yusuke1997/dblp-id-title huggingface dataset:
SAMPL7 Host-Guest Challenge Overview: assessing the reliability of polarizable and non-polarizable methods for binding free energy calculations
Insights into the binding of GABA to the insect RDL receptor from atomistic simulations: a comparison of models
Stacking Gaussian processes to improve pK a predictions in the SAMPL7 challenge
Conformations of large cycloalkanes: Cyclooctadecane, cyclononadecane and cycloicosane
Discovery of novel polyamine analogs with anti-protozoal activity by computer guided drug repositioning
QSAR using 2D descriptors and TRIPOS SIMCA
Identification of hub necroptosis-related targets and discovery of potential natural inhibitors in ulcerative colitis based on bioinformatics and computer-aided drug design
Computational discovery of putative quorum sensing inhibitors against LasR and RhlR receptor proteins of Pseudomonas aeruginosa
De novo design of molecular architectures by evolutionary assembly of drug-derived building blocks
Strategies II
Structural models in the assessment of protein druggability based on HTS data
Receptor-based 3D QSAR analysis of estrogen receptor ligands - merging the accuracy of receptor-based alignments with the computational efficiency of ligand-based methods
Exploring binding positions and backbone conformations of peptide ligands of proteins with a backbone-centred statistical energy function
Hydrophile-lipophile balance of alkyl ethoxylated surfactants as a function of intermolecular energies
Assessing the accuracy of octanol-water partition coefficient predictions in the SAMPL6 Part II log P Challenge
Adapting the semi-explicit assembly solvation model for estimating water-cyclohexane partitioning with the SAMPL5 molecules
Conformational search by potential energy annealing: Algorithm and application to cyclosporin A
Evaluating docked complexes with the HINT exponential function and empirical atomic hydrophobicities
Allosteric antagonist binding sites in class B GPCRs: corticotropin receptor 1
An insight to the molecular interactions of the FDA approved HIV PR drugs against L38L↑N↑L PR mutant
DP-BINDER: machine learning model for prediction of DNA-binding proteins by fusing evolutionary and physicochemical information
In silico prediction of drug toxicity
Assessment of the tautomeric population of benzimidazole derivatives in solution: a simple and versatile theoretical-experimental approach
Community benchmarks for virtual screening
Structure of a cyclic peptide with a catalytic triad, determined by computer simulation and NMR spectroscopy
A crystallographic perspective on sharing data and knowledge
Investigating the ameliorative effect of Kalanchoe pinnata on neuroinflammation-associated Alzheimer's disease using network pharmacology, molecular docking, and in vitro studies
Multiobjective optimization of combinatorial libraries
Development of purely structure-based pharmacophores for the topoisomerase I-DNA-ligand binding pocket
Detection of ligand binding hot spots on protein surfaces via fragment-based methods: application to DJ-1 and glucocerebrosidase
Automatic search for maximum similarity between molecular electrostatic potential distributions
A comparative study of ligand-receptor complex binding affinity prediction methods based on glycogen phosphorylase inhibitors
Understanding the mechanism of cellulose dissolution in 1-butyl-3-methylimidazolium chloride ionic liquid via quantum chemistry calculations and molecular dynamics simulations
Qualitative prediction of blood-brain barrier permeability on a large and refined dataset
Visualizing protein-ligand binding with chemical energy-wise decomposition (CHEWD): application to ligand binding in the kallikrein-8 S1 Site
Novel algorithms for searching conformational space
Discovering promising drug candidates for Parkinson's disease: integrating miRNA and DEG analysis with molecular dynamics and MMPBSA
Why relevant chemical information cannot be exchanged without disclosing structures
Is scaffold hopping a reliable indicator for the ability of computational methods to identify structurally diverse active compounds?
Molecular dynamics modeling and spectroscopic property prediction of V-type nerve agents for safe handling
Data-informed reparameterization of modified RNA and the effect of explicit water models: application to pseudouridine and derivatives
New developments in PEST shape/property hybrid descriptors
Mixed QM/MM molecular electrostatic potentials
Predicting partition coefficients of drug-like molecules in the SAMPL6 challenge with Drude polarizable force fields
Non-zero Lennard-Jones parameters for the Toukan-Rahman water model: more accurate calculations of the solvation free energy of organic substances
Evaluating the applicability domain in the case of classification predictive models for carcinogenicity based on the counter propagation artificial neural network
Fast H-DROP: A thirty times accelerated version of H-DROP for interactive SVM-based prediction of helical domain linkers
An exploration of a novel strategy for superposing several flexible molecules
Towards the chemometric dissection of peptide - HLA-A*0201 binding affinity: comparison of local and global QSAR models
A supermolecule study of the effect of hydration on the conformational behaviour of leucine-enkephalin
Incorporating significant amino acid pairs and protein domains to predict RNA splicing-related proteins with functional roles
Breast cancer diagnosis from histopathological images and molecular signatures by fusing features with an explainable AI-based residual tabular network model
Identification of novel EED-EZH2 PPI inhibitors using an in silico fragment mapping method
π-SCF-Molecular Mechanics PIMM: Formulation, parameters, applications
ALADDIN: An integrated tool for computer-assisted molecular design and pharmacophore recognition from geometric, steric, and substructure searching of three-dimensional molecular structures
Detection of tautomer proportions of dimedone in solution: a new approach based on theoretical and FT-IR viewpoint
Generation of a homology model of the human histamine H 3 receptor for ligand docking and pharmacophore-based screening
Novel phosphatidylinositol 4-kinases III beta (PI4KIIIβ) inhibitors discovered by virtual screening using free energy models
Relative free-energy calculations for scaffold hopping-type transformations with an automated RE-EDS sampling procedure
Electrostatic complementarity between proteins and ligands. 1. Charge disposition, dielectric and interface effects
An atomistic model of passive membrane permeability: application to a series of FDA approved drugs
Molecular modeling of the human vasopressin V2 receptor/agonist complex
A ligand's-eye view of protein binding
Computer simulation of the conformational behavior of cholecystokinin fragments: Conformational families of sulfated CCK8
BUILDER v.2: Improving the chemistry of a de novo design strategy
Enhancing sampling of water rehydration upon ligand binding using variants of grand canonical Monte Carlo
Methodological developments and strategies for a fast flexible superposition of drug-size molecules
Antitumor Agents 252. Application of validated QSAR models to database mining: discovery of novel tylophorine derivatives as potential anticancer agents
Molecular dynamics simulations on the inhibition of Cyclin-Dependent Kinases 2 and 5 in the presence of activators
Scoring confidence index: statistical evaluation of ligand binding mode predictions
DockBench as docking selector tool: the lesson learned from D3R Grand Challenge 2015
Structure-based identification and experimental evaluation of Oroxin A as a FYN kinase inhibitor
Ultrafast protein structure-based virtual screening with Panther
A molecular modeling study of inhibitors of nuclear factor kappa-B (p50) - DNA binding
An activity prediction model for steroidal and triterpenoidal inhibitors of Acetylcholinesterase enzyme
CDOCKER and λ-dynamics for prospective prediction in D3R Grand Challenge 2
Deep learning-guided rational engineering of synergistic PD-1 and LAG-3 blockade for enhanced tumor immunomodulation
Empowering pharmacoinformatics by linked life science data
A combined treatment of hydration and dynamical effects for the modeling of host-guest binding thermodynamics: the SAMPL5 blinded challenge
Measuring CAMD technique performance: A virtual screening case study in the design of validation experiments
Insights into the EGFR SAR of N-phenylquinazolin-4-amine-derivatives using quantum mechanical pairwise-interaction energies
mRAISE: an alternative algorithmic approach to ligand-based virtual screening
Triangulation algorithms for the representation of molecular surface properties
QSAR analyses on avian influenza virus neuraminidase inhibitors using CoMFA, CoMSIA, and HQSAR
Benchmarking ANI potentials as a rescoring function and screening FDA drugs for SARS-CoV-2 M pro
Investigation of the intermolecular recognition mechanism between the E3 ubiquitin ligase Keap1 and substrate based on multiple substrates analysis
Protein domain movement involved in binding of belinostat and HPOB as inhibitors of histone deacetylase 6 (HDAC6): a hybrid automated-interactive docking study
Focused Library Generator: case of Mdmx inhibitors
Differentiation of AmpC beta-lactamase binders vs. decoys using classification k NN QSAR modeling and application of the QSAR classifier to virtual screening
Interactions of peptide mimics of hyaluronic acid with the receptor for hyaluronan mediated motility (RHAMM)
Quantum-mechanical property prediction of solvated drug molecules: what have we learned from a decade of SAMPL blind prediction challenges?
The atom assignment problem in automated de novo drug design. 5. Tests for envelope-directed fragment placement based on molecular similarity
Morphological similarity: A 3D molecular similarity method correlated with protein-ligand recognition
Molecular modeling and bioinformatical analysis of the antibacterial target enzyme MurA from a drug design perspective
Comparative molecular field analysis of artemisinin derivatives: Ab initio versus semiempirical optimized structures
Pharmacophore modeling improves virtual screening for novel peroxisome proliferator-activated receptor-gamma ligands
Application of semi-empirical and ab initio quantum mechanical calculations
A molecular mechanism of P-loop pliability of Rho-kinase investigated by molecular dynamic simulation
Visualisation and subsets of the chemical universe database GDB-13 for virtual screening
Estimation of the size of drug-like chemical space based on GDB-17 data
On homology modeling of the M2 muscarinic acetylcholine receptor subtype
Boltzmann's principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structures
Docking studies on NSAID/COX-2 isozyme complexes using Contact Statistics analysis
Development and interpretation of a QSAR model for in vitro breast cancer (MCF-7) cytotoxicity of 2-phenylacrylonitriles
Recent advances in molecular diversity
Docking glycosaminoglycans to proteins: analysis of solvent inclusion
Molecular dynamics simulation of halogen bonding mimics experimental data for cathepsin L inhibition
Interactive essential dynamics
The configurational dependence of binding free energies: A Poisson-Boltzmann study of Neuraminidase inhibitors
User-centric design of a 3D search interface for protein-ligand complexes
Correction: Identification of hub necroptosis-related targets and discovery of potential natural inhibitors in ulcerative colitis based on bioinformatics and computer-aided drug design
Improving small molecule force fields by identifying and characterizing small molecules with inconsistent parameters
Epilogue to the Gerald Maggiora Festschrift: a tribute to an exemplary mentor, colleague, collaborator, and innovator
New insights into flavivirus biology: the influence of pH over interactions between prM and E proteins
Human topoisomerase I poisoning: docking protoberberines into a structure-based binding site model
Sample-distance Partial Least Squares: PLS optimized for many variables, with application to CoMFA
Predictive QSAR modeling based on diversity sampling of experimental datasets for the training and test set selection
Repurposing of known drugs for leishmaniasis treatment using bioinformatic predictions, in vitro validations and pharmacokinetic simulations
Developing 13C NMR quantitative spectrometric data-activity relationship (QSDAR) models of steroid binding to the corticosteroid binding globulin
Solvation free energies and partition coefficients with the coarse-grained and hybrid all-atom/coarse-grained MARTINI models
The probable conformation of substrates recognized by dipeptidyl-peptidase IV and some aspects of the Catalytic mechanism derived from theoretical investigations
Anti-inflammatory potential of isoquinoline alkaloids from Fumaria officinalis: in vitro, in vivo, and in silico evaluation
A noncanonical binding site of linezolid revealed via molecular dynamics simulations
Binding of the Zn 2+ ion to ferric uptake regulation protein from E. coli and the competition with Fe 2+ binding: a molecular modeling study of the effect on DNA binding and conformational changes of Fur
Medt5-bi: bidirectional translation between drug indications and molecular structures using a chemically-aware transformer
Discovery of DNA dyes Hoechst 34580 and 33342 as good candidates for inhibiting amyloid beta formation: in silico and in vitro study
Towards an identification of the pyrethroid pharmacophore. A molecular modelling study of some pyrethroid esters
Introduction to the special issue: Data Part 2: Experimental Data
Correction to: BRADSHAW: a system for automated molecular design
QSAR model based on weighted MCS trees approach for the representation of molecule data sets
Blinded predictions of host-guest standard free energies of binding in the SAMPL5 challenge
Quantum chemical predictions of water-octanol partition coefficients applied to the SAMPL6 logP blind challenge
Fragment-based lead discovery: challenges and opportunities
Epik: a software program for pK a prediction and protonation state generation for drug-like molecules
Simultaneous prediction of aqueous solubility and octanol/water partition coefficient based on descriptors derived from molecular structure
Improving drug discovery with a hybrid deep generative model using reinforcement learning trained on a Bayesian docking approximation
Binding site identification of G protein-coupled receptors through a 3D Zernike polynomials-based method: application to C. elegans olfactory receptors
Macrocycle modeling in ICM: benchmarking and evaluation in D3R Grand Challenge 4
Efficient overlay of small organic molecules using 3D pharmacophores
QSAR modeling and chemical space analysis of antimalarial compounds
Identification of novel inhibitors targeting PI3Kα via ensemble-based virtual screening method, biological evaluation and molecular dynamics simulation
In silico development of RNA aptamer candidates against thyroid receptor
Tautomerism in drug discovery
Exhaustive search and solvated interaction energy (SIE) for virtual screening and affinity prediction
Editorial: Contributions by Wendy Warr
Nucleotide-binding properties of adenylate kinase from Escherichia coli: A molecular dynamics study in aqueous and vacuum environments
A theoretical study of Zn ++ interacting with models of ligands present at the thermolysin active site
Computational study of the inhibitory mechanism of the kinase CDK5 hyperactivity by peptide p5 and derivation of a pharmacophore
A 3D QSAR CoMFA study of non-peptide angiotensin II receptor antagonists
Structural characterization and molecular dynamics simulations of the caprine and bovine solute carrier family 11 A1 (SLC11A1)
Predicting reactivity to drug metabolism: beyond P450s - modelling FMOs and UGTs
Megavariate analysis of hierarchical QSAR data
Scoring noncovalent protein-ligand interactions: A continuous differentiable function tuned to compute binding affinities
Predicting hydration free energies with a hybrid QM/MM approach: an evaluation of implicit and explicit solvation models in SAMPL4
High-throughput virtual screening and preclinical analysis identifies CB-1, a novel potent dual B-Raf/c-Raf inhibitor, effective against wild and mutant variants of B-Raf expression in colorectal carcinoma
Evolution of Support Vector Machine and Regression Modeling in Chemoinformatics and Drug Discovery
Computer simulation of the conformational behaviour of angiotensinogen (6-13) renin substrate
Fragment-based drug discovery
Quantitative structure-activity relationships from optimised ab initio bond lengths: steroid binding affinity and antibacterial activity of nitrofuran derivatives
Sparse QSAR modelling methods for therapeutic and regenerative medicine
Structure-activity relationships of diphenyl-ether as protoporphyrinogen oxidase inhibitors: insights from computational simulations
Design of chemical space networks using a Tanimoto similarity variant based upon maximum common substructures
Comparative assessment of physics-based in silico methods to calculate relative solubilities
Structure-based approach for identification of novel phenylboronic acids as serine-β-lactamase inhibitors
Comparative study of several algorithms for flexible ligand docking
Force matching as a stepping stone to QM/MM CB[8] host/guest binding free energies: a SAMPL6 cautionary tale
Replacement of steric 6-12 potential-derived interaction energies by atom-based indicator variables in CoMFA leads to models of higher consistency
AstexViewerTM: a visualisation aid for structure-based drug design
Visually impaired researchers get their hands on quantum chemistry: application to a computational study on the isomerization of a sterol
Combining conformational sampling and selection to identify the binding mode of zinc-bound amyloid peptides with bifunctional molecules
Substrate recognition by norovirus polymerase: microsecond molecular dynamics study
Leaving us with fond memories, smiles, SMILES and, alas, tears: a tribute to David Weininger, 1952-2016
Interaction with specific HSP90 residues as a scoring function: validation in the D3R Grand Challenge 2015
Pattern recognition study of QSAR substituent descriptors
Computation, experiment and molecular design
RNAHelix: computational modeling of nucleic acid structures with Watson-Crick and non-canonical base pairs
Prot2Prot: a deep learning model for rapid, photorealistic macromolecular visualization
Similarity and complementarity of molecular shapes: Applicability of a topological analysis approach
Design and tests of prospective property predictions for novel antimalarial 2-aminopropylaminoquinolones
Enhancing the diversity of a corporate database using chemical database clustering and analysis
ART-RRT: As-Rigid-As-Possible search for protein conformational transition paths
A molecular dynamics investigation of CDK8/CycC and ligand binding: conformational flexibility and implication in drug discovery
Design of new selective inhibitors of cyclooxygenase-2 by dynamic assembly of molecular building blocks
Binding models of reversible inhibitors to type-B monoamine oxidase
Data structures for computational compound promiscuity analysis and exemplary applications to inhibitors of the human kinome
Comparative and pharmacophore model for deacetylase SIRT1
In-silico Screening using Flexible Ligand Binding Pockets: A Molecular Dynamics-based Approach
3D-QSAR illusions
WONKA: objective novel complex analysis for ensembles of protein-ligand structures
An overview of the SAMPL8 host-guest binding challenge
Extend electron distributions applied to the molecular mechanics of some intermolecular interactions. II. Organic complexes
CoMFA-based comparison of two models of binding site on adenosine A1 receptor
Multi-targeted benzylpiperidine-isatin hybrids: Design, synthesis, biological and in silico evaluation as monoamine oxidases and acetylcholinesterase inhibitors for neurodegenerative disease therapies
Pharmacophore development for antagonists at alpha 1 adrenergic receptor subtypes
Investigating cyclic peptides inhibiting CD2-CD58 interactions through molecular dynamics and molecular docking methods
Remembrances of Corwin Hansch
Molecular dynamics simulations of cyclosporin A: The crystal structure and dynamic modelling of a structure in apolar solution based on NMR data
Force field development phase II: Relaxation of physics-based criteria... or inclusion of more rigorous physics into the representation of molecular energetics
Investigating the hydrogen-bond acceptor site of the nicotinic pharmacophore model: a computational and experimental study using epibatidine-related molecular probes
The use of an algorithmic method for small molecule superimpositions in the design of antiviral agents
Quantitative structure-agonist activity relationship of capsaicin analogues
Prediction of binding constants of protein ligands: A fast method for the prioritization of hits obtained from de novo design or 3D database search programs
Multi-phase Boltzmann weighting: accounting for local inhomogeneity in molecular simulations of water-octanol partition coefficients in the SAMPL6 challenge
Prediction of standard Gibbs energies of the transfer of peptide anions from aqueous solution to nitrobenzene based on support vector machine and the heuristic method
Computer simulation of liquid crystals
Design and characterization of an engineered gp41 protein from human immunodeficiency virus-1 as a tool for drug discovery
SMART: A solvent-accessible triangulated surface generator for molecular graphics and boundary element applications
RIP MDL information systems. Is this really the beginning of a new era?
Bayesian molecular design with a chemical language model
Reproducing the conformations of protein-bound ligands: A critical evaluation of several popular conformational searching tools
Screening of benzamidine-based thrombin inhibitors via a linear interaction energy in continuum electrostatics model
Antimalarial activity of synthetic 1, 2, 4-trioxanes and cyclic peroxy ketals, a quantum similarity study
Models for the binding of amiodarone to the thyroid hormone receptor
A validation study on the practical use of automated de novo design
Individually double minimum-distance definition of protein-RNA binding residues and application to structure-based prediction
Development of a pharmacophore for cruzain using oxadiazoles as virtual molecular probes: quantitative structure-activity relationship studies
Electrostatic-field and surface-shape similarity for virtual screening and pose prediction
Benchmarking ensemble docking methods in D3R Grand Challenge 4
Comparison of conformer distributions in the crystalline state with conformational energies calculated by ab initio techniques
DFT-based prediction of reactivity of short-chain alcohol dehydrogenase
Absolute binding free energies for the SAMPL6 cucurbit[8]uril host-guest challenge via the AMOEBA polarizable force field
Ab initio study on tautomerism of 2-thiouracil in the gas phase and in solution
A new procedure for improving the predictiveness of CoMFA models and its application to a set of dihydrofolate reductase inhibitors
Reaction mechanisms in peptide synthesis. Part 1. Semiquantitative characteristics of the reactivity of 2-methyl-5(4H)-oxazolone with water and ammonia in the gas phase and weakly polar media
Erratum to 'Neuronal nicotinic receptor agonists: a multi-approach development of the pharmacophore' [J. Comput. Aid. Mol. Des., Vol. 15 (2001) 859]
Tautomers and reference 3D-structures: the orphans of in silico drug design
Predicting the product specificity and coupling of cytochrome P450cam
Robust optimization of scoring functions for a target class
Computer-aided molecular and biological-immune modeling of illicium verum bioactive compounds employing the Egyptian Nile snail Biomphalaria alexandrina as a paradigm
Descriptor collision and confusion: Toward the design of descriptors to mask chemical structures
Using halogen bonds to address the protein backbone: a systematic evaluation
3D QSAR (COMFA) of a series of potent and highly selective VLA-4 antagonists
Ai-driven de novo design of customizable membrane permeable cyclic peptides
Prediction of the three-dimensional structure of the enzymatic domain of t-PA