yusuke1997/dblp-id-title huggingface dataset:
Comparison of two implementations of the incremental construction algorithm in flexible docking of thrombin inhibitors
The receptor-dependent LQTA-QSAR: application to a set of trypanothione reductase inhibitors
Monte Carlo on the manifold and MD refinement for binding pose prediction of protein-ligand complexes: 2017 D3R Grand Challenge
SAMPL7 protein-ligand challenge: A community-wide evaluation of computational methods against fragment screening and pose-prediction
Computation of 3D queries for ROCS based virtual screens
A hybrid approach for addressing ring flexibility in 3D database searching
Characterising the geometric diversity of functional groups in chemical databases
Intermediate states in the binding process of folic acid to folate receptor α: insights by molecular dynamics and metadynamics
Feature trees: A new molecular similarity measure based on tree matching
LUDI: rule-based automatic design of new substituents for enzyme inhibitor leads
The educational foundation of computational chemistry
LINGO-DL: a text-based approach for molecular similarity searching
Pharmacophore modelling of structurally unusual diltiazem mimics at L-type calcium channels
Stereochemistry of charged nitrogen-aromatic interactions and its involvement in ligand-receptor binding
Secure analysis of distributed chemical databases without data integration
A theoretical study of the Si-O bond in disiloxane and related molecules
Development of an automatic estimation system for both the partition coefficient and aqueous solubility
ConoDL: a deep learning framework for rapid generation and prediction of conotoxins
SCF-MO study of the polyglycine II structure
Water molecules in protein-ligand interfaces. Evaluation of software tools and SAR comparison
Conformational and receptor-binding properties of the insect neuropeptide proctolin and its analogues
Scoring functions: A view from the bench
Binding affinity prediction for binary drug-target interactions using semi-supervised transfer learning
A theoretical study of cis - trans isomerisation in H-ZSM5: probing the impact of cluster size and zeolite framework on energetics and structure
Common prevalence of alanine and glycine in mobile reactive centre loops of serpins and viral fusion peptides: Do prions possess a fusion peptide?
In vitro and in silico evaluation of synthesized 4-Anilinoquinazoline derivatives as potential anticancer agents
Effectiveness of graph-based and fingerprint-based similarity measures for virtual screening of 2D chemical structure databases
Molecular dynamics simulations as a guide for modulating small molecule aggregation
Towards a new age of virtual ADME/TOX and multidimensional drug discovery
De novo ligand design with explicit water molecules: an application to bacterial neuraminidase
Molecular modeling studies on the urease active site and the enzyme-catalyzed urea hydrolysis
MDFit: automated molecular simulations workflow enables high throughput assessment of ligands-protein dynamics
SAMPL7 blind predictions using nonequilibrium alchemical approaches
Calculating physical properties of organic compounds for environmental modeling from molecular structure
Advances in exploring activity cliffs
Systematic assessment of scaffold distances in ChEMBL: prioritization of compound data sets for scaffold hopping analysis in virtual screening
Time-efficient flexible superposition of medium-sized molecules
iScreen: world's first cloud-computing web server for virtual screening and de novo drug design based on TCM database@Taiwan
Comparing the performance of meta-classifiers - a case study on selected imbalanced data sets relevant for prediction of liver toxicity
Workflows and performances in the ranking prediction of 2016 D3R Grand Challenge 2: lessons learned from a collaborative effort
Calculations of protein-ligand binding entropy of relative and overall molecular motions
Elucidating the binding mechanism of 1,4-bis[(3-Piperidino)propanamido]anthracen-9,10-dione (1,4-BPAQ) to human telomeric G-quadruplexes: a multi-technique approach including spectroscopic, calorimetric and molecular docking insights
Covalent docking of selected boron-based serine beta-lactamase inhibitors
Source of oseltamivir resistance due to single E119D and double E119D/H274Y mutations in pdm09H1N1 influenza neuraminidase
Computational modeling and in-vitro/in-silico correlation of phospholipid-based prodrugs for targeted drug delivery in inflammatory bowel disease
Property distribution of drug-related chemical databases
A successful virtual screening application: prediction of anticonvulsant activity in MES test of widely used pharmaceutical and food preservatives methylparaben and propylparaben
Limiting assumptions in molecular modeling: electrostatics
E-state fields: Applications to 3D QSAR
A very short history of structure-based design: how did we get here and where do we need to go?
Binding mode similarity measures for ranking of docking poses: a case study on the adenosine A2A receptor
Comparative molecular field analysis of CCK-A antagonists using field-fit as an alignment technique. A convenient guide to design new CCK-A ligands
Consensus Induced Fit Docking (cIFD): methodology, validation, and application to the discovery of novel Crm1 inhibitors
De novo drug design through gradient-based regularized search in information-theoretically controlled latent space
Fast prediction and visualization of protein binding pockets with PASS
Site-Identification by Ligand Competitive Saturation (SILCS) assisted pharmacophore modeling
Chemical space networks: a powerful new paradigm for the description of chemical space
GEOM: A new tool for molecular modelling based on distance geometry calculations with NMR data
The slow but steady rise of binding free energy calculations in drug discovery
Computational chemogenomics: Is it more than inductive transfer?
Ligand-based virtual screening under partial shape constraints
The effects of tautomerism on the nature of molecules in the solid state
Pep-Calc.com: a set of web utilities for the calculation of peptide and peptoid properties and automatic mass spectral peak assignment
Construction of a full three-dimensional model of the transpeptidase domain of Streptococcus pneumoniae PBP2x starting from its C-alpha-atom coordinates
Erratum to: Predicting hydration free energies using all-atom molecular dynamics simulations and multiple starting conformations
Structural insights into binding of small molecule inhibitors to Enhancer of Zeste Homolog 2
MTD-ADJ: A multiconformational minimal topologic difference for determining bioactive conformers using adjusted biological activities
Predicting PAMPA permeability using the 3D-RISM-KH theory: are we there yet?
Hierarchical clustering analysis of flexible GBR 12909 dialkyl piperazine and piperidine analogs
Quantum simulations of SARS-CoV-2 main protease M pro enable high-quality scoring of diverse ligands
Molecular modeling of the neurophysin I/oxytocin complex
Atomistic insight into sequence-directed DNA bending and minicircle formation propensity in the absence and presence of phased A-tracts
Computer-assisted combinatorial design of bicyclic thymidine analogs as inhibitors of Mycobacterium tuberculosis thymidine monophosphate kinase
Bioactive focus in conformational ensembles: a pluralistic approach
The importance of molecular complexity in the design of screening libraries
Active site similarity between human and Plasmodium falciparum phosphodiesterases: considerations for antimalarial drug design
Rapid prediction of solvation free energy. 3. Application to the SAMPL2 challenge
Inhibition mechanism of MRTX1133 on KRAS G12D : a molecular dynamics simulation and Markov state model study
Discovery of a potential positive allosteric modulator of glucagon-like peptide 1 receptor through virtual screening and experimental study
Molecular docking, dynamics simulations, and in vivo studies of gallic acid in adenine-induced chronic kidney disease: targeting KIM-1 and NGAL
COSMO-RS: A novel view to physiological solvation and partition questions
R-group template CoMFA combines benefits of "ad hoc" and topomer alignments using 3D-QSAR for lead optimization
Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host-guest binding: II. regression and dielectric constant
New leads for selective GSK-3 inhibition: pharmacophore mapping and virtual screening studies
Theoretical descriptors for the quantitative rationalisation of plastocyanin mutant functional propertiess
VEGA - An open platform to develop chemo-bio-informatics applications, using plug-in architecture and script programming
ChEMBL. An interview with John Overington, team leader, chemogenomics at the European Bioinformatics Institute Outstation of the European Molecular Biology Laboratory (EMBL-EBI)
Modeling and active site refinement for G protein-coupled receptors: application to the β-2 adrenergic receptor
Automated site-directed drug design: An assessment of the transferability of atomic residual charges (CNDO) for molecular fragments
Refinement of Catalyst hypotheses using simplex optimisation
CADD medicine: design is the potion that can cure my disease
From bird's eye views to molecular communities: two-layered visualization of structure-activity relationships in large compound data sets
Heuristic lipophilicity potential for computer-aided rational drug design
Future structural genomics initiatives: an interview with Helen Berman, director of the Protein Data Bank
Evaluation of a novel molecular vibration-based descriptor (EVA) for QSAR studies: 2. Model validation using a benchmark steroid dataset
A quantum-mechanical study of the chain-length dependent stability of the extended and 3 10 -helix conformations in dehydroalanine oligopeptides
Ligand- and receptor-based docking with LiBELa
The backbone of our chemical computations
Comparative residue interaction analysis (CoRIA): a 3D-QSAR approach to explore the binding contributions of active site residues with ligands
Predicting skin permeability using the 3D-RISM-KH theory based solvation energy descriptors for a diverse class of compounds
Empirical scoring functions. II. The testing of an empirical scoring function for the prediction of ligand-receptor binding affinities and the use of Bayesian regression to improve the quality of the model
Pharmacophore model for bile acids recognition by the FPR receptor
Development of energetic pharmacophore for the designing of 1, 2, 3, 4-tetrahydropyrimidine derivatives as selective cyclooxygenase-2 inhibitors
Development of QSAR models for microsomal stability: identification of good and bad structural features for rat, human and mouse microsomal stability
Molecular simulations of paclitaxel binding to mutant β-tubulin: insights into chemotherapy resistance
Pose prediction and virtual screening performance of GOLD scoring functions in a standardized test
Exploring DrugCentral: from molecular structures to clinical effects
The orientation of N-H...O=C and N-H...N hydrogen bonds in biological systems: How good is a point charge as a model for a hydrogen bonding atom?
Binding pose and affinity prediction in the 2016 D3R Grand Challenge 2 using the Wilma-SIE method
Ligand docking and binding site analysis with PyMOL and Autodock/Vina
Deep learning model for activity cliffs prediction: a comprehensive approach to protein kinase inhibitors
DeepCOMO: from structure-activity relationship diagnostics to generative molecular design using the compound optimization monitor methodology
Application of artificial neural networks and DFT-based parameters for prediction of reaction kinetics of ethylbenzene dehydrogenase
Design of new imidazole derivatives with anti-HCMV activity: QSAR modeling, synthesis and biological testing
The AI-driven Drug Design (AIDD) platform: an interactive multi-parameter optimization system integrating molecular evolution with physiologically based pharmacokinetic simulations
A computational analysis of binding modes and conformation changes of MDM2 induced by p53 and inhibitor bindings
DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases
An improved theoretical approach to the empirical corrections of density functional theory
A computational study of cardiac glycosides from Vernonia amygdalina as PI3K inhibitors for targeting HER2 positive breast cancer
Structural dynamics of native and V260E mutant C-terminal domain of HIV-1 integrase
Modeling the inhibition of quadruple mutant Plasmodium falciparum dihydrofolate reductase by pyrimethamine derivatives
Application of the alchemical transfer and potential of mean force methods to the SAMPL8 host-guest blinded challenge
Protein-ligand pose and affinity prediction: Lessons from D3R Grand Challenge 3
Molecular basis of quantitative structure-properties relationships (QSPR): A quantum similarity approach
Predicting octanol/water partition coefficients for the SAMPL6 challenge using the SM12, SM8, and SMD solvation models
Erratum to: A desirability function-based scoring scheme for selecting fragment-like class A aminergic GPCR ligands
Rapid activity prediction of HIV-1 integrase inhibitors: harnessing docking energetic components for empirical scoring by chemometric and artificial neural network approaches
Identifying the binding mode of a molecular scaffold
Hit diffusion: limitations to drug discovery and structure-based design
The µ- and delta-opioid pharmacophore conformations of cyclic beta-casomorphin analogues indicate docking of the Phe 3 residue to different domains of the opioid receptors
Modeling activated states of GPCRs: the rhodopsin template
Side chain virtual screening of matched molecular pairs: a PDB-wide and ChEMBL-wide analysis
In silico screening for Plasmodium falciparum enoyl-ACP reductase inhibitors
Call for Papers: GRC, CADD, and statistics, and all that
The errors of our ways: taking account of error in computer-aided drug design to build confidence intervals for our next 25 years
SAMPL6 host-guest blind predictions using a non equilibrium alchemical approach
In silico exploration of natural xanthone derivatives as potential inhibitors of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replication and cellular entry
Influence of metal cofactors and water on the catalytic mechanism of creatininase-creatinine in aqueous solution from molecular dynamics simulation and quantum study
Synthesis, TD-DFT calculations, molecular docking and ADME studies of new spiro-oxindole derivatives containing 5(4H)-oxazolone as anti-viral and anti-bacterial agents
The future of molecular dynamics simulations in drug discovery
Structure-based virtual screening of small-molecule antagonists of platelet integrin αIIbβ3 that do not prime the receptor to bind ligand
Designing novel nicotinic agonists by searching a database of molecular shapes
Biosensor-based small molecule fragment screening with biolayer interferometry
Simplified, interpretable graph convolutional neural networks for small molecule activity prediction
Charge distribution from a simple molecular orbital type calculation and non-bonding interaction terms in the force field MAB
Targeting multiple pathways with virtual screening to identify the multi-target agent for Alzheimer's disease treatment
Investigating the extension of pairwise distance pharmacophore measures to triplet-based descriptors
First virtual screening and experimental validation of inhibitors targeting GES-5 carbapenemase
Toxigraphnet: a graph neural network framework for precise toxicity prediction of drug molecules
pK a measurements for the SAMPL6 prediction challenge for a set of kinase inhibitor-like fragments
Comparison of bioactive chemical space networks generated using substructure- and fingerprint-based measures of molecular similarity
A Virtual Active Compound Produced from the Negative Image of a Ligand-binding Pocket, and its Application to in-silico Drug Screening
SPROUT: A program for structure generation
Synthesis, characterization and density functional theory of a novel dichloro(2-(1-anthracene-9-ylmethyl)-1H-1,2,3-triazole-5-yl) pyridine)Cu(II) and polymeric dichloro(2-(1-anthracene-9-ylmethyl)-1H-1,2,3 -triazole-5-yl)pyridine) Cd(II) complexes
Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) of thiazolone derivatives as hepatitis C virus NS5B polymerase allosteric inhibitors
Binding mode prediction and MD/MMPBSA-based free energy ranking for agonists of REV-ERBα/NCoR
Forging the future
Predicting ligand binding affinity using on- and off-rates for the SAMPL6 SAMPLing challenge
Improving binding mode and binding affinity predictions of docking by ligand-based search of protein conformations: evaluation in D3R grand challenge 2015
Variable selection and specification of robust QSAR models from multicollinear data: arylpiperazinyl derivatives with affinity and selectivity for α 2 -adrenoceptors
Homology modeling, docking and structure-based pharmacophore of inhibitors of DNA methyltransferase
BRUTUS: Optimization of a grid-based similarity function for rigid-body molecular superposition. II. Description and characterization
Design, synthesis, characterization, in silico, in vitro and in vivo antidiabetic studies of novel benzothiophene derivatives
The computational design of test compounds with potentially specific biological activity: Histamine-H2 agonists derived from 5-HT/H2 antagonists
Scientific workflow systems: Pipeline Pilot and KNIME
A molecular dynamics simulation study decodes the early stage of the disassembly process abolishing the human SAMHD1 function
Understanding molecular structure from molecular mechanics
Effect of training data size and noise level on support vector machines virtual screening of genotoxic compounds from large compound libraries
Electrostatic complementarity between proteins and ligands. 3. Structural basis
Exploring the molecular basis of selectivity in A 1 adenosine receptors agonists: a case study
Homology modeling and molecular dynamics simulation of N -myristoyltransferase from protozoan parasites: active site characterization and insights into rational inhibitor design
Structure and dynamics of mesophilic variants from the homing endonuclease I-DmoI
MolGraph: a Python package for the implementation of molecular graphs and graph neural networks with TensorFlow and Keras
Similarity of molecular shape
The agonistic binding site at the histamine H 2 receptor. II. Theoretical investigations of histamine binding to receptor models of the seven alpha-helical transmembrane domain
Molecular modelling in design of crop protection chemicals
The role of zinc finger linkers in zinc finger protein binding to DNA
Identification of circadian rhythm-associated genes and therapeutic targets in myopia with dynamics simulation: a multiomics study using machine learning algorithms and Mendelian randomization
Quantitative Series Enrichment Analysis (QSEA): a novel procedure for 3D-QSAR analysis
Design of an activity landscape view taking compound-based feature probabilities into account
Validated ligand mapping of ACE active site
Feature-map vectors: a new class of informative descriptors for computational drug discovery
Ligand efficiency metrics considered harmful
Reactant- and product-based approaches to the design of combinatorial libraries
A desirability function-based scoring scheme for selecting fragment-like class A aminergic GPCR ligands
kScore: a novel machine learning approach that is not dependent on the data structure of the training set
The nature of topological parameters. I. Are topological parameters 'fundamental properties'?
Structure-based discovery of novel non-covalent small molecule inhibitors of USP30
Molecular modelling prediction of ligand binding site flexibility
Indices of differences of path lengths: Novel topological descriptors derived from electronic interferences in graphs
OVID and SUPER: Two overlap programs for drug design
A blind SAMPL6 challenge: insight into the octanol-water partition coefficients of drug-like molecules via a DFT approach
Warmr: a data mining tool for chemical data
Structural models of antibody variable fragments: A method for investigating binding mechanisms
Correction to: Computational workflow for discovering small molecular binders for shallow binding sites by integrating molecular dynamics simulation, pharmacophore modeling, and machine learning: STAT3 as case study
Classification scheme for the design of serine protease targeted compound libraries
Optimizing doped libraries by using genetic algorithms
Conformational analysis of nevirapine, a non-nucleoside HIV-1 reverse transcriptase inhibitor, based on quantum mechanical calculations
Challenging the gold standard for 3D-QSAR: template CoMFA versus X-ray alignment
Blind prediction of cyclohexane-water distribution coefficients from the SAMPL5 challenge
Reverse-docking as a computational tool for the study of asymmetric organocatalysis
On the importance of topological descriptors in understanding structure-property relationships
Parametrization of a force field for metals complexed to biomacromolecules: applications to Fe(II), Cu(II) and Pb(II)
Association of Cytochrome P450 Enzymes is a Determining Factor in their Catalytic Activity
Classification of auxin plant hormones by interaction property similarity indices
Molecular design of two sterol 14α-demethylase homology models and their interactions with the azole antifungals ketoconazole and bifonazole
A consistent description of HYdrogen bond and DEhydration energies in protein-ligand complexes: methods behind the HYDE scoring function
ALOHA: a novel probability fusion approach for scoring multi-parameter drug-likeness during the lead optimization stage of drug discovery
Unveiling the G4-PAMAM capacity to bind and protect Ang-(1-7) bioactive peptide by molecular dynamics simulations
Non-equilibrium approach for binding free energies in cyclodextrins in SAMPL7: force fields and software
New insights into the stereochemical requirements of the bradykinin B2 receptor antagonists binding
Molecular dynamics characterization of the SAMHD1 Aicardi-Goutières Arg145Gln mutant: structural determinants for the impaired tetramerization
ClogPalk: a method for predicting alkane/water partition coefficient
An overview of the diversity represented in commercially-available databases
Protein fragment reconstruction using various modeling techniques
RNA unrestrained molecular dynamics ensemble improves agreement with experimental NMR data compared to single static structure: a test case
Identification of novel small molecule TGF-β antagonists using structure-based drug design
Anticancer potential of novel benzothiazolyl piperidine-3-carboxamide derivatives as CDKs and VEGFR2 multi-target kinase inhibitors
Disruptor of telomeric silencing 1-like (DOT1L): disclosing a new class of non-nucleoside inhibitors by means of ligand-based and structure-based approaches
In search of new lead compounds for trypanosomiasis drug design: A protein structure-based linked-fragment approach
Binding of cyclic carboxylates to octa-acid deep-cavity cavitand
Computational study on mechanism of G-quartet oligonucleotide T40214 selectively targeting Stat3
SAMPL7 physical property prediction from EC-RISM theory
Molecular structure, DFT computations, and docking studies of an imidazo[1,2-a]pyridine derivative containing 1,2,3-triazole and 4-bromophenyl moieties
3D-QSAR using 'Multiconformer' alignment: The use of HASL in the analysis of 5-HT1A thienopyrimidinone ligands
Geometry optimization method versus predictive ability in QSPR modeling for ionic liquids
Synthesis and conformational analysis by 1 H NMR and restrained molecular dynamics simulations of the cyclic decapeptide [Ser-Tyr-Ser-Met-Glu-His-Phe-Arg-Trp-Gly]
Computational exploration and experimental validation to identify a dual inhibitor of cholinesterase and amyloid-beta for the treatment of Alzheimer's disease
Correlation of protein binding pocket properties with hits' chemistries used in generation of ultra-large virtual libraries
Essential dynamics/factor analysis for the interpretation of molecular dynamics trajectories
As-Rigid-As-Possible molecular interpolation paths
Computer-aided molecular modeling of a D 2 -agonist dopamine pharmacophore