yusuke1997/dblp-id-title huggingface dataset:
Solvent effect on the synthesis of clarithromycin: A molecular dynamics study
Structural insight into exosite binding and discovery of novel exosite inhibitors of botulinum neurotoxin serotype A through in silico screening
Integrating traditional and modern approaches for comprehensive pharmacophore map validation in drug discovery
Towards the automatic design of synthetically accessible protein ligands: Peptides, amides and peptidomimetics
ENPDA: an evolutionary structure-based de novo peptide design algorithm
Identification of HPr kinase/phosphorylase inhibitors: novel antimicrobials against resistant Enterococcus faecalis
Elucidating ligand recognition of reductive dehalogenases: the role of hydrophobic active site in organohalogen binding
Solvent effects on dimeric self-association of 2-pyrrolidinone: An ab initio study
A genetic algorithm for flexible molecular overlay and pharmacophore elucidation
Molecular modeling of a putative antagonist binding site on helix III of the β-adrenoceptor
Spatial chemical distance based on atomic property fields
The agonistic binding site at the histamine H 2 receptor. I. Theoretical investigations of histamine binding to an oligopeptide mimicking a part of the fifth transmembrane alpha-helix
A semiempirical study on inhibition of catechol O-methyltransferase by substituted catechols
Let's not forget tautomers
Molecular basis of P450 OleTJE: an investigation of substrate binding mechanism and major pathways
Phenylalkylamines in calcium channels: computational analysis of experimental structures
Imputation of sensory properties using deep learning
A pharmacophore model for NK2 antagonist comprising compounds from several structurally diverse classes
Role of the tautomerism of 2-azaadenine and 2-azahypoxanthine in substrate recognition by xanthine oxidase
The evolution of drug design at Merck Research Laboratories
An in silico approach for screening flavonoids as P-glycoprotein inhibitors based on a Bayesian-regularized neural network
Glycogen synthase kinase-3 inhibition by 3-anilino-4-phenylmaleimides: insights from 3D-QSAR and docking
Computational and experimental studies of the interaction between phospho-peptides and the C-terminal domain of BRCA1
Ligand-based and structure-based studies to develop predictive models for SARS-CoV-2 main protease inhibitors through the 3d-qsar.com portal
Quantitative structure-activity relationships by neural networks and inductive logic programming. I. The inhibition of dihydrofolate reductase by pyrimidines
Mixed learning algorithms and features ensemble in hepatotoxicity prediction
Combinatorial library-based design with Basis Products
Continuous indicator fields: a novel universal type of molecular fields
Atomistic computer simulations on multi-loaded PAMAM dendrimers: a comparison of amine- and hydroxyl-terminated dendrimers
Guidelines for the analysis of free energy calculations
Linear and nonlinear functions on modeling of aqueous solubility of organic compounds by two structure representation methods
Molecular modelling of poly(aryl ether ketones). I. Aryl··aryl interactions in crystal structures
The SAMPL2 blind prediction challenge: introduction and overview
A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE)
Q-fit: A probabilistic method for docking molecular fragments by sampling low energy conformational space
Understanding the relationship between preferential interactions of peptides in water-acetonitrile mixtures with protein-solvent contact surface area
An informatic pipeline for managing high-throughput screening experiments and analyzing data from stereochemically diverse libraries
Exploring the structural and electronic properties of boron nitride nanotube (BNNT) as nanocarrier for drug delivery applications: DFT approach
Binding free energies for the SAMPL8 CB8 "Drugs of Abuse" challenge from umbrella sampling combined with Hamiltonian replica exchange
New designs for MRI contrast agents
Thermodynamic integration to predict host-guest binding affinities
Prediction and interpretation of the lipophilicity of small peptides
In silico rationalization of the structural and physicochemical requirements for photobiological activity in angelicine derivatives and their heteroanalogues
Multi-stage variational autoencoders for hierarchical molecular generation and activity optimization
Modeling dimerizations of transmembrane proteins using Brownian dynamics simulations
Optimization of a mathematical topological pattern for the prediction of antihistaminic activity
Allosteric modulation model of the mu opioid receptor by herkinorin, a potent not alkaloidal agonist
Erratum to: Design of chemical space networks using a Tanimoto similarity variant based upon maximum common substructures
Peroxisome Proliferator-Activated Receptors target family landscape: A chemometrical approach to ligand selectivity based on protein binding site analysis
Performance of the IEF-MST solvation continuum model in the SAMPL2 blind test prediction of hydration and tautomerization free energies
Yada: a novel tool for molecular docking calculations
Comparative conformational analysis of [D-Pen 2 , D-Pen 5 ]enkephalin (DPDPE): A molecular mechanics study
Pharmacophore-driven identification of PPARγ agonists from natural sources
Refined homology model of monoacylglycerol lipase: toward a selective inhibitor
QSPR modeling of UV absorption intensities
The active analog approach applied to the pharmacophore identification of benzodiazepine receptor ligands
Derivatives in discrete mathematics: a novel graph-theoretical invariant for generating new 2/3D molecular descriptors. I. Theory and QSPR application
From mundane to surprising nonadditivity: drivers and impact on ML models
PLS modelling of structure-activity relationships of catechol O-methyltransferase inhibitors
Assessment of tautomer distribution using the condensed reaction graph approach
Supervised molecular dynamics for exploring the druggability of the SARS-CoV-2 spike protein
3D QSAR studies on binding affinities of coumarin natural products for glycosomal GAPDH of Trypanosoma cruzi
Theoretical studies on effective metal-to-ligand charge transfer characteristics of novel ruthenium dyes for dye sensitized solar cells
Efficient calculation of SAMPL4 hydration free energies using OMEGA, SZYBKI, QUACPAC, and Zap TK
Effects of point mutations on the thermostability of B. subtilis lipase: investigating nonadditivity
Protein Alpha Shape Similarity Analysis (PASSA): A new method for mapping protein binding sites. Application in the design of a selective inhibitor of Tyrosine kinase 2
Distinct binding of cetirizine enantiomers to human serum albumin and the human histamine receptor H 1
Improving virtual screening results with MM/GBSA and MM/PBSA rescoring
Computer-aided drug design platform using PyMOL
A genetic algorithm for structure-based de novo design
Structure-based CoMFA and CoMSIA study of indolinone inhibitors of PDK1
Molecular electrostatic potentials as input for the alignment of HIV-1 integrase inhibitors in 3D QSAR
Surrogate data - a secure way to share corporate data
Surflex-Dock: Docking benchmarks and real-world application
Influence of conformation on the representation of small flexible molecules at low resolution: alignment of endothiapepsin ligands
Virtual fragment screening: an exploration of various docking and scoring protocols for fragments using Glide
Automated docking of ligands to an artificial active site: augmenting crystallographic analysis with computer modeling
Combining NMR spectral and structural data to form models of polychlorinated dibenzodioxins, dibenzofurans, and biphenyls binding to the AhR
Validating the validation: reanalyzing a large-scale comparison of deep learning and machine learning models for bioactivity prediction
The tower of babel
Polygalic acid inhibits african swine fever virus polymerase activity: findings from machine learning and in vitro testing
Exploring conformational search protocols for ligand-based virtual screening and 3-D QSAR modeling
Molecular motions in drug design: the coming age of the metadynamics method
A benchmark study of loop modeling methods applied to G protein-coupled receptors
Molecular dynamics simulations reveal the inhibition mechanism of Cdc42 by RhoGDI1
How accurate are continuum solvation models for drug-like molecules?
A remark on the efficiency of the double-system/single-box nonequilibrium approach in the SAMPL6 SAMPLing challenge
C-QSAR: a database of 18, 000 QSARs and associated biological and physical data
Characterization of low-energy conformational domains for Met-enkephalin
Enhancing water sampling of buried binding sites using nonequilibrium candidate Monte Carlo
Prediction of the binding mode of N2-phenylguanine derivative inhibitors to herpes simplex virus type 1 thymidine kinase
Identification of protoberberine alkaloids as novel histone methyltransferase G9a inhibitors by structure-based virtual screening
Comprehensive analysis of beta-lactamase genes in clinical strains of Escherichia coli and Klebsiella pneumoniae: molecular characterization, and in Silico predictions
Time dependent analysis of assay comparability: a novel approach to understand intra- and inter-site variability over time
SAMPL6: calculation of macroscopic pK a values from ab initio quantum mechanical free energies
Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection - What can we learn from earlier mistakes?
WhichP450: a multi-class categorical model to predict the major metabolising CYP450 isoform for a compound
Extended continuous similarity indices: theory and application for QSAR descriptor selection
pH-dependent solubility prediction for optimized drug absorption and compound uptake by plants
Structural rationale for the cross-resistance of tumor cells bearing the A399V variant of elongation factor eEF1A1 to the structurally unrelated didemnin B, ternatin, nannocystin A and ansatrienin B
The effect of numerical error on the reproducibility of molecular geometry optimizations
GPCRLigNet: rapid screening for GPCR active ligands using machine learning
Multi-task learning for pKa prediction
Topological side-chain classification of β-turns: Ideal motifs for peptidomimetic development
EuLoc: a web-server for accurately predict protein subcellular localization in eukaryotes by incorporating various features of sequence segments into the general form of Chou's PseAAC
Discovering New Classes of Brugia malayi Asparaginyl-tRNA Synthetase Inhibitors and Relating Specificity to Conformational Change
The multiple roles of computational chemistry in fragment-based drug design
Improving the binding affinity estimations of protein-ligand complexes using machine-learning facilitated force field method
A QM/MM study of the associative mechanism for the phosphorylation reaction catalyzed by protein kinase A and its D166A mutant
MM/GBSA and LIE estimates of host-guest affinities: dependence on charges and solvation model
Comparing predictive ability of QSAR/QSPR models using 2D and 3D molecular representations
Hydration in drug design. 2. Influence of local site surface shape on water binding
How the energy evaluation method used in the geometry optimization step affect the quality of the subsequent QSAR/QSPR models
Reactivities of acrylamide warheads toward cysteine targets: a QM/ML approach to covalent inhibitor design
Virtual screening with AutoDock Vina and the common pharmacophore engine of a low diversity library of fragments and hits against the three allosteric sites of HIV integrase: participation in the SAMPL4 protein-ligand binding challenge
Study of SQ109 analogs binding to mycobacterium MmpL3 transporter using MD simulations and alchemical relative binding free energy calculations
Molecular dynamics insights into the interactions of biocompatible synthetic polymer composites with carbon-based nanoparticle derivatives: a comparative study of PLGA and PCL interactions with GO/rGO
Development of a common 3D pharmacophore for delta-opioid recognition from peptides and non-peptides using a novel computer program
T-Analyst: a program for efficient analysis of protein conformational changes by torsion angles
Multitarget-directed ligands in Alzheimer's disease: identification of AChE and BACE1 inhibitors by in silico approaches
Prediction of blood-brain barrier permeation using quantum chemically derived information
Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics
Molecular dynamics simulation of Matrix Metalloproteinase 2: fluctuations and time evolution of recognition pockets
Functionality map analysis of the active site cleft of human thrombin
Discovery of small molecules binding to the normal conformation of prion by combining virtual screening and multiple biological activity evaluation methods
A Java applet for multiple linked visualization of protein structure and sequence
Energy minimization and molecular dynamics studies of Asn-102 elastase
Current methods for site-directed structure generation
Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4
Substructure and whole molecule approaches for calculating log P
On the detection of multiple-binding modes of ligands to proteins, from biological, structural, and modeling data
Conformation-activity relationships of opiate analgesics
Electron affinities of p-benzoquinone, p-benzoquinone imine and p-benzoquinone diimine, and spin densities of their p-benzosemiq
Comparison of the umbrella sampling and the double decoupling method in binding free energy predictions for SAMPL6 octa-acid host-guest challenges
Bond-based global and local (bond, group and bond-type) quadratic indices and their applications to computer-aided molecular design, 1. QSPR studies of diverse sets of organic chemicals
Mycobacterium tuberculosis FAS-II pathway targeted integrative deep learning based identification of potential anti-tubercular agents
Enhancing molecular representation via fusion of multimodal transformers with integrated periodic local and global features
Molecular modeling of class I and II alleles of the major histocompatibility complex in Salmo salar
Computational studies of new potential antimalarial compounds - Stereoelectronic complementarity with the receptor
Novel isoquinolone PDK1 inhibitors discovered through fragment-based lead discovery
Dual-targeted hit identification using pharmacophore screening
A molecular graphics study on structure-action relationships of calcium-antagonistic and agonistic 1, 4-dihydropyridines
A modification to the COSMIC parameterisation using ab initio constrained potential functions
Effective virtual screening protocol for CYP2C9 ligands using a screening site constructed from flurbiprofen and S-warfarin pockets
Evaluating computational and experimental approaches in early-stage Alzheimer's drug discovery: a systematic review
Computer-aided design and activity prediction of leucine aminopeptidase inhibitors
Recovery of known T-cell epitopes by computational scanning of a viral genome
Structural functionality, catalytic mechanism modeling and molecular allergenicity of phenylcoumaran benzylic ether reductase, an olive pollen (Ole e 12) allergen
Inhibitor discovery for the E. coli meningitis virulence factor IbeA from homology modeling and virtual screening
Visual exploration of structure-activity relationship using maximum common framework
Mapping protein pockets through their potential small-molecule binding volumes: QSCD applied to biological protein structures
Protein ligand docking based on empirical method for binding affinity estimation
Successful identification of key chemical structure modifications that lead to improved ADME profiles
COSMO-RS predictions of logP in the SAMPL7 blind challenge
Prediction of SAMPL3 host-guest affinities with the binding energy distribution analysis method (BEDAM)
Fungal metabolite Ochratoxin A inhibits MrkD1P of multidrug-resistant Klebsiella pneumoniae: Integrated computational and in vitro validation
Automatic log P estimation based on combined additive modeling methods
Cyclophosphamides as hypoxia-activated diffusible cytotoxins: A theoretical study
Exploring fragment-based target-specific ranking protocol with machine learning on cathepsin S
A comparison of progestin and androgen receptor binding using the CoMFA technique
Structural investigations and modeling of cavities in clathrates
How N-(pyridin-4-yl)pyridin-4-amine and its methyl and nitro derivatives are arranged in the interlayer space of zirconium sulfophenylphosphonate: a problem solved by experimental and calculation methods
Computation of affinity and selectivity: Binding of 2, 4-diaminopteridine and 2, 4-diaminoquinazoline inhibitors to dihydrofolate reductases
Absolute binding free energy calculations of CBClip host-guest systems in the SAMPL5 blind challenge
A pseudoreceptor docking study of 4, 5-alpha-epoxymorphinans with a range of dielectric constants
On the relevance of query definition in the performance of 3D ligand-based virtual screening
Biophysical approaches to G protein-coupled receptors: Structure, function and dynamics
Structure-based prediction of free energy changes of binding of PTP1B inhibitors
Nonparametric chemical descriptors for the calculation of ligand-biopolymer affinities with machine-learning scoring functions
Conformational study of insect adipokinetic hormones using NMR constrained molecular dynamics
Protein-ligand docking using FFT based sampling: D3R case study
Molecular determinants in the bioactivation of the dopaminergic neurotoxin N-methyl-4-phenyl-1, 2, 3, 6-tetrahydropyridine (MPTP)
D3R grand challenge 4: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies
Modeling lipophilicity from the distribution of electrostatic potential on a molecular surface
Phosphorylation and ATP-binding induced conformational changes in the PrkC, Ser/Thr kinase from B. subtilis
Investigation of classification methods for the prediction of activity in diverse chemical libraries
An improved relaxed complex scheme for receptor flexibility in computer-aided drug design
Docking and scoring with ICM: the benchmarking results and strategies for improvement
Inhibition and substrate recognition - a computational approach applied to HIV protease
Computational analysis of binding affinity and neural response at the L-alanine receptor
Computational studies on the interaction of ABO-active saccharides with the norovirus VA387 capsid protein can explain experimental binding data
Conformational landscape of platinum(II)-tetraamine complexes: DFT and NBO studies
Binding of Alpha-hydroxy-beta-amino acid inhibitors to methionine aminopeptidase. The performance of two types of scoring functions
Dependency of ligand free energy landscapes on charge parameters and solvent models
Generating conformational transition paths with low potential-energy barriers for proteins
Improved prediction and characterization of blood-brain barrier penetrating peptides using estimated propensity scores of dipeptides
Replica exchange Monte-Carlo simulations of helix bundle membrane proteins: rotational parameters of helices
3D-Pharmacophore mapping of thymidine-based inhibitors of TMPK as potential antituberculosis agents
Protein Data Bank Japan (PDBj): an interview with Haruki Nakamura of Osaka University
Implementation of Smooth Continuous Camera Trajectories for Viewing PDB and VRML Objects
TOPS-MODE versus DRAGON descriptors to predict permeability coefficients through low-density polyethylene
Revealing the importance of linkers in K-series oxime reactivators for tabun-inhibited AChE using quantum chemical, docking and SMD studies
Automated clustering of probe molecules from solvent mapping of protein surfaces: new algorithms applied to hot-spot mapping and structure-based drug design
Three-dimensional hydrogen-bond geometry and probability information from a crystal survey
Computational investigation of functional water molecules in GPCRs bound to G protein or arrestin
Substantial improvements in large-scale redocking and screening using the novel HYDE scoring function
A marriage made in torsional space: using GALAHAD models to drive pharmacophore multiplet searches
Bond-based 2D TOMOCOMD-CARDD approach for drug discovery: aiding decision-making in 'in silico' selection of new lead tyrosinase inhibitors
On the use of LUDI to search the Fine Chemicals Directory for ligands of proteins of known three-dimensional structure
Significantly different effects of tetrahydroberberrubine enantiomers on dopamine D1/D2 receptors revealed by experimental study and integrated in silico simulation
Managing missing measurements in small-molecule screens
Rational creation and systematic analysis of cervical cancer kinase-inhibitor binding profile
Comparison of logP and logD correction models trained with public and proprietary data sets
Molecular mechanism of thiamine pyrophosphate import into mitochondria: a molecular simulation study
Development and validation of an improved algorithm for overlaying flexible molecules
Binding affinities in the SAMPL3 trypsin and host-guest blind tests estimated with the MM/PBSA and LIE methods
Fast prediction of hydration free energies for SAMPL4 blind test from a classical density functional theory
Standard state free energies, not pK a s, are ideal for describing small molecule protonation and tautomeric states
In silico modeling of PAX8-PPARγ fusion protein in thyroid carcinoma: influence of structural perturbation by fusion on ligand-binding affinity
Revealing cytotoxic substructures in molecules using deep learning
An improved method to predict the entropy term with the MM/PBSA approach
In silico discovery and experimental validation of natural derivatives as inhibitor of phosphoinositide Kinase, PIKfyve
Discover binding pathways using the sliding binding-box docking approach: application to binding pathways of oseltamivir to avian influenza H5N1 neuraminidase
QSAR modeling of beta-lactam binding to human serum proteins
Side-chain conformational space analysis (SCSA): A multi conformation-based QSAR approach for modeling and prediction of protein-peptide binding affinities
QSAR application for the prediction of compound permeability with in silico descriptors in practical use
Development of SAAP3D force field and the application to replica-exchange Monte Carlo simulation for chignolin and C-peptide
Strategies to design pyrazolyl urea derivatives for p38 kinase inhibition: a molecular modeling study
Chemometric rationalization of the structural and physicochemical basis for selective cyclooxygenase-2 inhibition: Toward more specific ligands
Biologically relevant conformational features of linear and cyclic proteolipid protein (PLP) peptide analogues obtained by high-resolution nuclear magnetic resonance and molecular dynamics
Analysis of SM8 and Zap TK calculations and their geometric sensitivity
Steroid binding by antibodies and artificial receptors: Exploration of theoretical methods to determine the origins of binding affinities and specificities
Fast and accurate methods for predicting short-range constraints in protein models
Prediction of protein-ligand binding affinity by free energy simulations: assumptions, pitfalls and expectations
Docking flexible ligands in proteins with a solvent exposure- and distance-dependent dielectric function
Automated computational screening of the thiol reactivity of substituted alkenes
CAVEAT: A program to facilitate the design of organic molecules
Predictive potential of eigenvalue-based topological molecular descriptors
Molecular dynamics simulation of the ligand binding domain of mGluR1 in response to agonist and antagonist binding
Tautomerism in chemical information management systems
Structural analysis of the KGD sequence loop of barbourin, an alpha-IIb-beta-3-specific disintegrin
SAMPL4, a blind challenge for computational solvation free energies: the compounds considered
Novel approach to evolutionary neural network based descriptor selection and QSAR model development
In silico identification and in vitro antiviral validation of potential inhibitors against Chikungunya virus
QM assisted ML for 19 F NMR chemical shift prediction