Opioid Receptor Agonist Nalfurafine and 42B, Its 3-Dehydroxy Analogue: Disconnect between in Vitro Agonist Bias and in Vivo Pharmacological Effects
inferred← citeshttps://doi.org/10.1021/ci400367mopenalex-snapshot
Accounting for Target Flexibility and Water Molecules by Docking to Ensembles of Target Structures: The HCV NS5B Palm Site I Inhibitors Case Study
inferred← citeshttps://doi.org/10.1021/ci500520qopenalex-snapshot
Role of Water in Ligand Binding to Maltose-Binding Protein: Insight from a New Docking Protocol Based on the 3D-RISM-KH Molecular Theory of Solvation
inferred← citeshttps://doi.org/10.1021/cr5000283openalex-snapshot
Solvation Thermodynamics of Organic Molecules by the Molecular Integral Equation Theory: Approaching Chemical Accuracy
inferred← citeshttps://doi.org/10.1021/jacs.5b07940openalex-snapshot
Water Sites, Networks, And Free Energies with Grand Canonical Monte Carlo
inferred← citeshttps://doi.org/10.1039/c9cc07714fopenalex-snapshot
Water envelope has a critical impact on the design of protein–protein interaction inhibitors
inferred← citeshttps://doi.org/10.1142/s0219633619500275openalex-snapshot
Improving protein–ligand binding prediction by considering the bridging water molecules in Autodock
inferred← citeshttps://doi.org/10.1186/s42826-024-00225-3openalex-snapshot
Cleistopholis patens root bark extract exerts cardioprotective effect against doxorubicin-induced myocardial toxicity in rats
inferred← citeshttps://doi.org/10.12691/ajmo-3-3-2openalex-snapshot
How Important is to Account for Water When Modeling Biomolecular Complexes
inferred← citeshttps://doi.org/10.1371/journal.pone.0239364openalex-snapshot
Alkaloids of Abuta panurensis Eichler: In silico and in vitro study of acetylcholinesterase inhibition, cytotoxic and immunomodulatory activities
inferred← citeshttps://doi.org/10.1371/journal.pone.0268269openalex-snapshot
Molecular docking, simulation and binding free energy analysis of small molecules as PfHT1 inhibitors
inferred← citeshttps://doi.org/10.15476/elte.2016.194openalex-snapshot
Calculation of hydration structures of proteins and their complexes
inferred← citeshttps://doi.org/10.21323/2618-9771-2023-6-3-365-389openalex-snapshot
Network pharmacology and molecular docking study to reveal the potential anticancer activity of Oscillatoxin D, E, and F marine cytotoxins
inferred← citeshttps://doi.org/10.2147/dddt.s575242openalex-snapshot
Structure-Based Discovery of Glyoxalase-I Inhibitors: Evaluating the Role of Active Site Water Molecules
inferred← citeshttps://doi.org/10.22201/fesz.23958723e.2018.0.143openalex-snapshot
Acoplamiento Molecular: Avances Recientes y Retos
inferred← citeshttps://doi.org/10.26434/chemrxiv-2023-jh1kkopenalex-snapshot
A new protein-ligand docking software with an improved method of molecular conformation optimization
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/10.3390/ijms232213946openalex-snapshot
Identification of Active Compounds against Melanoma Growth by Virtual Screening for Non-Classical Human DHFR Inhibitors
inferred← citeshttps://doi.org/10.3390/ijms241411784openalex-snapshot
The Advances and Limitations of the Determination and Applications of Water Structure in Molecular Engineering
inferred← citeshttps://doi.org/10.3390/molecules21111604openalex-snapshot
AutoDock-GIST: Incorporating Thermodynamics of Active-Site Water into Scoring Function for Accurate Protein-Ligand Docking
inferred← citeshttps://doi.org/10.3390/molecules27144568openalex-snapshot
Protein–Ligand Docking in the Machine-Learning Era
inferred← citeshttps://doi.org/10.3390/molecules28124814openalex-snapshot
Structure-Based Design of Novel MAO-B Inhibitors: A Review
inferred← citeshttps://doi.org/10.3390/ph16121639openalex-snapshot
A Review on Molecular Docking on HDAC Isoforms: Novel Tool for Designing Selective Inhibitors
inferred← citeshttps://doi.org/10.4018/978-1-5225-0362-0.ch003openalex-snapshot
Molecular Docking Challenges and Limitations
inferred← citeshttps://doi.org/10.4018/978-1-5225-1762-7.ch030openalex-snapshot
Molecular Docking Challenges and Limitations
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.