yusuke1997/dblp-id-title huggingface dataset:
Molecular dynamics simulations give insight into d-glucose dioxidation at C2 and C3 by Agaricus meleagris pyranose dehydrogenase
Computational study of the catalytic domain of human neutrophil collagenase. Specific role of the S3 and S'3 subsites in the interaction with a phosphonate inhibitor
Structure-based design of alicyclic fused pyrazole derivatives for targeting TGF-β receptor I kinase: molecular docking and dynamics insights
Demystifying the pH dependent conformational changes of human heparanase pertaining to structure-function relationships: an in silico approach
Lipophilicity in PK design: methyl, ethyl, futile
ExcelAutomat: a tool for systematic processing of files as applied to quantum chemical calculations
Rationalizing fragment based drug discovery for BACE1: insights from FB-QSAR, FB-QSSR, multi objective (MO-QSPR) and MIF studies
Drug discovery using very large numbers of patents. General strategy with extensive use of match and edit operations
Ligand atom partial charges assignment for complementary electrostatic potentials
Theoretical models to predict the inhibitory effect of ligands of sphingosine kinase 1 using QTAIM calculations and hydrogen bond dynamic propensity analysis
Symposium overview Minnesota Conference on Supercomputing in Biology: Proteins, Nucleic Acids, and Water
Design of compound libraries for fragment screening
A theoretical model for the Gla-TSR-EGF-1 region of the anticoagulant cofactor protein S: From biostructural pathology to specie
Simulation-based cheminformatic analysis of organelle-targeted molecules: lysosomotropic monobasic amines
Role of water coordination at zinc binding site and its catalytic pathway of dizinc creatininase: insights from quantum cluster approach
Molecular dynamics simulations of oligonucleotides in solution: Visualisation of intrinsic curvature
Design, synthesis, deep learning-guided prediction, and biological evaluation of novel pyridine-thiophene-based imine-benzalacetophenone hybrids as promising antimicrobial agent
Covalent inhibitor reactivity prediction by the electrophilicity index - in and out of scope
Charge density distributions derived from smoothed electrostatic potential functions: design of protein reduced point charge models
Genetic algorithm for the design of molecules with desired properties
Structure determination of a tetradecapeptide mimicking the RXVRG consensus sequence recognized by a Xenopus laevis skin endoprotease: An approach based on simulated annealing and 1 H NMR
Closing the side-chain gap in protein loop modeling
Gaussian mapping of chemical fragments in ligand binding sites
Assessing and improving the performance of consensus docking strategies using the DockBox package
Overview of the SAMPL6 host-guest binding affinity prediction challenge
Model based on GRID-derived descriptors for estimating CYP3A4 enzyme stability of potential drug candidates
SpaceGrow: efficient shape-based virtual screening of billion-sized combinatorial fragment spaces
Discovery and validation of pyrrolopyrimidine-based VEGFR2 inhibitors targeting tumor angiogenesis via structure-based virtual screening, quantum chemical analysis, and in vitro assays
Lessons learned in induced fit docking and metadynamics in the Drug Design Data Resource Grand Challenge 2
PoseEdit: enhanced ligand binding mode communication by interactive 2D diagrams
BCL: : Mol2D - a robust atom environment descriptor for QSAR modeling and lead optimization
Drug-resistant molecular mechanism of CRF01_AE HIV-1 protease due to V82F mutation
Examining unsupervised ensemble learning using spectroscopy data of organic compounds
In search of novel ligands using a structure-based approach: a case study on the adenosine A2A receptor
Functional group placement in protein binding sites: a comparison of GRID and MCSS
The atom assignment problem in automated de novo drug design. 4. Tests for site-directed fragment placement based on molecular complementarity
The Royal Society of Chemistry and the delivery of chemistry data repositories for the community
A well deserved honor: Yvonne Martin, 2009 recipient of the Herman Skolnik Award
ChemStable: a web server for rule-embedded naïve Bayesian learning approach to predict compound stability
Count on kappa
Computer simulation study of the binding of an antiviral agent to a sensitive and a resistant human rhinovirus
Molecular insight into γ-γ tubulin lateral interactions within the γ-tubulin ring complex (γ-TuRC)
A computational model of the nicotinic acetylcholine binding site
Lead Finder docking and virtual screening evaluation with Astex and DUD test sets
Reconstruction of the 3D coordinates of alpha-carbon atoms of proteins from a pair of stereographic figures
Computational investigation on the properties of alkoxysilyl-anchored near-infrared porphyrin dyes for application in dye-sensitized solar cells
Discriminant and quantitative PLS analysis of competitive CYP2C9 inhibitors versus non-inhibitors using alignment independent GRIND descriptors
Molecular simulation methods in drug discovery: a prospective outlook
Computational Studies and Drug Design for HIV-1 Reverse Transcriptase Inhibitors of 3′, 4′-di-O-(S)-camphanoyl-(+)-cis-Khellactone (DCK) Analogs
Comparison of affinity ranking using AutoDock-GPU and MM-GBSA scores for BACE-1 inhibitors in the D3R Grand Challenge 4
Local neighborhood behavior in a combinatorial library context
A structure-based design approach for the identification of novel inhibitors: application to an alanine racemase
Protein secondary structure templates derived from bioactive natural products - Combinatorial chemistry meets structure-based design
Mechanistic insights into protonation state as a critical factor in hFPPS enzyme inhibition
In silico strategies for the selection of chelating compounds with potential application in metal-promoted neurodegenerative diseases
Molecular dynamics: Deciphering the data
Role of protein structure and the role of individual fingers in zinc finger protein-DNA recognition: a molecular dynamics simulation study and free energy calculations
An approximate but efficient method to calculate free energy trends by computer simulation: Application to dihydrofolate reductase-inhibitor complexes
RigFit: A new approach to superimposing ligand molecules
Design, synthesis and in vitro kinetic study of tranexamic acid prodrugs for the treatment of bleeding conditions
FLOG: A system to select 'quasi-flexible' ligands complementary to a receptor of known three-dimensional structure
"In silico" study of the binding of two novel antagonists to the nociceptin receptor
BODIL: a molecular modeling environment for structure-function analysis and drug design
Presenting data in such a fashion that they can be used by other scientists
Multiconformational composite molecular potential fields in the analysis of drug action. I. Methodology and first evaluation using 5-HT and histamine action as examples
CoMFA and docking study of novel estrogen receptor subtype selective ligands
Effective prediction of bacterial type IV secreted effectors by combined features of both C-termini and N-termini
Docking and multivariate methods to explore HIV-1 drug-resistance: a comparative analysis
Applications of momentum-space similarity
A consistent S-Adenosylmethionine force field improved by dynamic Hirshfeld-I atomic charges for biomolecular simulation
Three-dimensional quantitative structure-activity relationship (3D QSAR) and pharmacophore elucidation of tetrahydropyran derivatives as serotonin and norepinephrine transporter inhibitors
Prediction of cyclohexane-water distribution coefficient for SAMPL5 drug-like compounds with the QMPFF3 and ARROW polarizable force fields
The statistics of virtual screening and lead optimization
Fine specificity of antigen binding to two class I major histocompatibility proteins (B*2705 and B*2703) differing in a single amino acid residue
EVA: A new theoretically based molecular descriptor for use in QSAR/QSPR analysis
A support vector machine approach to classify human cytochrome P450 3A4 inhibitors
Blinded evaluation of cathepsin S inhibitors from the D3RGC3 dataset using molecular docking and free energy calculations
Blind prediction of SAMPL4 cucurbit[7]uril binding affinities with the mining minima method
Assessing the performance of three resveratrol in binding with SIRT1 by molecular dynamics simulation and MM/GBSA methods: the weakest binding of resveratrol 3 to SIRT1 triggers a possibility of dissociation from its binding site
New insights into human farnesyl pyrophosphate synthase inhibition by second-generation bisphosphonate drugs
An approach to computer-aided inhibitor design: Application to cathepsin L
A molecular modelling study of the interaction of noradrenaline with the β 2 -adrenergic receptor
Combining self- and cross-docking as benchmark tools: the performance of DockBench in the D3R Grand Challenge 2
Structure-based ligand design for flexible proteins: Application of new F-DycoBlock
Outliers in SAR and QSAR: 3. Importance of considering the role of water molecules in protein-ligand interactions and quantitative structure-activity relationship studies
A deep learning approach for the blind logP prediction in SAMPL6 challenge
Distance geometry analysis of ligand binding to drug receptor sites
Conformational studies on (+)-anatoxin-a and derivatives
Democratization of computational chemistry and Chem(o)informatics
Structure-activity relationships of pyrethroid insecticides. Part 2. The use of molecular dynamics for conformation searching and average parameter calculation
De novo design and synthetic accessibility
Unraveling the distinctive features of hemorrhagic and non-hemorrhagic snake venom metalloproteinases using molecular simulations
Structure-based design, synthesis and biological evaluation of β-glucuronidase inhibitors
NMR-restrained docking of a peptidic inhibitor to the N-terminal domain of the phosphoenolpyruvate: sugar phosphotransferase enzyme I
Is there a common allosteric binding site for G-protein coupled receptors?
A pose prediction approach based on ligand 3D shape similarity
Correction: Exploring DrugCentral: from molecular structures to clinical effects
A Monte Carlo pharmacophore generation procedure: Application to the human PAF receptor
Systematic mining of analog series with related core structures in multi-target activity space
Engineering strategy to improve peptide analogs: from structure-based computational design to tumor homing
Molecular insight of isotypes specific β-tubulin interaction of tubulin heterodimer with noscapinoids
Insight into the molecular mechanism of yeast acetyl-coenzyme A carboxylase mutants F510I, N485G, I69E, E477R, and K73R resistant to soraphen A
Incorporating partial matches within multiobjective pharmacophore identification
Development and validation of a modular, extensible docking program: DOCK 5
Comparison of a 3D-model of the classical Alpha-scorpion toxin V from Leiurus quinquestriatus quinquestriatus with other scorpion toxins
Modified AutoDock for accurate docking of protein kinase inhibitors
Integrated machine learning and deep learning-based virtual screening framework identifies novel natural GSK-3β inhibitors for Alzheimer's disease
Detailed potential of mean force studies on host-guest systems from the SAMPL6 challenge
Molecular mechanism of R-bicalutamide switching from androgen receptor antagonist to agonist induced by amino acid mutations using molecular dynamics simulations and free energy calculation
A computational analysis of the binding model of MDM2 with inhibitors
A reverse combination of structure-based and ligand-based strategies for virtual screening
Convolidine as potent BACE1 inhibitor for Alzheimer's disease; in-silico coupled with in-vitro assessment
Computational study of the heterodimerization between µ and delta receptors
The nature of topological parameters. II. The composition of topological parameters
Electrostatic and structural similarity of classical and non-classical lactam compounds
Computer simulation of the binding of quinocarcin to DNA. Prediction of mode of action and absolute configuration
Designing the molecular future
Evaluation of a novel infrared range vibration-based descriptor (EVA) for QSAR studies. 1. General application
Assembling of phenyl substituted halogens in the C3-position of substituted isatins by mono wave assisted synthesis: development of a new class of monoamine oxidase inhibitors
Hybrid receptor structure/ligand-based docking and activity prediction in ICM: development and evaluation in D3R Grand Challenge 3
Interpreting physicochemical experimental data sets
The centroidal algorithm in molecular similarity and diversity calculations on confidential datasets
Molecular docking studies on tetrahydroimidazo-[4, 5, 1-jk][1, 4]-benzodiazepinone (TIBO) derivatives as HIV-1 NNRT inhibitors
Druggable exosites of the human kino-pocketome
Cooperative and structural relationships of the trimeric Spike with infectivity and antibody escape of the strains Delta (B.1.617.2) and Omicron (BA.2, BA.5, and BQ.1)
Placement of medium-sized molecular fragments into active sites of proteins
A new approach to analysis and display of local lipophilicity/hydrophilicity mapped on molecular surfaces
Molecular dynamics simulation of S100B protein to explore ligand blockage of the interaction with p53 protein
Tales from the war on error: the art and science of curating QSAR data
On the NS-DSSB unidirectional estimates in the SAMPL6 SAMPLing challenge
The search for a new model structure of beta-Factor XIIa
Crystal structure of an antiviral ankyrin targeting the HIV-1 capsid and molecular modeling of the ankyrin-capsid complex
Molecular dynamics simulation of cyclosophoroheptadecaose (Cys-A)
Target identification for repurposed drugs active against SARS-CoV-2 via high-throughput inverse docking
3CL pro of SARS-CoV-2 as a new target for bufadienolides: in silico and in vitro study
Artificial intelligence for prediction of biological activities and generation of molecular hits using stereochemical information
Mappability of drug-like space: towards a polypharmacologically competent map of drug-relevant compounds
MiR-146/TNF-α/IL-6/osteocalcin crosstalk in anti-rheumatic potential of Galleria mellonella hemolymph from computational molecular modeling to in-vivo validation
Understanding the molecular interactions of different radical scavengers with ribonucleotide reductase M2 (hRRM2) domain: opening the gates and gaining access
Molecular structure matching by simulated annealing. III. The incorporation of null correspondences into the matching problem
Coupling enhanced sampling of the apo-receptor with template-based ligand conformers selection: performance in pose prediction in the D3R Grand Challenge 4
Impediments to the scientific method
Interactions of GF-17 derived from LL-37 antimicrobial peptide with bacterial membranes: a molecular dynamics simulation study
On the suitability of semiempirical calculations as sources of force field parameters
Exploring aromatic cage flexibility of the histone methyllysine reader protein Spindlin1 and its impact on binding mode prediction: an in silico study
Docking and scoring of metallo-β-lactamases inhibitors
Flexibases: A way to enhance the use of molecular docking methods
GenStar: A method for de novo drug design
QSAR: dead or alive?
GREEN: A program package for docking studies in rational drug design
Analysis of the activation mechanism of the guinea-pig Histamine H 1 -receptor
In silico identification of new ligands for GPR17: a promising therapeutic target for neurodegenerative diseases
A Comparative Molecular Similarity Index Analysis (CoMSIA) study identifies an HLA-A2 binding supermotif
Molecular dynamics and docking simulations as a proof of high flexibility in E. coli FabH and its relevance for accurate inhibitor modeling
Selective assembly of cyclodextrins on poly(ethylene oxide)-poly(propylene oxide) block copolymers
Computer-aided molecular modelling: Research study or research tool?
Does your model weigh the same as a Duck?
Imidazole-containing farnesyltransferase inhibitors: 3D quantitative structure-activity relationships and molecular docking
Modelling of carbohydrate-aromatic interactions: ab initio energetics and force field performance
A pharmacophore model for dopamine D4 receptor antagonists
Binding-affinity predictions of HSP90 in the D3R Grand Challenge 2015 with docking, MM/GBSA, QM/MM, and free-energy simulations
Comparative molecular field analysis and energy interaction studies of thrombin-inhibitor complexes
3D-QSAR methods on the basis of ligand-receptor complexes. Application of COMBINE and GRID/GOLPE methodologies to a series of CYP1A2 ligands
SAMPL4 & DOCK3.7: lessons for automated docking procedures
The computer program LUDI: A new method for the de novo design of enzyne inhibitors
Complex peptide macrocycle optimization: combining NMR restraints with conformational analysis to guide structure-based and ligand-based design
Molecular level model for the agonist/antagonist selectivity of the 1, 4-dihydropyridine calcium channel receptor
Structure and reaction based evaluation of synthetic accessibility
Discovery of a novel serine protease inhibitor utilizing a structure-based and experimental selection of fragments technique
An extensive ecdysteroid CoMFA
PAPQMD parametrization of molecular systems with cyclopropyl rings: Conformational study of homopeptides constituted by 1-aminocyclopropane-1-carboxylic acid
Is the reductionist paradox an Achilles Heel of drug discovery?
Elucidating allosteric signal disruption in PBP2a: impact of N146K/E150K mutations on ceftaroline resistance in methicillin-resistant Staphylococcus aureus
Tautomerism, Hammett sigma, and QSAR
Computational and experimental repositioning of quinoline analogues as KSP inhibitors: insights from free energy landscape and PCA analysis
Modeling of the structure and interactions of the B. anthracis antitoxin, MoxX: deletion mutant studies highlight its modular structure and repressor function
Deciphering common failures in molecular docking of ligand-protein complexes
Prediction of SAMPL3 host-guest binding affinities: evaluating the accuracy of generalized force-fields
Similarity searching in files of three-dimensional chemical structures: Representation and searching of molecular electrostatic potentials using field-graphs
Computational combinatorial ligand design: Application to human alpha-thrombin
A comparative study of fragment screening methods on the p38α kinase: new methods, new insights
Evaluation of docking performance in a blinded virtual screening of fragment-like trypsin inhibitors
A computational study of the molecular basis of antibiotic resistance in a DXR mutant
Rational selection of training and test sets for the development of validated QSAR models
Vascular endothelial growth factor receptor-2 (VEGFR-2) inhibitors: development and validation of predictive 3-D QSAR models through extensive ligand- and structure-based approaches
Molecular dynamics of 5-HT1A and 5-HT2A serotonin receptors with methylated buspirone analogues
Investigating the role of glycans in Omicron sub-lineages XBB.1.5 and XBB.1.16 binding to host receptor using molecular dynamics and binding free energy calculations
Validation of tautomeric and protomeric binding modes by free energy calculations. A case study for the structure based optimization of d-amino acid oxidase inhibitors
AI-powered IC50 prediction for p53 inhibitors drug-target interaction via hybrid graph neural networks
Molecular simulation and docking studies of Gal1p and Gal3p proteins in the presence and absence of ligands ATP and galactose: implication for transcriptional activation of GAL genes
Electrostatic complementarity between proteins and ligands. 2. Ligand moieties
Computational analysis of local membrane properties
Asp746 to Glycine Change May have a Greater Influence than Cys751 to Serine Change in Accounting for Ligand Selectivity between EGFR and HER-2 at the ATP Site
Energetic basis for drug resistance of HIV-1 protease mutants against amprenavir
Pushing the boundaries of 3D-QSAR
Global 3D-QSAR methods: MS-WHIM and autocorrelation
Assessing protein-ligand binding modes with computational tools: the case of PDE4B
Binding free energy predictions of farnesoid X receptor (FXR) agonists using a linear interaction energy (LIE) approach with reliability estimation: application to the D3R Grand Challenge 2
Data modelling with neural networks: Advantages and limitations
Identification of antipsychotic drug fluspirilene as a potential p53-MDM2 inhibitor: a combined computational and experimental study
Models of protein-ligand crystal structures: trust, but verify
Testing the semi-explicit assembly model of aqueous solvation in the SAMPL4 challenge
An in-vitro and in-silico approaches in exploring the molecular contact of COVID-19 antiviral drug molnupiravir with human serum albumin: effect of binding on protein structure
The effect of physical organic properties on hydrophobic fields
Electrostatic evaluation of isosteric analogues
Molecular mechanics and dynamics study of DNA-furocoumarins complexes: Effect of methylation of the angular derivatives on the intercalation geometry
Development of predictive pharmacophore model for in silico screening, and 3D QSAR CoMFA and CoMSIA studies for lead optimization, for designing of potent tumor necrosis factor alpha converting enzyme inhibitors
Anticancer potential of 2,2′-bipyridine hydroxamic acid derivatives in head and neck cancer therapy
QSAR of conformationally flexible molecules: Comparative molecular field analysis of protein-tyrosine kinase inhibitors
SAMPL6 Octanol-water partition coefficients from alchemical free energy calculations with MBIS atomic charges
SPLICE: A program to assemble partial query solutions from three-dimensional database searches into novel ligands
Computer-assisted study on the reaction between pyruvate and ylide in the pathway leading to lactyl-ThDP
The measurement of molecular diversity by receptor site interaction simulation
The perspectives of computational chemistry modeling
Defining the nucleotide binding sites of P2Y receptors using rhodopsin-based homology modeling
Triple hydrogen bonding in a circular arrangement: ab initio, DFT and first-principles MD studies of tris-hydroxyaryl enamines
Autocorrelation descriptor improvements for QSAR: 2DA_Sign and 3DA_Sign
Classical QSAR and comparative molecular field analyses of the host-guest interaction of organic molecules with cyclodextrins
Uncovering abnormal changes in logP after fluorination using molecular dynamics simulations
A Bayesian molecular interaction library
Ligand-, structure- and pharmacophore-based molecular fingerprints: a case study on adenosine A1, A2A, A2B, and A3 receptor antagonists
Computational and experimental studies to discover a promising lead compound, chemically related to natural acetylene acetogenins from Porcelia macrocarpa, against amastigotes of Leishmania (L.) infantum
Development of in silico models for human liver microsomal stability
Milestones in electron crystallography
CORCEMA evaluation of the potential role of intermolecular transferred NOESY in the characterization of ligand-receptor complexes
Blinded evaluation of farnesoid X receptor (FXR) ligands binding using molecular docking and free energy calculations
Predicting water-to-cyclohexane partitioning of the SAMPL5 molecules using dielectric balancing of force fields
Multiple automatic base selection: Protein-ligand docking based on incremental construction without manual intervention
A shape- and chemistry-based docking method and its use in the design of HIV-1 protease inhibitors
Book Review: Andrew R. Leach and Valerie J. Gillet. An Introduction to Chemoinformatics
Structure-guided optimization of small molecule c-Abl activators
Blind prediction of solvation free energies from the SAMPL4 challenge
QSAR workbench: automating QSAR modeling to drive compound design
A new method for estimating the relative binding free energy, derived from a free energy variational principle for the Pim-1-kinase-ligand and FKBP-ligand systems
Determination of clefts in receptor structures
FreeSolv: a database of experimental and calculated hydration free energies, with input files