yusuke1997/dblp-id-title huggingface dataset:
QSAR of benzene derivatives: comparison of classical descriptors, quantum theoretic parameters and flip regression, exemplified by phenylalkylamine hallucinogens
Structural insights of a PI3K/mTOR dual inhibitor with the morpholino-triazine scaffold
MENTHOR, a database system for the storage and retrieval of three-dimensional molecular structures and associated data searchable by substructural, biologic, physical, or geometric properties
Touching proteins with virtual bare hands - Visualizing protein-drug complexes and their dynamics in self-made virtual reality using gaming hardware
Automated QSPR through Competitive Workflow
Design and synthesis of type-III mimetics of omega-conotoxin GVIA
Quantum chemical studies on tautomerism of barbituric acid in gas phase and in solution
Philip S. Magee: a life in QSAR
Computational approaches for predicting mutant protein stability
Interactions between anti-ErbB2 antibody A21 and the ErbB2 extracellular domain provide a basis for improving A21 affinity
Lessons learned from the design of chemical space networks and opportunities for new applications
A molecular model of the folate binding site of Pneumocystis carinii dihydrofolate reductase
Hydrophobic Molecular Similarity from MST Fractional Contributions to the Octanol/water Partition Coefficient
Design of a colicin E7 based chimeric zinc-finger nuclease
Inflation of correlation in the pursuit of drug-likeness
Improving ligand 3D shape similarity-based pose prediction with a continuum solvent model
SAMPL2 challenge: prediction of solvation energies and tautomer ratios
Assessing the stability of free-energy perturbation calculations by performing variations in the method
On the interpretation and interpretability of quantitative structure-activity relationship models
ANVAS: Artificial Neural Variables Adaptation System for descriptor selection
Distant collaboration in drug discovery: The LINK3D project
Pharmacophore identification by molecular modeling and chemometrics: The case of HMG-CoA reductase inhibitors
Conformational analysis of kainate in aqueous solution in relation to its binding to AMPA and kainic acid receptors
Free energy calculations offer insights into the influence of receptor flexibility on ligand-receptor binding affinities
Symposium overview computer simulation of inorganic solids
A search for sources of drug resistance by the 4D-QSAR analysis of a set of antimalarial dihydrofolate reductase inhibitors
Pattern recognition display methods for the analysis of computed molecular properties
LiteBoost: a lightweight and explainable boosting model for predicting polymer density from SMILES data
Protein-small molecule docking with receptor flexibility in iMOLSDOCK
Quantum chemical and molecular mechanics studies on the assessment of interactions between resveratrol and mutant SOD1 (G93A) protein
Conformational flexibility of DENV NS2B/NS3pro: from the inhibitor effect to the serotype influence
De novo and inverse folding predictions of protein structure and dynamics
Prediction of cyclohexane-water distribution coefficients for the SAMPL5 data set using molecular dynamics simulations with the OPLS-AA force field
Superimposition evaluation of ecdysteroid agonist chemotypes through multidimensional QSAR
Learning epistatic interactions from sequence-activity data to predict enantioselectivity
Parameterization of an empirical model for the prediction of n -octanol, alkane and cyclohexane/water as well as brain/blood partition coefficients
Genetic neural network modeling of the selective inhibition of the intermediate-conductance Ca 2+ -activated K + channel by some triarylmethanes using topological charge indexes descriptors
Mechanism of enhanced conversion of 1, 2, 3-trichloropropane by mutant haloalkane dehalogenase revealed by molecular modeling
An explicit-solvent hybrid QM and MM approach for predicting pKa of small molecules in SAMPL6 challenge
Optimization of biaryl piperidine and 4-amino-2-biarylurea MCH1 receptor antagonists using QSAR modeling, classification techniques and virtual screening
Design of a tripartite network for the prediction of drug targets
GADRC: a graph-based approach for drug repositioning with deep residual networks and computational feature-guided undersampling
Insight into the sequence-specific elements leading to increased DNA bending and ligase-mediated circularization propensity by antitumor trabectedin
Turbo prediction: a new approach for bioactivity prediction
Discovery of a small-molecule inhibitor of Dvl-CXXC5 interaction by computational approaches
Enhancing reaction-based de novo design using a multi-label reaction class recommender
Chain melting temperature estimation for phosphatidyl cholines by quantum mechanically derived quantitative structure property relationships
A practical procedure for the determination of electrostatic charges of large molecules
Computational methods for the structural alignment of molecules
Combined experimental and computational investigation of vildagliptin: spectroscopy, electronic structure, MD and Docking to EGFR, VEGFR2, and HER2 anticancer targets
A least-squares-fitting procedure for an efficient preclinical ranking of passive transport across the blood-brain barrier endothelium
Prediction of SAMPL4 host-guest binding affinities using funnel metadynamics
Development of QSARs for cysteine-containing di- and tripeptides with antioxidant activity:influence of the cysteine position
A structure-activity relationship study of catechol-O-methyltransferase inhibitors combining molecular docking and 3D QSAR methods
Active site acidic residues and structural analysis of modelled human aromatase: A potential drug target for breast cancer
Exploring ensembles of bioactive or virtual analogs of X-ray ligands for shape similarity searching
Biomolecular force fields: where have we been, where are we now, where do we need to go and how do we get there?
Design, structure-based focusing and in silico screening of combinatorial library of peptidomimetic inhibitors of Dengue virus NS2B-NS3 protease
Conformational behaviour and molecular similarity of some beta 1 -adrenergic ligands
Predicting hydration free energies with chemical accuracy: the SAMPL4 challenge
Defining scaffold geometries for interacting with proteins: geometrical classification of secondary structure linking regions
Chemistry, information and Frank: a tribute to Frank Brown
IsoStar: A library of information about nonbonded interactions
Affinity prediction using deep learning based on SMILES input for D3R grand challenge 4
Relative free energies of binding to thymidylate synthase of 2- and/or 4-thio and/or 5-fluoro analogues of dUMP
Blind prediction of distribution in the SAMPL5 challenge with QM based protomer and p K a corrections
1001 Ways to run AutoDock Vina for virtual screening
Identification of target-specific bioisosteric fragments from ligand-protein crystallographic data
Extracting ligands from receptors by reversed targeted molecular dynamics
A density functional reactivity theory (DFRT) based approach to understand the interaction of cisplatin analogues with protecting agents
Forces in molecular recognition: Comparison of experimental data and molecular mechanics calculations
Prediction of the binding sites of huperzine A in acetylcholinesterase by docking studies
Interpretation of machine learning models using shapley values: application to compound potency and multi-target activity predictions
2D and 3D QSAR studies of diarylpyrimidine HIV-1 reverse transcriptase inhibitors
5-HT1A receptor pharmacophores to screen for off-target activity of α1-adrenoceptor antagonists
Predicting the effects of amino acid replacements in peptide hormones on their binding affinities for class B GPCRs and application to the design of secretin receptor antagonists
Designing a multi-epitope mRNA vaccine to combat human metapneumovirus based on consensus sequence using reverse vaccinology
The character of molecular modeling
Antagonist-perturbation mechanism for activation function-2 fixed motifs: active conformation and docking mode of retinoid X receptor antagonists
3D-chiral Atom, Atom-type, and Total Non-stochastic and Stochastic Molecular Linear Indices and their Applications to Central Chirality Codification
eFindSite: Improved prediction of ligand binding sites in protein models using meta-threading, machine learning and auxiliary ligands
Alignment of flexible molecules at their receptor site using 3D descriptors and Hi-PCA
Molecular modeling of protein structure and function: A bioinformatic approach
Experimental versus predicted affinities for ligand binding to estrogen receptor: iterative selection and rescoring of docked poses systematically improves the correlation
QSID Tool: a new three-dimensional QSAR environmental tool
Computer-aided drug discovery research at a global contract research organization
Hydrogen bonding and dimeric self-association of 2-pyrrolidinone: An ab initio study
Inclusion of conserved buried water molecules in the model structure of rat submaxillary kallikrein
QMOD: physically meaningful QSAR
Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset
Binding affinities of the farnesoid X receptor in the D3R Grand Challenge 2 estimated by free-energy perturbation and docking
In vitro and in silico studies of anticancer activities of pectic acid and pectin oligosaccharide in Epstein-Barr virus-positive nasopharyngeal carcinoma
Derivation of a 3D pharmacophore model for the angiotensin-II site one receptor
3D-QSAR and docking studies on 4-anilinoquinazoline and 4-anilinoquinoline epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors
Structural and functional analysis of a novel psychrophilic β-mannanase from Glaciozyma antarctica PI12
Distilling the essential features of a protein surface for improving protein-ligand docking, scoring, and virtual screening
Automated site-directed drug design: Searches of the Cambridge Structural Database for bond lengths in molecular fragments to be used for automated structure assembly
Ring system-based chemical graph generation for de novo molecular design
Enabling drug discovery project decisions with integrated computational chemistry and informatics
High accuracy quantum-chemistry-based calculation and blind prediction of macroscopic pKa values in the context of the SAMPL6 challenge
Elaborate ligand-based modeling coupled with QSAR analysis and in silico screening reveal new potent acetylcholinesterase inhibitors
Electrostatics and computational modelling Editorial overview
Support vector inductive logic programming outperforms the naive Bayes classifier and inductive logic programming for the classification of bioactive chemical compounds
Enhancing accuracy of virtual kinase profiling via application of graph neural network to 3D pharmacophore ensembles
Modeling the interactions of a peptide-major histocompatibility class I ligand with its receptors. I. Recognition by two alpha-beta T cell receptors
Computational design of bio-inspired carnosine-based HOBr antioxidants
CoMFA and CoMSIA 3D-quantitative structure-activity relationship model on benzodiazepine derivatives, inhibitors of phosphodiesterase IV
Identification of potential inhibitors of Mycobacterium tuberculosis shikimate kinase: molecular docking, in silico toxicity and in vitro experiments
Docking and quantitative structure-activity relationship studies for 3-fluoro-4-(pyrrolo[2, 1- f ][1, 2, 4]triazin-4-yloxy)aniline, 3-fluoro-4-(1H-pyrrolo[2, 3-b]pyridin-4-yloxy)aniline, and 4-(4-amino-2-fluorophenoxy)-2-pyridinylamine derivatives as c-Met kinase inhibitors
Predictions of hydration free energies from continuum solvent with solute polarizable models: the SAMPL2 blind challenge
Structural insights for the design of new PPARgamma partial agonists with high binding affinity and low transactivation activity
Estimation of relative binding free energy based on a free energy variational principle for the FKBP-ligand system
Cavity search: An algorithm for the isolation and display of cavity-like binding regions
Discovery of novel human acrosin inhibitors by virtual screening
Conformational analysis of [Met5]-enkephalin: Solvation and ionization considerations
Modelling of α-lactalbumin from the known structure of hen egg white lysozyme using molecular dynamics
Stability and free energy calculation of LNA modified quadruplex: a molecular dynamics study
Prediction of hydration free energies for the SAMPL4 data set with the AMOEBA polarizable force field
Molecular dynamics simulations of halide glasses
Advanced investigation of the adsorption process of geosmin molecules on polar bear and camel olfactory receptors: statistical physics treatment, in-depth DFT-modeling, and docking analysis
'ValleyScan': A new two-bond drive technique for the calculation of potential energy surfaces with less computational effort
A proposed common spatial pharmacophore and the corresponding active conformations of some peptide leukotriene receptor antagonists
Computer-aided drug design at Boehringer Ingelheim
On the active site of mononuclear B1 metallo β-lactamases: a computational study
An eleven amino acid residue deletion expands the substrate specificity of acetyl xylan esterase II (AXE II) from Penicillium purpurogenum
Prediction of activity cliffs on the basis of images using convolutional neural networks
Molecular structure matching by simulated annealing. II. An exploration of the evolution of configuration landscape problems
Theoretical studies on the reaction of mono- and ditriflate derivatives of 1, 4: 3, 6-dianhydro-d-mannitol with trimethylamine - Can a quaternary ammonium salt be a source of the methyl group?
The measurement of molecular diversity: A three-dimensional approach
An ab initio theoretical study of the stereoisomers of tetrahydrocannabinols
Converging free energies of binding in cucurbit[7]uril and octa-acid host-guest systems from SAMPL4 using expanded ensemble simulations
Comparative molecular field analysis of non-steroidal aromatase inhibitors related to fadrozole
Lead-like, drug-like or "Pub-like": how different are they?
Molecular dynamics modeling the synthetic and biological polymers interactions pre-studied via docking - Anchors modified polyanions interference with the HIV-1 fusion mediator
Novel inhibitors to Taenia solium Cu/Zn superoxide dismutase identified by virtual screening
Fragment-based prediction of skin sensitization using recursive partitioning
Composite multi-parameter ranking of real and virtual compounds for design of MC4R agonists: Renaissance of the Free-Wilson methodology
An improved adaptive genetic algorithm for protein-ligand docking
Homology modeling and molecular interaction field studies of α-glucosidases as a guide to structure-based design of novel proposed anti-HIV inhibitors
Identification of novel Trypanosoma cruzi prolyl oligopeptidase inhibitors by structure-based virtual screening
Investigation of structures and properties of cyclic peptide nanotubes by experiment and molecular dynamics
A molecular-field-based similarity study of non-nucleoside HIV-1 reverse transcriptase inhibitors
Computational atomistic blueprinting of novel conducting copolymers using particle swarm optimization
Molecular dynamics simulations of ligand-induced backbone conformational changes in the binding site of the periplasmic lysine-, arginine-, ornithine-binding protein
Network-based piecewise linear regression for QSAR modelling
A computational docking study on the pH dependence of peptide binding to HLA-B27 sub-types differentially associated with ankylosing spondylitis
How to do an evaluation: pitfalls and traps
Sequence specificity in DNA-drug intercalation: MD simulation and density functional theory approaches
The SAMPL5 host-guest challenge: computing binding free energies and enthalpies from explicit solvent simulations by the attach-pull-release (APR) method
TargetCPP: accurate prediction of cell-penetrating peptides from optimized multi-scale features using gradient boost decision tree
QM/MM based 3D QSAR models for potent B-Raf inhibitors
StackHCV: a web-based integrative machine-learning framework for large-scale identification of hepatitis C virus NS5B inhibitors
A very large diversity space of synthetically accessible compounds for use with drug design programs
Do benzodiazepines mimic reverse-turn structures?
Molecular structure matching by simulated annealing. IV. Classification of atom correspondences in sets of dissimilar molecules
A new peptide docking strategy using a mean field technique with mutually orthogonal Latin square sampling
Structural analysis of the Aβ(11-42) amyloid fibril based on hydrophobicity distribution
Design and characterization of chemical space networks for different compound data sets
QSAR and molecular docking for the search of AOX inhibitors: a rational drug discovery approach
Application of the 3D-RISM-KH molecular solvation theory for DMSO as solvent
Pyridones as NNRTIs against HIV-1 mutants: 3D-QSAR and protein informatics
Solvation and formal charge corrections to the Piecewise-Linear Potential
The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure
Molecular modelling studies and the chromatographic behaviour of oxiracetam and some closely related molecules
Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host-guest binding: I. Standard procedure
CoMFA validation of the superposition of six classes of compounds which block GABA receptors non-competitively
Undersampling: case studies of flaviviral inhibitory activities
Fast estimation of hydrogen-bonding donor and acceptor propensities: a GMIPp study
Predicting anticonvulsant activity of benzamides/benzylamines: computational approach using topological descriptors
Evaluation of different virtual screening strategies on the basis of compound sets with characteristic core distributions and dissimilarity relationships
Structure-based design of Aurora A & B inhibitors
DFT-based QSAR and QSPR models of several cis -platinum complexes: solvent effect
Discovery of novel wee1 inhibitors via structure-based virtual screening and biological evaluation
Furan-based benzene mono- and dicarboxylic acid derivatives as multiple inhibitors of the bacterial Mur ligases (MurC-MurF): experimental and computational characterization
Physicochemical QSAR analysis of hERG inhibition revisited: towards a quantitative potency prediction
Performance of the SMD and SM8 models for predicting solvation free energy of neutral solutes in methanol, dimethyl sulfoxide and acetonitrile
Modeling of peptides containing D-amino acids: implications on cyclization
Fine tuning for success in structure-based virtual screening
Applications of rule-induction in the derivation of quantitative structure-activity relationships
Alchemical prediction of hydration free energies for SAMPL
Theoretical investigation of AKT1 mutations in breast cancer: a computational approach to structural and functional insights
Improved docking, screening and selectivity prediction for small molecule nuclear receptor modulators using conformational ensembles
Molecular modelling evaluation of the cytotoxic activity of podophyllotoxin analogues
Genetic algorithms as a tool for helix design - computational and experimental studies on prion protein helix 1
Decoding the multifunctional potential of ursolic acid: antioxidant, antiproliferative, molecular dynamics, and biodegradability evaluations of a mangrove-derived terpenoid
Homo-timeric structural model of human microsomal prostaglandin E synthase-1 and characterization of its substrate/inhibitor binding interactions
Design criteria for molecular mimics of fragments of the beta-turn. 1. C-alpha atom analysis
A pseudoreceptor modelling study of the varicella-zoster virus and human thymidine kinase binding sites
Structure-activity correlation study of HIV-1 inhibitors: Electronic and molecular parameters
BEDAM binding free energy predictions for the SAMPL4 octa-acid host challenge
In silico molecular docking analysis of the human Argonaute 2 PAZ domain reveals insights into RNA interference
Computational study on QSAR modeling, molecular docking, and ADMET profiling of pyrazole-modified catalpol derivatives as prospective dual inhibitors of VEGFR-2/BRAF V600E
Discovery of novel inhibitors of human galactokinase by virtual screening
Computer-aided structure-affinity relationships in a set of piperazine and 3, 8-diazabicyclo[3.2.1]octane derivatives binding to the µ-opioid receptor
Binding energy calculations for hevein-carbohydrate interactions using expanded ensemble molecular dynamics simulations
Towards the comprehensive, rapid, and accurate prediction of the favorable tautomeric states of drug-like molecules in aqueous solution
DR2DI: a powerful computational tool for predicting novel drug-disease associations
The SAMPL4 host-guest blind prediction challenge: an overview
Silver threads
A homology-based model of the human 5-HT2A receptor derived from an in silico activated G-protein coupled receptor
Optimization of CAMD techniques 3. Virtual screening enrichment studies: a help or hindrance in tool selection?
MASSA Algorithm: an automated rational sampling of training and test subsets for QSAR modeling
Prediction of ligand binding mode among multiple cross-docking poses by molecular dynamics simulations
In tribute to Corwin Hansch, father of QSAR
Why you should read Dr. Cramer's perspective
The coordination of the catalytic zinc ion in alcohol dehydrogenase studied by combined quantum-chemical and molecular mechanics calculations
Meta-iPVP: a sequence-based meta-predictor for improving the prediction of phage virion proteins using effective feature representation
Exploring fragment spaces under multiple physicochemical constraints
Shape information from a critical point analysis of calculated electron density maps: Application to DNA-drug systems
The structure-activity relationship of inhibitors of serotonin uptake and receptor binding
Heuristic lipophilicity potential for computer-aided rational drug design: Optimizations of screening functions and parameters
AM1-SM2 and PM3-SM3 parameterized SCF solvation models for free energies in aqueous solution
Strategies for the determination of pharmacophoric 3D database queries
BALLView: An object-oriented molecular visualization and modeling framework
PROGEN: An automated modelling algorithm for the generation of complete protein structures from the alpha-carbon atomic coordinates
Molecular modeling of cytochrome P450 3A4
Comparison of three GPCR structural templates for modeling of the P2Y 12 nucleotide receptor
Characterization of PD-L1 binding sites by a combined FMO/GRID-DRY approach
PRO_LIGAND: An approach to de novo molecular design. 4. Application to the design of peptides
MCDOCK: A Monte Carlo simulation approach to the molecular docking problem
In silico probing and biological evaluation of SETDB1/ESET-targeted novel compounds that reduce tri-methylated histone H3K9 (H3K9me3) level
The SAMPL6 challenge on predicting octanol-water partition coefficients from EC-RISM theory
Computer simulations in zeolite chemistry
Ab initio calculations on iron-porphyrin model systems for intermediates in the oxidative cycle of cytochrome P450s
Dimer asymmetry in superoxide dismutase studied by molecular dynamics simulation
Computational investigation to identify multi-targeted anti-hyperglycemic potential of substituted 2-Mercaptobenzimidazole derivatives and synthesis of new α-glucosidase inhibitors
A functional feature analysis on diverse protein-protein interactions: application for the prediction of binding affinity
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
Outliers in SAR and QSAR: Is unusual binding mode a possible source of outliers?
Conformational specificity of non-canonical base pairs and higher order structures in nucleic acids: crystal structure database analysis
Subunit rotation models activation of serotonin 5-HT 3AB receptors by agonists
Exploring Oxazolidinone scaffolds for future antibiotics: synthesis and computational insights with DFT, docking, ADME and MD simulation