yusuke1997/dblp-id-title huggingface dataset:
Categorical QSAR models for skin sensitization based on local lymph node assay measures and both ground and excited state 4D-fingerprint descriptors
Predicting relative binding affinities of non-peptide HIV protease inhibitors with free energy perturbation calculations
Conformational behaviour of the antineoplastic peptide dolastatin-10 and of two mutated derivatives
Multi-task generative topographic mapping in virtual screening
Challenges of fragment screening
Theoretical models for the conformations and the protonation of triacetonamine
Structural evaluation of an alternative Protein A biomimetic ligand for antibody purification
MathDL: mathematical deep learning for D3R Grand Challenge 4
Improved convergence of binding affinities with free energy perturbation: Application to nonpeptide ligands with pp60src SH2 domain
VSDMIP 1.5: an automated structure- and ligand-based virtual screening platform with a PyMOL graphical user interface
Optimal affinity ranking for automated virtual screening validated in prospective D3R grand challenges
Modeling Epac1 interactions with the allosteric inhibitor AM-001 by co-solvent molecular dynamics
Optimizing Dvl PDZ domain inhibitor by exploring chemical space
Can free energy calculations be fast and accurate at the same time? Binding of low-affinity, non-peptide inhibitors to the SH2 domain of the src protein
Bioactive constituents isolated from the leaves of Phyllostachys Bambusoides with potent soluble epoxide hydrolase inhibitory activity: enzyme kinetics, molecular docking, and molecular dynamics simulations
Improvement of multi-task learning by data enrichment: application for drug discovery
Locally Linear Embedding for dimensionality reduction in QSAR
Improving the accuracy of ultrafast ligand-based screening: incorporating lipophilicity into ElectroShape as an extra dimension
Development, interpretation and temporal evaluation of a global QSAR of hERG electrophysiology screening data
Artificial intelligence in protein-based detection and inhibition of AMR pathways
Recommendations for evaluation of computational methods
QSAR modeling based on the bias/variance compromise: a harmonious
Molecular modeling study of the induced-fit effect on kinase inhibition: the case of fibroblast growth factor receptor 3 (FGFR3)
Structure-based QSAR study on differential inhibition of human prostaglandin endoperoxide H synthase-2 (COX-2) by nonsteroidal anti-inflammatory drugs
Identification and biological assessment of amino benzoxazole derivatives as KDR inhibitors and potential anti-cancer agents
Reinforcing the membrane-mediated mechanism of action of the anti-tuberculosis candidate drug thioridazine with molecular simulations
Mur ligase F as a new target for the flavonoids quercitrin, myricetin, and (-)-epicatechin
Automated conformational analysis: Algorithms for the efficient construction of low-energy conformations
Homology modeling of the receptor binding domain of human thrombopoietin
Multiple receptor-ligand based pharmacophore modeling and molecular docking to screen the selective inhibitors of matrix metalloproteinase-9 from natural products
Obtaining QM/MM binding free energies in the SAMPL8 drugs of abuse challenge: indirect approaches
Binding free energy predictions in host-guest systems using Autodock4. A retrospective analysis on SAMPL6, SAMPL7 and SAMPL8 challenges
The implementation of ab initio quantum chemistry calculations on transputers
Energetic analysis of fragment docking and application to structure-based pharmacophore hypothesis generation
Computational docking simulations of a DNA-aptamer for argininamide and related ligands
Pharmacophore modeling and parallel screening for PPAR ligands
The Protein Data Bank archive as an open data resource
The importance of short structural motifs in protein structure analysis
Azahar: a PyMOL plugin for construction, visualization and analysis of glycan molecules
Matching organic libraries with protein-substructures
Charge calculations in molecular mechanics. Part 8 Partial atomic charges from classical calculations
A CADD-alog of strategies in pharma
A semiempirical SCF-MO study of the tautomeric forms of 3-acetyl tetronic- and tetramic acids
pKa prediction for small molecules: an overview of experimental, quantum, and machine learning-based approaches
An electron-conformational method of identification of pharmacophore and anti-pharmacophore shielding: Application to rice blast activity
Automated site-directed drug design: The generation of a basic set of fragments to be used for automated structure assembly
Pharmacophore refinement of gpIIb/IIIa antagonists based on comparative studies of antiadhesive cyclic and acyclic RGD peptides
New products and rumors of new products
FILO (Field Interaction Ligand Optimization): A simplex strategy for searching the optimal ligand interaction field in drug design
What is computational chemistry?
Wavelets and molecular structure
In silico model for P-glycoprotein substrate prediction: insights from molecular dynamics and in vitro studies
Energy-entropy prediction of octanol-water logP of SAMPL7 N-acyl sulfonamide bioisosters
Insights into resistance mechanism of the macrolide biosensor protein MphR(A) binding to macrolide antibiotic erythromycin by molecular dynamics simulation
Computational exploration and molecular dynamics simulations for investigating the potential inhibitory mechanism of amantadine on the ion channel activity of bovine viral diarrhea virus p7
Automated molecular design: A new fragment-joining algorithm
The histamine H1-receptor antagonist binding site. Part I: Active conformation of cyproheptadine
Computational chemistry at Janssen
SAMPL3: blinded prediction of host-guest binding affinities, hydration free energies, and trypsin inhibitors
Application of target repositioning and in silico screening to exploit fatty acid binding proteins (FABPs) from Echinococcus multilocularis as possible drug targets
Computer graphic study on models of the molybdenum cofactor of xanthine oxidase
MM/GBSA prediction of relative binding affinities of carbonic anhydrase inhibitors: effect of atomic charges and comparison with Autodock4 Zn
Inhibitors of prolyl endopeptidase: Characterization of the pharmacophoric pattern using conformational analysis and 3D-QSAR
Theoretical study of selective methylation in the synthesis of azithromycin
Galileo: Three-dimensional searching in large combinatorial fragment spaces on the example of pharmacophores
Dynamic models of G-protein coupled receptor dimers: indications of asymmetry in the rhodopsin dimer from molecular dynamics simulations in a POPC bilayer
Resolving the problem of trapped water in binding cavities: prediction of host-guest binding free energies in the SAMPL5 challenge by funnel metadynamics
Ultrafast de novo docking combining pharmacophores and combinatorics
Role of R292K mutation in influenza H7N9 neuraminidase toward oseltamivir susceptibility: MD and MM/PB(GB)SA study
The Journal of Computer-Aided Molecular Design: a bibliometric note
Tautomers and topomers: challenging the uncertainties of direct physicochemical modeling
Rethinking the applicability domain analysis in QSAR models
Computer-aided active-site-directed modeling of the Herpes Simplex Virus 1 and human thymidine kinase
Plausible compounds drawn from plants as curative agents for neurodegeneration: An in-silico approach
ADis-QSAR: a machine learning model based on biological activity differences of compounds
An online repository of solvation thermodynamic and structural maps of SARS-CoV-2 targets
New insights from molecular dynamic simulation studies of the multiple binding modes of a ligand with G-quadruplex DNA
Prediction of the binding site of 1-benzyl-4-[(5, 6-dimethoxy-l-indanon-2-yl)methyl]piperidine in acetylcholinesterase by docking studies with the SYSDOC program
QSAR with experimental and predictive distributions: an information theoretic approach for assessing model quality
Using diverse potentials and scoring functions for the development of improved machine-learned models for protein-ligand affinity and docking pose prediction
Comparison of correlation vector methods for ligand-based similarity searching
A review of protein-small molecule docking methods
Identification and neuroprotective evaluation of a potential c-Jun N-terminal kinase 3 inhibitor through structure-based virtual screening and in-vitro assay
Promoter recognition specificity of Corynebacterium glutamicum stress response sigma factors σ D and σ H deciphered using computer modeling and point mutagenesis
Towards an understanding of the molecular basis of hydrophobicity
Activity prediction of substrates in NADH-dependent carbonyl reductase by docking requires catalytic constraints and charge parameterization of catalytic zinc environment
Modeling and conformation analysis of β-cyclodextrin complexes
Molecular shape and electrostatics in the encoding of relevant chemical information
Simplified activity cliff network representations with high interpretability and immediate access to SAR information
Does a diol cyclic urea inhibitor of HIV-1 protease bind tighter than its corresponding alcohol form? A study by free energy perturbation and continuum electrostatics calculations
Exploring the dynamics and interaction of a full ErbB2 receptor and Trastuzumab-Fab antibody in a lipid bilayer model using Martini coarse-grained force field
MM3(96) parameterization for camptothecin analogs: An ab initio and molecular mechanics study
Structural insights into transient receptor potential vanilloid type 1 (TRPV1) from homology modeling, flexible docking, and mutational studies
Identifying and characterising promising small molecule inhibitors of kinesin spindle protein using ligand-based virtual screening, molecular docking, molecular dynamics and MM‑GBSA calculations
Simulation of MDM2 N-terminal domain conformational lability in the presence of imidazoline based inhibitors of MDM2-p53 protein-protein interaction
Assessing the performance of docking, FEP, and MM/GBSA methods on a series of KLK6 inhibitors
Activity, assay and target data curation and quality in the ChEMBL database
Molecular docking and 3D-quantitative structure activity relationship analyses of peptidyl vinyl sulfones: Plasmodium Falciparum cysteine proteases inhibitors
The SAMPL4 hydration challenge: evaluation of partial charge sets with explicit-water molecular dynamics simulations
Conserved network properties of helical membrane protein structures and its implication for improving membrane protein homology modeling at the twilight zone
Comparative docking studies on ligand binding to the multispecific antibodies IgE-La2 and IgE-Lb4
MAB, a generally applicable molecular force field for structure modelling in medicinal chemistry
Generation of in-silico cytochrome P450 1A2, 2C9, 2C19, 2D6, and 3A4 inhibition QSAR models
Predicting infinite dilution activity coefficients of organic compounds in water by quantum-connectivity descriptors
Impact of distance-based metric learning on classification and visualization model performance and structure-activity landscapes
MS-WHIM, new 3D theoretical descriptors derived from molecular surface properties: A comparative 3D QSAR study in a series of steroids
What is research?
Markov model-based polymer assembly from force field-parameterized building blocks
A multiway 3D QSAR analysis of a series of (S)-N-[(1-ethyl-2-pyrrolidinyl)methyl]-6-methoxybenzamides
Predicting partition coefficients for the SAMPL7 physical property challenge using the ClassicalGSG method
Can we separate active from inactive conformations?
Shifting the paradigm of diabetes mellitus therapeutics: synthesis of novel fused pyrrolo-Imidazolidinone derivatives and their kinetic and computational profiling
Molecular surface-volume and property matching to superpose flexible dissimilar molecules
Gazing into the crystal ball; the future of computer-aided drug design
From UK-2A to florylpicoxamid: Active learning to identify a mimic of a macrocyclic natural product
Advanced Editorial to announce a JCAMD Special Issue on Artificial Intelligence and Machine Learning
PRO_SELECT: Combining structure-based drug design and combinatorial chemistry for rapid lead discovery. 1. Technology
A replica exchange umbrella sampling (REUS) approach to predict host-guest binding free energies in SAMPL8 challenge
The inevitable QSAR renaissance
Neuronal nicotinic receptor agonists: a multi-approach development of the pharmacophore
In silico analysis of the histaprodifen induced activation pathway of the guinea-pig histamine H 1 -receptor
DBMAKER: A set of programs to generate three-dimensional databases based upon user-specified criteria
Factor Xa: Simulation studies with an eye to inhibitor design
A Python tool to set up relative free energy calculations in GROMACS
Exploring the interaction mechanism between antagonist and the jasmonate receptor complex by molecular dynamics simulation
Identification of novel target sites and an inhibitor of the dengue virus E protein
Using steered molecular dynamics to study the interaction between ADP and the nucleotide-binding domain of yeast Hsp70 protein Ssa1
In silico ADME/Tox: why models fail
Quantum mechanics study of the hydroxyethylamines-BACE-1 active site interaction energies
QXP: Powerful, rapid computer algorithms for structure-based drug design
Design, synthesis and experimental validation of novel potential chemopreventive agents using random forest and support vector machine binary classifiers
Rethinking 3D-QSAR
The critical role of QM/MM X-ray refinement and accurate tautomer/protomer determination in structure-based drug design
Weak interactions in furan dimers
A mechanism-based 3D-QSAR approach for classification and prediction of acetylcholinesterase inhibitory potency of organophosphate and carbamate analogs
A novel view of modelling interactions between synthetic and biological polymers via docking
Erratum to: A combined treatment of hydration and dynamical effects for the modeling of host-guest binding thermodynamics: the SAMPL5 blinded challenge
Molecular dynamics to enhance structure-based virtual screening on cathepsin B
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
Monomer structure fingerprints: an extension of the monomer composition version for peptide databases
A Monte Carlo method for finding important ligand fragments from receptor data
Molecular dynamics study on micelle-small molecule interactions: developing a strategy for an extensive comparison
Strategies I
Identification of novel and potent small-molecule inhibitors of tubulin with antitumor activities by virtual screening and biological evaluations
A model of the human M 2 muscarinic acetylcholine receptor
Comparing pharmacophore models derived from crystallography and NMR ensembles
Improving homology modeling of G-protein coupled receptors through multiple-template derived conserved inter-residue interactions
Towards discovering dual functional inhibitors against both wild type and K103N mutant HIV-1 reverse transcriptases: molecular docking and QSAR studies on 4, 1-benzoxazepinone analogues
Overview adcm43.bhtof the SAMPL5 host-guest challenge: Are we doing better?
Integrated in silico approaches for the prediction of Ames test mutagenicity
A binding mode hypothesis for prothioconazole binding to CYP51 derived from first principles quantum chemistry
The effect of CH 3 , F and NO 2 substituents on the individual hydrogen bond energies in the adenine-thymine and guanine-cytosine base pairs
Integrated strategy for screening direct Keap1-Nrf2 PPI inhibitors from traditional Chinese medicine: a case study of Achyranthis bidentatae Radix
Combining MOSCED with molecular simulation free energy calculations or electronic structure calculations to develop an efficient tool for solvent formulation and selection
Prediction of P-glycoprotein inhibitors with machine learning classification models and 3D-RISM-KH theory based solvation energy descriptors
Quantum chemical studies on anion specificity of CαNN motif in functional proteins
Strategies for modelling of catalysts
Predicting cyclohexane/water distribution coefficients for the SAMPL5 challenge using MOSCED and the SMD solvation model
Prodrug-ML: prodrug-likeness prediction via machine learning on sampled negative decoys
Evolutionary algorithms in computer-aided molecular design
Our gratitude to outgoing Editor-in-Chief Andrew Leach and a hearty welcome to new Editor-in-Chief, Richards Lewis
Automated docking of 82 N-benzylpiperidine derivatives to mouse acetylcholinesterase and comparative molecular field analysis with 'natural' alignment
Computer based screening of compound databases: 1. Preselection of benzamidine-based thrombin inhibitors
Towards the understanding of the activity of G9a inhibitors: an activity landscape and molecular modeling approach
DTBA-net: Drug-Target Binding Affinity prediction using feature selection in hybrid CNN model
Quantitative Structure-activity Relationship Analysis of Pyridinone HIV-1 Reverse Transcriptase Inhibitors using the k Nearest Neighbor Method and QSAR-based Database Mining
RDPSOVina: the random drift particle swarm optimization for protein-ligand docking
Structure-activity relationship of Ca2+ channel blockers: A study using conformational analysis and chemometric methods
Identification of family-specific residue packing motifs and their use for structure-based protein function prediction: II. Case studies and applications
Some conclusions regarding the predictions of tautomeric equilibria in solution based on the SAMPL2 challenge
Generation of multiple pharmacophore hypotheses using multiobjective optimisation techniques
Software to obtain spatially localized functions from different radial functions
Conformational landscape of β-cyclodextrin: a computational resource for host-guest modeling in supramolecular systems
Compass: A shape-based machine learning tool for drug design
Applying forces to elastic network models of large biomolecules using a haptic feedback device
On the molecular interaction between lactoferrin and the dye Red HE-3B. A novel approach for docking a charged and highly flexible molecule to protein surfaces
A model for the binding of low molecular weight inhibitors to the active site of thrombin
In memoriam Professor Corwin Hansch: birth pangs of QSAR before 1961
Alchemical Grid Dock (AlGDock) calculations in the D3R Grand Challenge 3 - Binding free energies between flexible ligands and rigid receptors
AZT acts as an anti-influenza nucleotide triphosphate targeting the catalytic site of A/PR/8/34/H1N1 RNA dependent RNA polymerase
Future in biomolecular computation
The reductionist paradox: are the laws of chemistry and physics sufficient for the discovery of new drugs?
Comparison of substructural epitopes in enzyme active sites using self-organizing maps
Multi-Omics Analysis of the virulence factors and designing of next-generation multi-epitopes Vaccines against Rickettsia prowazekii: a computer-aided vaccine designing approach
Towards a rational spacer design for bivalent inhibition of estrogen receptor
FitScore: a fast machine learning-based score for 3D virtual screening enrichment
In silico inspired design and synthesis of a novel tubulin-binding anti-cancer drug: folate conjugated noscapine (Targetin)
Computational study of the effects of protein tyrosine nitrations on the catalytic activity of human thymidylate synthase
Enhancing the accuracy of virtual screening: molecular dynamics with quantum-refined force fields
Prediction of cyclohexane-water distribution coefficients with COSMO-RS on the SAMPL5 data set
Guest editorial for special issue on "ADME and Physical Properties"
Scoring protein-protein docked structures based on the balance and tightness of binding
Ranking docking poses by graph matching of protein-ligand interactions: lessons learned from the D3R Grand Challenge 2
Protein A-like peptide generation based on generalized diffusion model
A structure-guided approach for protein pocket modeling and affinity prediction
Calculating the knowledge-based similarity of functional groups using crystallographic data
Alignment-independent technique for 3D QSAR analysis
Data sharing as an issue
IS-Dom: a dataset of independent structural domains automatically delineated from protein structures
Virtual reality and cheminformatics-driven discovery of a potential broad-spectrum natural antagonist against flaviviral methyltransferases and its cytotoxicity evaluation
Structure-based design of potent CDK1 inhibitors derived from olomoucine
Validation of an empirical RNA-ligand scoring function for fast flexible docking using RiboDock
Interaction force diagrams: new insight into ligand-receptor binding
Elucidating the druggability of the human proteome with eFindSite
Predicting the affinity of Farnesoid X Receptor ligands through a hierarchical ranking protocol: a D3R Grand Challenge 2 case study
The 3D Structure of the Binding Pocket of the Human Oxytocin Receptor for Benzoxazine Antagonists, Determined by Molecular Docking, Scoring Functions and 3D-QSAR Methods
Correction to: Assessing the performance of docking, FEP, and MM/GBSA methods on a series of KLK6 inhibitors
Benefits of statistical molecular design, covariance analysis, and reference models in QSAR: a case study on acetylcholinesterase
Exploiting activity cliffs for building pharmacophore models and comparison with other pharmacophore generation methods: sphingosine kinase 1 as case study
Using particle swarms for the development of QSAR models based on K-nearest neighbor and kernel regression
Combined experimental and quantum mechanical elucidation of the synthetically accessible stereoisomers of Hydroxyestradienone (HED), the starting material for vilaprisan synthesis
Pharmacophore and receptor models for neurokinin receptors
Frozen out: molecular modeling in the age of cryocrystallography
Combinatorial-computational-chemoinformatics (C 3 ) approach to finding and analyzing low-energy tautomers
Modeling ligand recognition at the P2Y12 receptor in light of X-ray structural information
Computational fragment-based drug design to explore the hydrophobic sub-pocket of the mitotic kinesin Eg5 allosteric binding site
The role of water and protein flexibility in the structure-based virtual screening of allosteric GPCR modulators: an mGlu5 receptor case study
Identification and energetic ranking of possible docking sites for pterin on dihydrofolate reductase
Rational design, synthesis and biological evaluations of amino-noscapine: a high affinity tubulin-binding noscapinoid
Molecular docking studies of a group of hydroxamate inhibitors with gelatinase-A by molecular dynamics
Insight into microtubule destabilization mechanism of 3, 4, 5-trimethoxyphenyl indanone derivatives using molecular dynamics simulation and conformational modes analysis
The application of three approximate free energy calculations methods to structure based ligand design: Trypsin and its complex with inhibitors
Modeling receptor flexibility in the structure-based design of KRAS G12C inhibitors
Resveratrol as a nontoxic excipient stabilizes insulin in a bioactive hexameric form
Darwinian Docking
Cytotoxic and gene expression effects of deltamethrin and acetamiprid on MDA-MB-231 breast cancer cells: a molecular and functional study
CAL3JHH: a Java program to calculate the vicinal coupling constants ( 3 J H, H ) of organic molecules
Prediction of free energies of hydration with COSMO-RS on the SAMPL4 data set
SAMPL6 host-guest binding affinities and binding poses from spherical-coordinates-biased simulations
Comparative molecular modelling study of the calcium channel blockers nifedipine and black mamba toxin FS2
DFT calculation of four new potential agents muscarinic of bispyridinium type: structure, synthesis, biological activity, hydration, and relations with the potents W84 and DUO-3O
Molecular recognition of thiaclopride by Aplysia californica AChBP: new insights from a computational investigation
Screening the molecular surface of human anticoagulant protein C: A search for interaction sites
Protein-ligand co-design: a case for improving binding affinity between type II NADH:quinone oxidoreductase and quinones