Epik: a software program for pK( a ) prediction and protonation state generation for drug-like molecules (scientific article published on 27 September 2007)

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Q44126096	Identification of 15d-PGJ2 as an antagonist of farnesoid X receptor: molecular modeling with biological evaluation
Q54491300	Identification of N-phenyl-2-(N-phenylphenylsulfonamido)acetamides as new RORγ inverse agonists: Virtual screening, structure-based optimization, and biological evaluation.
Q34515674	Identification of Novel Disruptor of Telomeric Silencing 1-like (DOT1L) Inhibitors through Structure-Based Virtual Screening and Biological Assays
Q41436449	Identification of Novel Non-secosteroidal Vitamin D Receptor Agonists with Potent Cardioprotective Effects and devoid of Hypercalcemia
Q46646513	Identification of Plasmodium falciparum spermidine synthase active site binders through structure-based virtual screening
Q52718343	Identification of Selective, Cell Active Inhibitors of Protein Arginine Methyltransferase 5 through Structure-Based Virtual Screening and Biological Assays.
Q94938641	Identification of a Covalent Molecular Inhibitor of Anti-apoptotic BFL-1 by Disulfide Tethering
Q89230946	Identification of a Potent Tryptophan-Based TRPM8 Antagonist With in Vivo Analgesic Activity
Q46478346	Identification of a new binding site in E. coli FabH using Molecular dynamics simulations: validation by computational alanine mutagenesis and docking studies
Q35742387	Identification of dengue viral RNA-dependent RNA polymerase inhibitor using computational fragment-based approaches and molecular dynamics study
Q97905427	Identification of key interactions between SARS-CoV-2 main protease and inhibitor drug candidates
Q36016417	Identification of matrine as a promising novel drug for hepatic steatosis and glucose intolerance with HSP72 as an upstream target
Q48365472	Identification of natural inhibitors of Bcr-Abl for the treatment of chronic myeloid leukemia.
Q102054755	Identification of new IDH2R140Q inhibitors by discriminatory analysis-based molecular docking and biological evaluation
Q92217026	Identification of new NIK inhibitors by discriminatory analysis-based molecular docking and biological evaluation
Q102321979	Identification of novel human neutrophil elastase inhibitors from dietary phytochemicals using in silico and in vitro studies
Q36370537	Identification of novel serotonin reuptake inhibitors targeting central and allosteric binding sites: A virtual screening and molecular dynamics simulations study.
Q28733552	Identification of novel small molecule inhibitors against NS2B/NS3 serine protease from Zika virus
Q49106909	Identification of novel small-molecule inhibitors targeting menin-MLL interaction, repurposing the antidiarrheal loperamide.
Q41904886	Identification of novel tyrosine kinase inhibitors for drug resistant T315I mutant BCR-ABL: a virtual screening and molecular dynamics simulations study
Q51630891	Identification of phenoxyacetamide derivatives as novel DOT1L inhibitors via docking screening and molecular dynamics simulation.
Q90964866	Identification of potent L,D-transpeptidase 5 inhibitors for Mycobacterium tuberculosis as potential anti-TB leads: virtual screening and molecular dynamics simulations
Q104793085	Identification of potential SARS-CoV-2 M^pro inhibitors integrating molecular docking and water thermodynamics
Q57284496	Identification of potential drugs targeting L,L-diaminopimelate aminotransferase of Chlamydia trachomatis: An integrative pharmacoinformatics approach
Q101453668	Identification of selective Lyn inhibitors from the chemical databases through integrated molecular modelling approaches
Q56987439	Identification of the first surrogate agonists for the G protein-coupled receptor GPR132
Q39936129	Identification of transmembrane domain 5 as a critical molecular determinant of menthol sensitivity in mammalian TRPA1 channels
Q90391781	Identifying Oxacillinase-48 Carbapenemase Inhibitors Using DNA-Encoded Chemical Libraries
Q89671929	Identifying new piperazine-based PARP1 inhibitors using text mining and integrated molecular modeling approaches
Q104692156	Identifying the natural polyphenol catechin as a multi-targeted agent against SARS-CoV-2 for the plausible therapy of COVID-19: an integrated computational approach
Q34956542	Impact of distinct chemical structures for the development of a methamphetamine vaccine
Q64063487	Importance of Incorporating Protein Flexibility in Molecule Modeling: A Theoretical Study on Type I NIK Inhibitors
Q92951662	Impressive Enrichment of Semiempirical Quantum Mechanics-Based Scoring Function: HSP90 Protein with 4541 Inhibitors and Decoys
Q51550011	Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKa Values.
Q92908497	Improved homology modeling of the human & rat EP4 prostanoid receptors
Q56984194	In Silico ADME/Tox Predictions
Q42221010	In Silico Designing and Analysis of Inhibitors against Target Protein Identified through Host-Pathogen Protein Interactions in Malaria
Q90632638	In Silico Insights towards the Identification of NLRP3 Druggable Hot Spots
Q55880715	In Silico Prediction of Ionization
Q64970494	In Silico and In Vitro Analysis of the 4,4',4''-((1,3,5-Triazine-2,4,6-triyl)tris(azanediyl))triphenol), an Antioxidant Agent with a Possible Anti-Inflammatory Function.
Q104493683	In Silico/In Vitro Hit-to-Lead Methodology Yields SMYD3 Inhibitor That Eliminates Unrestrained Proliferation of Breast Carcinoma Cells
Q28820807	In search of novel ligands using a structure-based approach: a case study on the adenosine A2A receptor
Q96435322	In silico Druggability Assessment of the NUDIX Hydrolase Protein Family as a Workflow for Target Prioritization
Q57456522	In silico Screening and Evaluation of Plasmodium falciparum Protein Kinase 5 (PK5) Inhibitors
Q89544798	In silico approaches for investigating the binding propensity of apigenin and luteolin against class I HDAC isoforms
Q99555228	In silico characterization of adipokinetic hormone receptor and screening for pesticide candidates against stick insect, Carausius morosus
Q88913754	In silico design of novel proton-pump inhibitors with reduced adverse effects
Q47402960	In silico identification and in vivo characterization of small molecule therapeutic hypothermia mimetics.
Q100443847	In silico identification of angiotensin-1 converting enzyme inhibitors using text mining and virtual screening
Q100994555	In silico identification of drug candidates against COVID-19
Q56343057	In silico identification of inhibitors against Plasmodium falciparum histone deacetylase 1 (PfHDAC-1)
Q100951663	In silico identification of small molecule modulators for disruption of Hsp90-Cdc37 protein-protein interaction interface for cancer therapeutic application
Q92383888	In silico probing exercises, bioactive-conformational and dynamic simulations strategies for designing and promoting selective therapeutics against Helicobacter pylori strains
Q35693310	In silico screening for agonists and blockers of the β(2) adrenergic receptor: implications of inactive and activated state structures
Q50097350	In vitro and in silico perspectives on biological and phytochemical profile of three halophyte species-A source of innovative phytopharmaceuticals from nature.
Q98772801	In vitro and in silico studies on the structural and biochemical insight of anti-biofilm activity of andrograpanin from Andrographis paniculata against Pseudomonas aeruginosa
Q89752520	In vitro investigation of the effect of mesalazine on amyloid fibril formation of hen egg-white lysozyme and defibrillation lysozyme fibrils
Q90375092	Inclusion of enclosed hydration effects in the binding free energy estimation of dopamine D3 receptor complexes
Q38300058	Increased efficiency of Campylobacter jejuni N-oligosaccharyltransferase PglB by structure-guided engineering
Q91710511	Indenoisoquinoline Topoisomerase Inhibitors Strongly Bind and Stabilize the MYC Promoter G-Quadruplex and Downregulate MYC
Q40171626	Influence of Ethanol on Darunavir Hepatic Clearance and Intracellular PK/PD in HIV-Infected Monocytes, and CYP3A4-Darunavir Interactions Using Inhibition and in Silico Binding Studies
Q43654904	Inhibition and biochemical characterization of methicillin-resistant Staphylococcus aureus shikimate dehydrogenase: an in silico and kinetic study.
Q92161698	Inhibition of Human Serum Paraoxonase-I with Antimycotic Drugs: In Vitro and In Silico Studies
Q91645685	Inhibition of Porcine Aminopeptidase M (pAMP) by the Pentapeptide Microginins
Q60919746	Inhibition of acetylcholinesterase and butyrylcholinesterase with uracil derivatives: kinetic and computational studies
Q99549976	Inhibition of amyloid fibrillation of HEWL by 4-methylcoumarin and 4- methylthiocoumarin derivatives
Q34490095	Inhibition of angiotensin-converting enzyme activity by flavonoids: structure-activity relationship studies.
Q104751536	Inhibition of biofilm formation, quorum sensing and other virulence factors in Pseudomonas aeruginosa by polyphenols of Gynura procumbens leaves
Q89725994	Inhibition of human CYP1 enzymes by a classical inhibitor α-naphthoflavone and a novel inhibitor N-(3, 5-dichlorophenyl)cyclopropanecarboxamide: An in vitro and in silico study
Q52370460	Inhibition of human monoamine oxidase A and B by flavonoids isolated from two Algerian medicinal plants.
Q47652352	Inhibition of myeloperoxidase activity by the alkaloids of Peganum harmala L. (Zygophyllaceae).
Q34632021	Inhibition of secreted phospholipases A₂ by 2-oxoamides based on α-amino acids: Synthesis, in vitro evaluation and molecular docking calculations.
Q90975231	Inhibition of translation termination by small molecules targeting ribosomal release factors
Q35932496	Inhibitor design against JNK1 through e-pharmacophore modeling docking and molecular dynamics simulations.
Q38851160	Inhibitory effect of positively charged triazine antagonists of prokineticin receptors on the transient receptor vanilloid type-1 (TRPV1) channel.
Q92923746	Innovative Three-Step Microwave-Promoted Synthesis of N-Propargyltetrahydroquinoline and 1,2,3-Triazole Derivatives as a Potential Factor Xa (FXa) Inhibitors: Drug Design, Synthesis, and Biological Evaluation
Q92959118	Insight into the screening of potential beta-lactamase inhibitors as anti-bacterial chemical agents through pharmacoinformatics study
Q90734464	Insight into the selective mechanism of phosphoinositide 3-kinase γ with benzothiazole and thiazolopiperidine γ-specific inhibitors by in silico approaches
Q57990988	Insights into the structural determinants for selective inhibition of nitric oxide synthase isoforms
Q50964984	Insights into unbound-bound states of GPR142 receptor in a membrane-aqueous system using molecular dynamics simulations.
Q97543863	Integrated Binary QSAR-Driven Virtual Screening and in vitro Studies for Finding Novel hMAO-B-Selective Inhibitors
Q93200291	Integrating Ligand and Target-Driven Based Virtual Screening Approaches With in vitro Human Cell Line Models and Time-Resolved Fluorescence Resonance Energy Transfer Assay to Identify Novel Hit Compounds Against BCL-2
Q47652129	Integrating computational methods to predict mutagenicity of aromatic azo compounds
Q55295867	Integration of in vitro and in silico perspectives to explain chemical characterization, biological potential and anticancer effects of Hypericum salsugineum: A pharmacologically active source for functional drug formulations.
Q89860412	Integration of multi-scale molecular modeling approaches with experiments for the in silico guided design and discovery of novel hERG-Neutral antihypertensive oxazalone and imidazolone derivatives and analysis of their potential restrictive effects
Q47522548	Interacting with GPCRs: Using Interaction Fingerprints for Virtual Screening
Q47093607	Interaction of Cholesterol with Perfringolysin O: What Have We Learned from Functional Analysis?
Q90162275	Interaction of Coumarin Phytoestrogens with ERα and ERβ: A Molecular Dynamics Simulation Study
Q46043111	Interaction of arylsulfatase-A (ASA) with its natural sulfoglycolipid substrates: a computational and site-directed mutagenesis study
Q38878454	Interactions of omeprazole-based analogues with cytochrome P450 2C19: a computational study
Q56992142	Interspecies comparison of putative ligand binding sites of human, rat and mouse P-glycoprotein
Q90241352	Investigation of Phospholipase Cγ1 Interaction with SLP76 Using Molecular Modeling Methods for Identifying Novel Inhibitors
Q92016866	Investigation of Potential Paraoxonase-I Inhibitors by Kinetic and Molecular Docking Studies: Chemotherapeutic Drugs
Q96120502	Investigation of novel indole-based HIV-1 protease inhibitors using virtual screening and text mining
Q57138721	Investigations into the therapeutic potential of Asphodeline liburnica roots: In vitro and in silico biochemical and toxicological perspectives
Q92975707	Involvement of monoaminergic targets in the antidepressant- and anxiolytic-like effects of the synthetic alkamide riparin IV: Elucidation of further mechanisms through pharmacological, neurochemistry and computational approaches
Q104076087	Isobenzofuran-1(3H)-ones as new tyrosinase inhibitors: Biological activity and interaction studies by molecular docking and NMR
Q90011399	Isolation, purification and characterization of naturally derived Crocetin beta-d-glucosyl ester from Crocus sativus L. against breast cancer and its binding chemistry with ER-alpha/HDAC2
Q36938240	Knowledge-Based Methods To Train and Optimize Virtual Screening Ensembles
Q41056037	L-2-Hydroxyglutarate production arises from noncanonical enzyme function at acidic pH
Q54250623	LASSBio-1829 Hydrochloride: Development of a New Orally Active N-Acylhydrazone IKK2 Inhibitor with Anti-inflammatory Properties.
Q98567577	Large-Scale Assessment of Binding Free Energy Calculations in Active Drug Discovery Projects
Q36059863	Large-scale prediction and testing of drug activity on side-effect targets
Q53241398	Ligand Binding Pathways of Clozapine and Haloperidol in the Dopamine D2 and D3 Receptors.
Q28533835	Ligand induced conformational changes of the human serotonin transporter revealed by molecular dynamics simulations
Q52672698	Ligand-Based Pharmacophore Screening Strategy: a Pragmatic Approach for Targeting HER Proteins.
Q62849215	Ligand-Induced Structural Changes in TEM-1 Probed by Molecular Dynamics and Relative Binding Free Energy Calculations
Q95313279	Lycorine ameliorates bleomycin-induced pulmonary fibrosis via inhibiting NLRP3 inflammasome activation and pyroptosis
Q90746831	Machine learning meets pK a
Q51036226	Macrocycle conformational sampling with MacroModel.
Q46353864	Mechanism of Sirt1 NAD+-dependent Protein Deacetylase Inhibition by Cysteine S-Nitrosation.
Q57998781	Mechanistic Analysis of Muraymycin Analogues: A Guide to the Design of MraY Inhibitors
Q89257053	Mechanistic Insights into Stereospecific Bioactivity and Dissipation of Chiral Fungicide Triticonazole in Agricultural Management
Q103822196	Mechanistic insight on the remdesivir binding to RNA-Dependent RNA polymerase (RdRp) of SARS-cov-2
Q34041202	Mechanistic insights into the allosteric modulation of opioid receptors by sodium ions
Q94560621	Metadynamics as a Post-Processing Method for Virtual Screening with Application to the Pseudokinase Domain of JAK2
Q104499069	Mining Natural Products for Macrocycles to Drug Difficult Targets
Q39290519	Modeling androgen receptor flexibility: a binding mode hypothesis of CYP17 inhibitors/antiandrogens for prostate cancer therapy
Q52682791	Modeling of alcohol oxidase enzyme of Candida boidinii and in silico analysis of competitive binding of proton ionophores and FAD with enzyme.
Q91471721	Modelling the binding mode of macrocycles: Docking and conformational sampling
Q92020497	Modification of the lead molecule: Tryptophan and piperidine appended triazines reversing inflammation and hyeperalgesia in rats
Q92197933	Molecular Docking and Quantum Studies of Lawsone Dimers Derivatives: New Investigation of Antioxidant Behavior and Antifungal Activity
Q57210507	Molecular Docking of Potential Inhibitors of Broccoli Myrosinase
Q91452095	Molecular Dynamics Simulation reveals the mechanism by which the Influenza Cap-dependent Endonuclease acquires resistance against Baloxavir marboxil
Q104132303	Molecular and functional characterization of buffalo nasal epithelial odorant binding proteins and their structural insights by in silico and biochemical approaches
Q91918668	Molecular basis for the different interactions of congeneric substrates with the polyspecific transporter AcrB
Q42277716	Molecular design and synthesis of HCV inhibitors based on thiazolone scaffold
Q42925147	Molecular docking and 3D-QSAR CoMFA studies on indole inhibitors of GIIA secreted phospholipase A(2).
Q86708262	Molecular docking and dynamic simulation studies evidenced plausible immunotherapeutic anticancer property by Withaferin A targeting indoleamine 2,3-dioxygenase
Q97684787	Molecular docking and dynamics study of natural compound for potential inhibition of main protease of SARS-CoV-2
Q109745333	Molecular docking and oxidation kinetics of 3-phenyl coumarin derivatives by human CYP2A13
Q40637614	Molecular docking study of natural alkaloids as multi-targeted hedgehog pathway inhibitors in cancer stem cell therapy
Q91712536	Molecular dynamics investigations for the prediction of molecular interaction of cauliflower mosaic virus transmission helper component protein complex with Myzus persicae stylet's cuticular protein and its docking studies with annosquamosin-A encap
Q40844559	Molecular dynamics of sialic acid analogues complex with cholera toxin and DFT optimization of ethylene glycol-mediated zinc nanocluster conjugation
Q91034093	Molecular dynamics simulation of biased agonists at the dopamine D2 receptor suggests the mechanism of receptor functional selectivity
Q39391532	Molecular modeling on pyrimidine-urea inhibitors of TNF-α production: an integrated approach using a combination of molecular docking, classification techniques, and 3D-QSAR CoMSIA.
Q50536056	Multiconformation, Density Functional Theory-Based pKa Prediction in Application to Large, Flexible Organic Molecules with Diverse Functional Groups.
Q88594026	Multidirectional investigations on different parts of Allium scorodoprasum L. subsp. rotundum (L.) Stearn: Phenolic components, in vitro biological, and in silico propensities
Q89345556	Multifunctional quinoline-triazole derivatives as potential modulators of amyloid-β peptide aggregation
Q52326894	Multiple e-Pharmacophore modeling to identify a single molecule that could target both streptomycin and paromomycin binding sites for 30S ribosomal subunit inhibition.
Q84230608	Multiple ligand docking by Glide: implications for virtual second-site screening
Q89874938	Na+/K+-ATPase-Targeted Cytotoxicity of (+)-Digoxin and Several Semisynthetic Derivatives
Q46411760	New azole derivatives showing antimicrobial effects and their mechanism of antifungal activity by molecular modeling studies
Q96680623	Nitrogen Catabolite Repression in members of Paracoccidioides complex
Q38749449	Non-Acidic Free Fatty Acid Receptor 4 Agonists with Antidiabetic Activity
Q92961686	Novel AChE and BChE inhibitors using combined virtual screening, text mining and in vitro binding assays
Q48105075	Novel Bacterial Topoisomerase Inhibitors Exploit Asp83 and the Intrinsic Flexibility of the DNA Gyrase Binding Site.
Q47271707	Novel Mixed-Type Inhibitors of Protein Tyrosine Phosphatase 1B. Kinetic and Computational Studies.
Q89880858	Novel and potent inhibitors for dihydropteroate synthase of Helicobacter pylori
Q51564174	Novel bis-arylalkylamines as myeloperoxidase inhibitors: Design, synthesis, and structure-activity relationship study.
Q47271789	Novel in vitro and in silico insights of the multi-biological activities and chemical composition of Bidens tripartita L.
Q34402678	Novel insights of structure-based modeling for RNA-targeted drug discovery
Q48633041	Novel series of tacrine-tianeptine hybrids: Synthesis, cholinesterase inhibitory activity, S100B secretion and a molecular modeling approach.
Q50088311	Novel sulfonamide incorporating piperazine, aminoalcohol and 1,3,5-triazine structural motifs with carbonic anhydrase I, II and IX inhibitory action.
Q91180404	Novel sulfonamides incorporating 1,3,5-triazine and amino acid structural motifs as inhibitors of the physiological carbonic anhydrase isozymes I, II and IV and tumor-associated isozyme IX
Q90489766	Novel tumor necrosis factor-α (TNF-α) inhibitors from small molecule library screening for their therapeutic activity profiles against rheumatoid arthritis using target-driven approaches and binary QSAR models
Q27681884	Novel β-amino acid derivatives as inhibitors of cathepsin A
Q88385614	Nε-Acryloyllysine Piperazides as Irreversible Inhibitors of Transglutaminase 2: Synthesis, Structure-Activity Relationships, and Pharmacokinetic Profiling
Q38971591	On the fly estimation of host-guest binding free energies using the movable type method: participation in the SAMPL5 blind challenge
Q41469400	On the origin of fluorescence in bacteriophytochrome infrared fluorescent proteins
Q58556734	Overview of the SAMPL6 host-guest binding affinity prediction challenge
Q111149480	Overview of the SAMPL6 pKa challenge: evaluating small molecule microscopic and macroscopic pKa predictions
Q48156672	Oxime Ethers of (E)-11-Isonitrosostrychnine as Highly Potent Glycine Receptor Antagonists.
Q38973272	PAC-1 and isatin derivatives are weak matrix metalloproteinase inhibitors
Q86063074	Para-(benzoyl)-phenylalanine as a potential inhibitor against LpxC of Leptospira spp.: homology modeling, docking, and molecular dynamics study
Q92399576	Partially inserted nascent chain unzips the lateral gate of the Sec translocon
Q47797655	Performance of multiple docking and refinement methods in the pose prediction D3R prospective Grand Challenge 2016.
Q99610890	Pharmacoinformatic investigation of medicinal plants from East Africa
Q96647549	Pharmacoinformatics and molecular dynamics simulation studies reveal potential covalent and FDA-approved inhibitors of SARS-CoV-2 main protease 3CLpro
Q90841227	Pharmacological and polyphenolic profiles of Phyllanthus phillyreifolius var. commersonii Müll. Arg: An unexplored endemic species from Mauritius
Q39859925	Pharmacophore modeling and structure-based virtual screening to identify potent inhibitors targeting LuxP of Vibrio harveyi
Q58870401	Phenolic profile and pharmacological propensities of Gynandriris sisyrinchium through in vitro and in silico perspectives
Q58870415	Phytochemical characterization, in vitro and in silico approaches for three Hypericum species
Q35747460	Policresulen, a novel NS2B/NS3 protease inhibitor, effectively inhibits the replication of DENV2 virus in BHK-21 cells
Q100486784	Potent novel inhibitors against hepatitis C virus NS3 (HCV NS3 GT-3a) protease domain
Q83363874	Practical calculation of molecular acidity with the aid of a reference molecule
Q49984769	Preclinical characterization of anlotinib, a highly potent and selective vascular endothelial growth factor receptor-2 inhibitor.
Q91340094	Preclinical toxicity of innovative molecules: In vitro, in vivo and metabolism prediction
Q39384465	Predicting and improving the membrane permeability of peptidic small molecules.
Q44103023	Predicting pK(a) values of substituted phenols from atomic charges: comparison of different quantum mechanical methods and charge distribution schemes
Q94479342	Predicting pKa Using a Combination of Semi-Empirical Quantum Mechanics and Radial Basis Function Methods
Q39535428	Predicting pKa Values in Aqueous Solution for the Guanidine Functional Group from Gas Phase Ab Initio Bond Lengths
Q91876611	Predicting pKa for Small Molecules on Public and In-house Datasets Using Fast Prediction Methods Combined with Data Fusion
Q37585236	Predicting pKa.
Q91214765	Predicting resistance of clinical Abl mutations to targeted kinase inhibitors using alchemical free-energy calculations
Q90737973	Predicting the Magnitude of σ-Holes Using VmaxPred, a Fast and Efficient Tool Supporting the Application of Halogen Bonds in Drug Discovery
Q37549125	Predicting water-to-cyclohexane partitioning of the SAMPL5 molecules using dielectric balancing of force fields
Q90919827	Prediction of pKa Using Machine Learning Methods with Rooted Topological Torsion Fingerprints: Application to Aliphatic Amines
Q48092459	Prediction of pKa Values for Druglike Molecules Using Semiempirical Quantum Chemical Methods
Q35164065	Prediction of substrates for glutathione transferases by covalent docking
Q47119940	Predictive compound accumulation rules yield a broad-spectrum antibiotic
Q59355967	Probing the "fingers" domain binding pocket of Hepatitis C virus NS5B RdRp and D559G resistance mutation via molecular docking, molecular dynamics simulation and binding free energy calculations
Q83888592	Probing the alpha-helical structural stability of stapled p53 peptides: molecular dynamics simulations and analysis
Q41680944	Prohexadione, a plant growth regulator, inhibits histone lysine demethylases and modulates epigenetics
Q93093382	Proline autocatalysis in the origin of biological enantioenriched chirality
Q92159276	Proof of Principle that Molecular Modeling Followed by a Biophysical Experiment Can Develop Small Molecules that Restore Function to the Cardiac Thin Filament in the Presence of Cardiomyopathic Mutations
Q92515827	Propafenone analogue with additional H-bond acceptor group shows increased inhibitory activity on P-glycoprotein
Q37108546	Proposed Mode of Binding and Action of Positive Allosteric Modulators at Opioid Receptors
Q88405678	Proposing Novel MAO-B Hit Inhibitors Using Multidimensional Molecular Modeling Approaches and Application of Binary QSAR Models for Prediction of Their Therapeutic Activity, Pharmacokinetic and Toxicity Properties
Q97638606	Proposing novel MDM2 inhibitors: Combined physics-driven high-throughput virtual screening and in vitro studies
Q91160035	Proposing novel TNFα direct inhibitor Scaffolds using fragment-docking based e-pharmacophore modeling and binary QSAR-based virtual screening protocols pipeline
Q92609329	Protection of Primary Dopaminergic Midbrain Neurons Through Impact of Small Molecules Using Virtual Screening of GPR139 Supported by Molecular Dynamic Simulation and Systems Biology
Q44012277	Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments
Q98468985	Protein reliability analysis and virtual screening of natural inhibitors for SARS-CoV-2 main protease (Mpro) through docking, molecular mechanic & dynamic, and ADMET profiling
Q35013427	Protocols utilizing constant pH molecular dynamics to compute pH-dependent binding free energies
Q35171617	Protonated form: the potent form of potassium-competitive acid blockers
Q96589902	Pseudouridylation defect due to DKC1 and NOP10 mutations causes nephrotic syndrome with cataracts, hearing impairment, and enterocolitis
Q92076465	Pyridine derivatives as anticancer lead compounds with Fatty Acid Synthase as the target: An in silico-guided in vitro study
Q92079181	Pyridinylimidazoles as dual glycogen synthase kinase 3β/p38α mitogen-activated protein kinase inhibitors
Q52645960	QSAR-Driven Design and Discovery of Novel Compounds With Antiplasmodial and Transmission Blocking Activities.
Q37616239	QSAR-Driven Discovery of Novel Chemical Scaffolds Active against Schistosoma mansoni
Q108768387	Quantitative Proteomics Reveals that Hsp90 Inhibition Dynamically Regulates Global Protein Synthesis in Leishmania mexicana
Q91803815	Quantum Chemical Calculation of Molecular and Periodic Peptide and Protein Structures
Q92316344	Quantum chemical calculation and binding modes of H1R; a combined study of molecular docking and DFT for suggesting therapeutically potent H1R antagonist
Q43265131	Quantum mechanical scoring for protein docking.
Q46860944	Quantum polarized ligand docking investigation to understand the significance of protonation states in histone deacetylase inhibitors
Q91693944	Rapid approach to complex boronic acids
Q43624519	Rapid context-dependent ligand desolvation in molecular docking
Q42698668	Rational Design of Small Peptides for Optimal Inhibition of Cyclooxygenase-2: Development of a Highly Effective Anti-Inflammatory Agent
Q38722512	Rationally designed benzopyran fused isoxazolidines and derived β2,3,3-amino alcohols as potent analgesics: Synthesis, biological evaluation and molecular docking analysis
Q38884546	Re(I) and Tc(I) complexes for targeting nitric oxide synthase: influence of the chelator in the affinity for the enzyme.
Q104455795	Recent advances in constraint and machine learning-based metabolic modeling by leveraging stoichiometric balances, thermodynamic feasibility and kinetic law formalisms
Q92075356	Recognition of PDL1/L2 by different induced-fit mechanisms of PD1: a comparative study of molecular dynamics simulations
Q51698294	Redesign of a Fluorogenic Labeling System To Improve Surface Charge, Brightness, and Binding Kinetics for Imaging the Functional Localization of Bromodomains.
Q99400402	Reductive domino reaction to access chromeno[2,3-c]isoquinoline-5-amines with antiproliferative activities against human tumor cells
Q48050957	Relative Binding Free Energy Calculations Applied to Protein Homology Models
Q37159748	Repositioning organohalogen drugs: a case study for identification of potent B-Raf V600E inhibitors via docking and bioassay
Q104064469	Repurposing of FDA approved ring systems through bi-directional target-ring system dual screening
Q57467585	Reverse screening on indicaxanthin from Opuntia ficus-indica as natural chemoactive and chemopreventive agent
Q38061451	Rigorous incorporation of tautomers, ionization species, and different binding modes into ligand-based and receptor-based 3D-QSAR methods.
Q98206799	SARS-CoV-2 RNA Dependent RNA polymerase (RdRp) - A drug repurposing study
Q45805013	SFCscore(RF): a random forest-based scoring function for improved affinity prediction of protein-ligand complexes
Q62652639	Salt Bridge in Ligand–Protein Complexes—Systematic Theoretical and Statistical Investigations
Q34911055	Screen of pseudopeptidic inhibitors of human sirtuins 1-3: two lead compounds with antiproliferative effects in cancer cells
Q91570312	Screening of FDA approved drugs for finding potential inhibitors against Granzyme B as a potent drug-repurposing target
Q61814552	Searching for Chymase Inhibitors among Chamomile Compounds Using a Computational-Based Approach
Q41681901	Searching for anthranilic acid-based thumb pocket 2 HCV NS5B polymerase inhibitors through a combination of molecular docking, 3D-QSAR and virtual screening
Q51734710	Selecting an optimal number of binding site waters to improve virtual screening enrichments against the adenosine A2A receptor.
Q45892090	Shape and pharmacophore-based virtual screening to identify potential cytochrome P450 sterol 14α-demethylase inhibitors
Q53342097	Simplified in vitro refolding and purification of recombinant human granulocyte colony stimulating factor using protein folding cation exchange chromatography.
Q90727527	Small-Molecule Covalent Modification of Conserved Cysteine Leads to Allosteric Inhibition of the TEAD⋅Yap Protein-Protein Interaction
Q101238345	Small-Molecule Inhibition of the uPAR•uPA Interaction by Conformational Selection
Q36172936	Small-molecule factor D inhibitors targeting the alternative complement pathway
Q100385854	Solution structure of the Hop TPR2A domain and investigation of target druggability by NMR, biochemical and in silico approaches
Q98387838	Some calcium-channel blockers: kinetic and in silico studies on paraoxonase-I
Q89690113	Standard state free energies, not pKas, are ideal for describing small molecule protonation and tautomeric states
Q90098652	Stereoselective bioactivity of the chiral triazole fungicide prothioconazole and its metabolite
Q92441413	Strictinin, a novel ROR1-inhibitor, represses triple negative breast cancer survival and migration via modulation of PI3K/AKT/GSK3ß activity
Q27676926	Structural Basis for Molecular Recognition at Serotonin Receptors
Q55039422	Structural Changes Due to Antagonist Binding in Ligand Binding Pocket of Androgen Receptor Elucidated Through Molecular Dynamics Simulations.
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P8978	DBLP publication ID	journals/jcamd/ShelleyCFGTU07
P356	DOI	10.1007/S10822-007-9133-Z
P2888	exact match	https://scigraph.springernature.com/pub.10.1007/s10822-007-9133-z
P698	PubMed publication ID	17899391

P2093	author name string	Jeremy R Greenwood
		Anuradha Cholleti
		John C Shelley
		Leah L Frye
		Makoto Uchimaya
		Mathew R Timlin
P2860	cites work	pK a Prediction for Organic Acids and Bases	Q55921625
P433	issue	12
P921	main subject	software	Q7397
P304	page(s)	681-691
P577	publication date	2007-09-27
P1433	published in	Journal of Computer - Aided Molecular Design	Q15766522
P1476	title	Epik: a software program for pK( a ) prediction and protonation state generation for drug-like molecules
P478	volume	21

Epik: a software program for pK( a ) prediction and protonation state generation for drug-like molecules

scientific article published on 27 September 2007

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