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Ligand−Protein Docking with Water Molecules
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Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1002/(sici)1097-0134(199707)28:3<313::aid-prot2>3.0.co;2-dopenalex-snapshot
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inferredcites →https://doi.org/10.1002/(sici)1097-0134(19980501)31:2<201::aid-prot9>3.0.co;2-oopenalex-snapshot
Accessibility to internal cavities and ligand binding sites monitored by protein crystallographic thermal factors
inferredcites →https://doi.org/10.1002/(sici)1097-0134(19980815)32:3<381::aid-prot12>3.0.co;2-5openalex-snapshot
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inferredcites →https://doi.org/10.1002/(sici)1097-0134(19990101)34:1<17::aid-prot3>3.0.co;2-1openalex-snapshot
The particle concept: placing discrete water molecules during protein-ligand docking predictions
inferredcites →https://doi.org/10.1002/(sici)1097-0134(19990701)36:1<117::aid-prot10>3.0.co;2-hopenalex-snapshot
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inferredcites →https://doi.org/10.1002/1097-0134(20001201)41:4<545::aid-prot110>3.0.co;2-8openalex-snapshot
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inferredcites →https://doi.org/10.1002/anie.200200539openalex-snapshot
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inferredcites →https://doi.org/10.1002/jcc.10100openalex-snapshot
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inferredcites →https://doi.org/10.1002/jcc.20022openalex-snapshot
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inferredcites →https://doi.org/10.1002/pro.5560041004openalex-snapshot
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inferredcites →https://doi.org/10.1002/pro.5560071002openalex-snapshot
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inferredcites →https://doi.org/10.1002/prot.10028openalex-snapshot
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inferredcites →https://doi.org/10.1002/prot.20026openalex-snapshot
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inferredcites →https://doi.org/10.1002/prot.21014openalex-snapshot
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inferredcites →https://doi.org/10.1002/prot.340230103openalex-snapshot
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inferredcites →https://doi.org/10.1006/jmbi.1996.0746openalex-snapshot
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inferredcites →https://doi.org/10.1006/jmbi.1999.2795openalex-snapshot
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inferredcites →https://doi.org/10.1006/jmbi.1999.3101openalex-snapshot
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inferredcites →https://doi.org/10.1006/jmbi.1999.3180openalex-snapshot
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inferredcites →https://doi.org/10.1006/jmbi.1999.3195openalex-snapshot
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inferredcites →https://doi.org/10.1016/0022-2836(92)91054-sopenalex-snapshot
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inferredcites →https://doi.org/10.1016/0079-6107(84)90007-5openalex-snapshot
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inferredcites →https://doi.org/10.1016/1074-5521(95)90050-0openalex-snapshot
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inferredcites →https://doi.org/10.1016/1074-5521(95)90097-7openalex-snapshot
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inferredcites →https://doi.org/10.1016/j.bmc.2004.11.024openalex-snapshot
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inferredcites →https://doi.org/10.1016/j.cplett.2005.04.072openalex-snapshot
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inferredcites →https://doi.org/10.1016/j.jmb.2006.01.053openalex-snapshot
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inferredcites →https://doi.org/10.1016/s0006-3495(95)79955-6openalex-snapshot
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inferredcites →https://doi.org/10.1016/s0009-2614(02)01925-5openalex-snapshot
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inferredcites →https://doi.org/10.1016/s0021-9258(18)47079-2openalex-snapshot
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inferredcites →https://doi.org/10.1016/s0022-2836(02)00975-0openalex-snapshot
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inferredcites →https://doi.org/10.1016/s0022-2836(02)01408-0openalex-snapshot
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inferredcites →https://doi.org/10.1021/jm0306430openalex-snapshot
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inferredcites →https://doi.org/10.1093/protein/11.1.11openalex-snapshot
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inferredcites →https://doi.org/10.1093/protein/12.12.1021openalex-snapshot
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inferredcites →https://doi.org/10.1098/rsta.2001.0863openalex-snapshot
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inferredcites →https://doi.org/10.2174/0929867043363929openalex-snapshot
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What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1002/9783527633326.ch10openalex-snapshot
Consideration of Water and Solvation Effects in Virtual Screening
inferred← citeshttps://doi.org/10.1002/9783527645947.ch8openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/9783527840748.ch20openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/ange.200904410openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/anie.200904410openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/cbdv.202000290openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/chem.201102571openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/chem.201103369openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/chem.201405764openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/chin.200821218openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/fsn3.71878openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jcc.21775openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jcc.23108openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jcc.26965openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/minf.201000007openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/minf.201100086openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/slct.202303307openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/wcms.1544openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/wcms.18openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/7355_2014_42openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/s00894-015-2834-7openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/s10822-022-00452-7openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/s12272-015-0640-5openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/s12539-015-0126-7openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.abb.2015.05.011openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.bpj.2010.02.034openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.ddtec.2013.08.002openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.ejmech.2025.117846openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.febslet.2012.04.057openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.jmgm.2010.03.007openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.jmgm.2011.09.006openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.jmgm.2018.04.011openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.jmgm.2019.107510openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.molliq.2022.119393openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.ymeth.2014.10.019openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/acs.chemrev.4c00807openalex-snapshot
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Statistical Analysis, Investigation, and Prediction of the Water Positions in the Binding Sites of Proteins
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.jcim.7b00520openalex-snapshot
Prediction of Ordered Water Molecules in Protein Binding Sites from Molecular Dynamics Simulations: The Impact of Ligand Binding on Hydration Networks
inferred← citeshttps://doi.org/10.1021/acs.jcim.9b00645openalex-snapshot
Incorporating Explicit Water Molecules and Ligand Conformation Stability in Machine-Learning Scoring Functions
inferred← citeshttps://doi.org/10.1021/acs.jctc.5b00839openalex-snapshot
Prediction of Water Binding to Protein Hydration Sites with a Discrete, Semiexplicit Solvent Model
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.7b00057openalex-snapshot
The Roles of Water in the Protein Matrix: A Largely Untapped Resource for Drug Discovery
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/acsomega.4c00517openalex-snapshot
General Characterization of Properties of Ordered and Disordered Proteins by Wide-Line 1H NMR
inferred← citeshttps://doi.org/10.1021/ci100329zopenalex-snapshot
Quantum Mechanics/Molecular Mechanics Strategies for Docking Pose Refinement: Distinguishing between Binders and Decoys in CytochromecPeroxidase
inferred← citeshttps://doi.org/10.1021/ci100510mopenalex-snapshot
Molecular Docking with Ligand Attached Water Molecules
inferred← citeshttps://doi.org/10.1021/ci200150popenalex-snapshot
AcquaAlta: A Directional Approach to the Solvation of Ligand–Protein Complexes
inferred← citeshttps://doi.org/10.1021/ci400052wopenalex-snapshot
Investigation on the Effect of Key Water Molecules on Docking Performance in CSARdock Exercise
inferred← citeshttps://doi.org/10.1021/ci4003409openalex-snapshot
Combining Solvent Thermodynamic Profiles with Functionality Maps of the Hsp90 Binding Site to Predict the Displacement of Water Molecules
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/ci4006047openalex-snapshot
Flexibility and Explicit Solvent in Molecular-Dynamics-Based Docking of Protein–Glycosaminoglycan Systems
inferred← citeshttps://doi.org/10.1021/ci5000455openalex-snapshot
Selecting an Optimal Number of Binding Site Waters To Improve Virtual Screening Enrichments Against the Adenosine A2A Receptor
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/ci900293eopenalex-snapshot
Role of Water in Molecular Docking Simulations of Cytochrome P450 2D6
inferred← citeshttps://doi.org/10.1021/ci900345hopenalex-snapshot
Ligand−Protein Cross-Docking with Water Molecules
inferred← citeshttps://doi.org/10.1021/ci9004157openalex-snapshot
Accuracy Assessment of Protein-Based Docking Programs against RNA Targets
inferred← citeshttps://doi.org/10.1021/ja809696sopenalex-snapshot
Free Energies and Entropies of Water Molecules at the Inhibitor−Protein Interface of DNA Gyrase
inferred← citeshttps://doi.org/10.1021/jm2005145openalex-snapshot
A Force Field with Discrete Displaceable Waters and Desolvation Entropy for Hydrated Ligand Docking
inferred← citeshttps://doi.org/10.1021/jm8006239openalex-snapshot
Exploiting Ordered Waters in Molecular Docking
inferred← citeshttps://doi.org/10.1021/jm9010127openalex-snapshot
Discovery of a Novel Class of Potent Coumarin Monoamine Oxidase B Inhibitors: Development and Biopharmacological Profiling of 7-[(3-Chlorobenzyl)oxy]-4-[(methylamino)methyl]-2H-chromen-2-one Methanesulfonate (NW-1772) as a Highly Potent, Selective, Reversible, and Orally Active Monoamine Oxidase B…
inferred← citeshttps://doi.org/10.1021/jp2066106openalex-snapshot
Local Order and Mobility of Water Molecules around Ambivalent Helices
inferred← citeshttps://doi.org/10.1021/jp5053612openalex-snapshot
Docking and Free Energy Perturbation Studies of Ligand Binding in the Kappa Opioid Receptor
inferred← citeshttps://doi.org/10.1021/jp802795aopenalex-snapshot
Hydration Water and Bulk Water in Proteins Have Distinct Properties in Radial Distributions Calculated from 105 Atomic Resolution Crystal Structures
inferred← citeshttps://doi.org/10.1021/jp9047456openalex-snapshot
Prediction of the Water Content in Protein Binding Sites
inferred← citeshttps://doi.org/10.1038/s41598-018-33354-6openalex-snapshot
Identification of novel acetylcholinesterase inhibitors designed by pharmacophore-based virtual screening, molecular docking and bioassay
inferred← citeshttps://doi.org/10.1038/s41598-020-70369-4openalex-snapshot
Insights on small molecule binding to the Hv1 proton channel from free energy calculations with molecular dynamics simulations
inferred← citeshttps://doi.org/10.1038/s41598-022-25464-zopenalex-snapshot
A novel small molecule inhibitor of human Drp1
inferred← citeshttps://doi.org/10.1039/d0nj02537bopenalex-snapshot
Combinatorial library generation, molecular docking and molecular dynamics simulations for enhancing the isoflavone scaffold in phosphodiesterase inhibition
inferred← citeshttps://doi.org/10.1039/d2cp04584bopenalex-snapshot
Uncovering water effects in protein–ligand recognition: importance in the second hydration shell and binding kinetics
inferred← citeshttps://doi.org/10.1039/d3cp05687bopenalex-snapshot
Insight into the activation mechanism of carbonic anhydrase( ii ) through 2-(2-aminoethyl)-pyridine: a promising pathway for enhanced enzymatic activity
inferred← citeshttps://doi.org/10.1039/d5em00084jopenalex-snapshot
Molecular docking for screening chemicals of environmental health concern: insight from a case study on bisphenols
inferred← citeshttps://doi.org/10.1080/08927022.2012.696113openalex-snapshot
Docking and molecular dynamics studies of new potential inhibitors of the human epidermal receptor 2
inferred← citeshttps://doi.org/10.1080/17460441.2021.1929921openalex-snapshot
Computational representations of protein–ligand interfaces for structure-based virtual screening
inferred← citeshttps://doi.org/10.1093/bib/bbab474openalex-snapshot
A point cloud-based deep learning strategy for protein–ligand binding affinity prediction
inferred← citeshttps://doi.org/10.1093/bioinformatics/btv093openalex-snapshot
Mobility-based prediction of hydration structures of protein surfaces
inferred← citeshttps://doi.org/10.1126/sciadv.abo5083openalex-snapshot
The mechanisms of catalysis and ligand binding for the SARS-CoV-2 NSP3 macrodomain from neutron and x-ray diffraction at room temperature
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/10.1155/2022/9444502openalex-snapshot
Computational Modeling of T Cell Hypersensitivity during Coronavirus Infections Leading to Autoimmunity and Lethality
inferred← citeshttps://doi.org/10.11606/d.9.2019.tde-28012019-115311openalex-snapshot
Otimização de novos inibidores da di-idrofolato redutase de Mycobaterium tuberculosis (mtDHFR): Docking molecular, síntese, avaliação da inibição enzimática e da atividade antimicobacte
inferred← citeshttps://doi.org/10.11606/d.9.2022.tde-29072022-231426openalex-snapshot
Potenciais inibidores de di-idrofolato redutase de>i< Mycobacterium tuberculosis>/i< (>i /i<): >i /i< molecular, síntese e avaliação enzimática de derivados dos ácidos aminobenzóico e >i /i<-aminocinâmico
inferred← citeshttps://doi.org/10.1186/s12941-018-0266-9openalex-snapshot
Ginger (Zingiber officinale) phytochemicals—gingerenone-A and shogaol inhibit SaHPPK: molecular docking, molecular dynamics simulations and in vitro approaches
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/10.12691/ajmo-4-3-2openalex-snapshot
Docking and Ligand Binding Affinity: Uses and Pitfalls
inferred← citeshttps://doi.org/10.1371/journal.pone.0032036openalex-snapshot
Rapid and Accurate Prediction and Scoring of Water Molecules in Protein Binding Sites
inferred← citeshttps://doi.org/10.1371/journal.pone.0067536openalex-snapshot
Towards Ligand Docking Including Explicit Interface Water Molecules
inferred← citeshttps://doi.org/10.1371/journal.pone.0249866openalex-snapshot
Structural and thermodynamic analysis of factors governing the stability and thermal folding/unfolding of SazCA
inferred← citeshttps://doi.org/10.1517/17425255.4.5.513openalex-snapshot
Computational prediction of drug binding and rationalisation of selectivity towards cytochromes P450
inferred← citeshttps://doi.org/10.1517/17460441.2011.534452openalex-snapshot
Accounting for water molecules in drug design
inferred← citeshttps://doi.org/10.1517/17460441.3.5.579openalex-snapshot
Designing a ligand for pharmaceutical purposes
inferred← citeshttps://doi.org/10.1517/17460441.3.8.841openalex-snapshot
What has virtual screening ever done for drug discovery?
inferred← citeshttps://doi.org/10.15476/elte.2016.194openalex-snapshot
Calculation of hydration structures of proteins and their complexes
inferred← citeshttps://doi.org/10.2174/0115734099370189250416024026openalex-snapshot
In Silico Identification of 2,4-Diaryl-6-styrylpyridine Derivatives as Orthosteric-allosteric EGFR Inhibitors
inferred← citeshttps://doi.org/10.2174/0929867311320180002openalex-snapshot
Protein-Ligand Docking in the New Millennium – A Retrospective of 10 Years in the Field
inferred← citeshttps://doi.org/10.2174/0929867325666180514110824openalex-snapshot
Advances in the Treatment of Explicit Water Molecules in Docking and Binding Free Energy Calculations
inferred← citeshttps://doi.org/10.2174/0929867329666220208095122openalex-snapshot
Computational Strategies to Identify New Drug Candidates against Neuroinflammation
inferred← citeshttps://doi.org/10.2174/1381612811319230011openalex-snapshot
Correct Protonation States and Relevant Waters = Better Computational Simulations?
inferred← citeshttps://doi.org/10.2174/1386207322666190927143026openalex-snapshot
From the Explored to the Unexplored: Computer-Tailored Drug Design Attempts in the Discovery of Selective Caspase Inhibitors
inferred← citeshttps://doi.org/10.2174/1568026622666220726114407openalex-snapshot
The Role of Water Network Chemistry in Proteins: A Structural Bioinformatics Perspective in Drug Discovery and Development
inferred← citeshttps://doi.org/10.2174/157340909789577856openalex-snapshot
Modeling Reality for Optimal Docking of Small Molecules to Biological Targets
inferred← citeshttps://doi.org/10.22201/fesz.23958723e.2018.0.143openalex-snapshot
Acoplamiento Molecular: Avances Recientes y Retos
inferred← citeshttps://doi.org/10.3390/chemengineering8050104openalex-snapshot
In Silico Analysis of Vitamin D Interactions with Aging Proteins: Docking, Molecular Dynamics, and Solvation Free Energy Studies
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/ijms27156840openalex-snapshot
Comparative Structure-Based Analysis of Predicted BZD9L1 Binding Modes Across Human Sirtuins
inferred← citeshttps://doi.org/10.3390/molecules22081210openalex-snapshot
Chalcone Derivatives: Promising Starting Points for Drug Design
inferred← citeshttps://doi.org/10.3390/molecules23092321openalex-snapshot
Multi-Body Interactions in Molecular Docking Program Devised with Key Water Molecules in Protein Binding Sites
inferred← citeshttps://doi.org/10.3390/molecules24152808openalex-snapshot
Pharmacophoric Site Identification and Inhibitor Design for Autotaxin
inferred← citeshttps://doi.org/10.3390/molecules24173174openalex-snapshot
The Effect of Flavonoid Aglycones on the CYP1A2, CYP2A6, CYP2C8 and CYP2D6 Enzymes Activity
inferred← citeshttps://doi.org/10.3390/molecules27217403openalex-snapshot
Weak Noncovalent Interactions in Three Closely Related Adamantane-Linked 1,2,4-Triazole N-Mannich Bases: Insights from Energy Frameworks, Hirshfeld Surface Analysis, In Silico 11β-HSD1 Molecular Docking and ADMET Prediction
inferred← citeshttps://doi.org/10.3390/molecules28093906openalex-snapshot
Past, Present, and Future Perspectives on Computer-Aided Drug Design Methodologies
inferred← citeshttps://doi.org/10.3390/ph18111680openalex-snapshot
Exploring the Impact of 3-O-Methylquercetin on Wnt/β-Catenin Pathway Activity and Its Potential in Neural Processes
inferred← citeshttps://doi.org/10.3390/ph4091196openalex-snapshot
In Silico Veritas: The Pitfalls and Challenges of Predicting GPCR-Ligand Interactions
inferred← citeshttps://doi.org/10.34626/0hnm-hn65openalex-snapshot
New Computational Methods to Calculate Drug-Receptor Binding Free Energies
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
inferred← citeshttps://doi.org/10.56042/ijbb.v60i9.4029openalex-snapshot
The role of water molecules and its dynamics to the binding site of β-lactamase enzyme with respect to β-lactamase inhibitor
inferred← citeshttps://doi.org/10.70675/1a4f06f0zdfa4z41efza87az70239c45c50copenalex-snapshot
Conception d'un logiciel pour la recherche de nouvelles molécules bioactives
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