yusuke1997/dblp-id-title huggingface dataset:
Deciphering the conformational transitions of LIMK2 active and inactive states to ponder specific druggable states through microsecond scale molecular dynamics simulation
The analysis of the market success of FDA approvals by probing top 100 bestselling drugs
Compilation and physicochemical classification analysis of a diverse hERG inhibition database
Prospective evaluation of shape similarity based pose prediction method in D3R Grand Challenge 2015
QSAR of heterocyclic antifungal agents by flip regression
Deploying the drug repurposing approach for the identification of selective monoamine oxidase-B inhibitors against neurological disabilities: an in Silico and in vitro approach
Chasing allosteric inhibition of the SARS-CoV-2 PLpro via molecular dynamics simulations with flooding fragments (MDFFr)
An automated PLS search for biologically relevant QSAR descriptors
Bigger data, collaborative tools and the future of predictive drug discovery
Computational chemistry in 25 years
Modelling and mutation studies on the histamine H 1 -receptor agonist binding site reveal different binding modes for H 1 -agonists: Asp 116 (TM3) has a constitutive role in receptor stimulation
Thermodynamic cycle integration by computer simulation as a tool for obtaining free energy differences in molecular chemistry
Scoring Functions - the First 100 Years
Selectivity analysis of 5-(arylthio)-2, 4-diaminoquinazolines as inhibitors of Candida albicans dihydrofolate reductase by molecular dynamics simulations
2D- and 3D-QSAR studies of a series of benzopyranes and benzopyrano[3, 4b][1, 4]-oxazines as inhibitors of the multidrug transporter P-glycoprotein
Active-site mobility inhibits reductive dehalogenation of 1, 1, 1-trichloroethane by cytochrome P450cam
Mathematical deep learning for pose and binding affinity prediction and ranking in D3R Grand Challenges
Elucidating zerumbone's low-efficacy agonism at the μ-opioid receptor via molecular dynamics simulation and Markov state modeling
Ligand binding affinity prediction by linear interaction energy methods
TargIDe: a machine-learning workflow for target identification of molecules with antibiofilm activity against Pseudomonas aeruginosa
Extensive structural change of the envelope protein of dengue virus induced by a tuned ionic strength: conformational and energetic analyses
FLASHFLOOD: A 3D Field-based similarity search and alignment method for flexible molecules
Measuring experimental cyclohexane-water distribution coefficients for the SAMPL5 challenge
Finding potential DNA-binding compounds by using molecular shape
Warfarin: history, tautomerism and activity
Blind prediction of host-guest binding affinities: a new SAMPL3 challenge
Quantitative measurement of protease ligand conformation
Development of a conformational search strategy for flexible ligands: A study of the potent μ-selective opioid analgesic fentanyl
One site fits both: A model for the ternary complex of folate + NADPH in R67 dihydrofolate reductase, a D2 symmetric enzyme
Structure-based identification of inhibitors disrupting the CD2-CD58 interactions
Application of multivariate data analysis methods to Comparative Molecular Field Analysis (CoMFA) data: Proton affinities and pKa prediction for nucleic acids components
Relative solvation free energies calculated using an ab initio QM/MM-based free energy perturbation method: dependence of results on simulation length
Consensus scoring evaluated using the GPCR-Bench dataset: Reconsidering the role of MM/GBSA
Computational fragment-based screening using RosettaLigand: the SAMPL3 challenge
A flexible triangulation method to describe the solvent-accessible surface of biopolymers
HCV genotyping and rational computational designing of an immunogenic multiepitope vaccine against genotype 3a
Hydration in drug design. 1. Multiple hydrogen-bonding features of water molecules in mediating protein-ligand interactions
In silico design of dehydrophenylalanine containing peptide activators of glucokinase using pharmacophore modelling, molecular dynamics and machine learning: implications in type 2 diabetes
Design of Recombinant Stem Cell Factor-macrophage Colony Stimulating Factor Fusion Proteins and their Biological Activity In Vitro
Fragment-based drug discovery: what really works. An interview with Sandy Farmer of Boehringer Ingelheim
A theoretical approach to the influence of the macrocycle conformation on the molecular electronic structure in Mg-porphyrins
Protein fold recognition
Molecular dynamics study of peptide segments of the BH3 domain of the proapoptotic proteins Bak, Bax, Bid and Hrk bound to the Bcl-xL and Bcl-2 proteins
Computational QSAR study of novel 2-aminothiazol-4(5H)-one derivatives as 11β-HSD1 inhibitors
The use of docking-based comparative intermolecular contacts analysis to identify optimal docking conditions within glucokinase and to discover of new GK activators
The IUPAC aqueous and non-aqueous experimental pKa data repositories of organic acids and bases
A collaborative environment for developing and validating predictive tools for protein biophysical characteristics
Deciphering structure, function and mechanism of Plasmodium IspD homologs from their evolutionary imprints
Engineering the Pseudomonas aeruginosa II lectin: designing mutants with changed affinity and specificity
D3R Grand Challenge 4: ligand similarity and MM-GBSA-based pose prediction and affinity ranking for BACE-1 inhibitors
Obituary: Corwin H. Hansch
Dynamic simulation as an essential tool in molecular modeling
Force-field parametrization and molecular dynamics simulations of Congo red
Use of molecular dynamics fingerprints (MDFPs) in SAMPL6 octanol-water log P blind challenge
Comparative review of molecular modelling software for personal computers
Conformational variety for the ansa chain of rifamycins: Comparison of observed crystal structures and molecular dynamics simulations
App-etite for change
Insight on the mechanism of hexameric Pseudin-4 against bacterial membrane-mimetic environment
The prediction of human oral absorption for diffusion rate-limited drugs based on heuristic method and support vector machine
H-DROP: an SVM based helical domain linker predictor trained with features optimized by combining random forest and stepwise selection
Optimisation of human VH domain antibodies specific to Mycobacterium tuberculosis heat shock protein (HSP16.3)
Very empirical treatment of solvation and entropy: a force field derived from Log Po/w
Prediction of SAMPL2 aqueous solvation free energies and tautomeric ratios using the SM8, SM8AD, and SMD solvation models
AI-driven peptide discovery for endometrial cancer: deep generative modeling and molecular simulation in the big data era
Orientation and structure-building role of the water molecules bound at the contact surface of the dihydrofolate reductase-methotrexate complex
Dynamical Aspects of TEM-1 β-Lactamase Probed by Molecular Dynamics
Estimation of influential points in any data set from coefficient of determination and its leave-one-out cross-validated counterpart
Class IV charge models: A new semiempirical approach in quantum chemistry
Diverse binding site structures revealed in homology models of polyreactive immunoglobulins
Similarity based SAR (SIBAR) as tool for early ADME profiling
Design of chemical space networks on the basis of Tversky similarity
Design of a multi-purpose fragment screening library using molecular complexity and orthogonal diversity metrics
Virtual screening applications: a study of ligand-based methods and different structure representations in four different scenarios
Structure-based design of ligands for protein basic domains: Application to the HIV-1 Tat protein
Prediction of inter-residue contacts map based on genetic algorithm optimized radial basis function neural network and binary input encoding scheme
Docking performance of the glide program as evaluated on the Astex and DUD datasets: a complete set of glide SP results and selected results for a new scoring function integrating WaterMap and glide
Computational prediction of ion permeation characteristics in the glycine receptor modified by photo-sensitive compounds
Crystal polymorphism and spectroscopical properties of sulfonamides in solid state by means of First Principles calculations
A β-solenoid model of the Pmel17 repeat domain: insights to the formation of functional amyloid fibrils
Active learning strategies with COMBINE analysis: new tricks for an old dog
A virtual high throughput screen for high affinity cytochrome P450cam substrates. Implications for in silico prediction of drug metabolism
SAMPL6 logP challenge: machine learning and quantum mechanical approaches
The in silico identification of novel broad-spectrum antidotes for poisoning by organophosphate anticholinesterases
The effect of isodensity surface sampling on ESP derived charges and the effect of adding bondcenters on DMA derived charges
HomologyPlot: Searching for homology to a family of proteins using a database of unique conserved patterns
Modelling study of protein kinase inhibitors: Binding mode of staurosporine and origin of the selectivity of CGP 52411
Homology model directed alignment selection for comparative molecular field analysis: Application to photosystem II inhibitors
Conformational analysis of a farnesyltransferase peptide inhibitor, CVIM
Conformational properties of amphotericin B amide derivatives - impact on selective toxicity
Quantitative structure-activity relationships of mutagenic activity from quantum topological descriptors: triazenes and halogenated hydroxyfuranones (mutagen-X) derivatives
A computational study on the relative reactivity of reductively activated 1, 4-benzoquinone and its isoelectronic analogs
D3R Grand Challenge 2: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies
Reliable gas-phase tautomer equilibria of drug-like molecule scaffolds and the issue of continuum solvation
FOUNDATION: A program to retrieve all possible structures containing a user-defined minimum number of matching query elements from three-dimensional databases
A molecular graphics study exploring a putative ligand binding site of the β -adrenoceptor
Rational design of biaryl pharmacophore inserted noscapine derivatives as potent tubulin binding anticancer agents
Statistical dictionaries for hypothetical in silico model of the early-stage intermediate in protein folding
Implicit solvation in the self-consistent mean field theory method: sidechain modelling and prediction of folding free energies of protein mutants
Association of transmembrane helices: what determines assembling of a dimer?
Electron-density-dependent fused-sphere surfaces derived from pseudopotential calculations
Docking of small molecules to farnesoid X receptors using AutoDock Vina with the Convex-PL potential: lessons learned from D3R Grand Challenge 2
Crystallographic modelling
Evaluation of designed ligands by a multiple screening method: Application to glycogen phosphorylase inhibitors constructed with a variety of approaches
The effects of characteristics of substituents on toxicity of the nitroaromatics: HiT QSAR study
The advent and evolution of QSAR at Pomona College
Visualisation of the chemical space of fragments, lead-like and drug-like molecules in PubChem
Mapping of the interaction sites of galanthamine: a quantitative analysis through pairwise potentials and quantum chemistry
Structure-based combinatorial library design: Discovery of non-peptidic inhibitors of caspases 3 and 8
Multidimensional in silico evaluation of fluorine-18 radiopharmaceuticals: integrating pharmacokinetics, ADMET, and clustering for diagnostic stratification
Comparing classification models - a practical tutorial
Automatic QSAR modeling of ADME properties: blood-brain barrier penetration and aqueous solubility
MLP Tools: a PyMOL plugin for using the molecular lipophilicity potential in computer-aided drug design
VolSurf analysis of pharmacokinetic properties for several antifungal sesquiterpene lactones isolated from Greek Centaurea sp
Annular tautomerism: experimental observations and quantum mechanics calculations
Free energy perturbation approach to the critical assessment of selective cyclooxygenase-2 inhibitors
Obituary: Toshio Fujita, QSAR pioneer
Shape similarity guided pose prediction: lessons from D3R Grand Challenge 3
Construction of 3D models of the CYP11B family as a tool to predict ligand binding characteristics
Strategic approaches to drug design. II. Modelling studies on phosphodiesterase substrates and inhibitors
Computational peptide discovery with a genetic programming approach
Conformational energies of reference organic molecules: benchmarking of common efficient computational methods against coupled cluster theory
Characterization of dipeptidylcarboxypeptidase of Leishmania donovani : a molecular model for structure based design of antileishmanials
Revisiting allostery in CREB-binding protein (CBP) using residue-based interaction energy
Explicit solvation thermodynamics in ionic solution: extending grid inhomogeneous solvation theory to solvation free energy of salt-water mixtures
Evaluating docking programs: keeping the playing field level
Quantitative structure-activity relationships by neural networks and inductive logic programming. II. The inhibition of dihydrofolate reductase by triazines
The continuous molecular fields approach to building 3D-QSAR models
Docking pose selection by interaction pattern graph similarity: application to the D3R grand challenge 2015
CONFIRM: connecting fragments found in receptor molecules
OpenCDLig: a free web application for sharing resources about cyclodextrin/ligand complexes
FastGrow: on-the-fly growing and its application to DYRK1A
Molecular dynamics studies of α-helix stability in fibril-forming peptides
Combinatorial docking and combinatorial chemistry: Design of potent non-peptide thrombin inhibitors
Variable selection and model validation of 2D and 3D molecular descriptors>
Structural insights into the mechanism of translational inhibition by the fungicide sordarin
Binding free energies in the SAMPL5 octa-acid host-guest challenge calculated with DFT-D3 and CCSD(T)
From closed to open: three dynamic states of membrane-bound cytochrome P450 3A4
This issue: Drug Design Data Resource Grand Challenge 4, first of two issues
AllChem: generating and searching 10 20 synthetically accessible structures
Structure-toxicity relationships of polycyclic aromatic hydrocarbons using molecular quantum similarity
Development and application of hybrid structure based method for efficient screening of ligands binding to G-protein coupled receptors
Binding free energy calculations to rationalize the interactions of huprines with acetylcholinesterase
Molecular structure matching by simulated annealing. I. A comparison between different cooling schedules
Prediction of octanol-water partition coefficients for the SAMPL6-log P molecules using molecular dynamics simulations with OPLS-AA, AMBER and CHARMM force fields
A k-nearest neighbor classification of hERG K+ channel blockers
Extensive all-atom Monte Carlo sampling and QM/MM corrections in the SAMPL4 hydration free energy challenge
Further development and validation of empirical scoring functions for structure-based binding affinity prediction
Evaluation of docking/scoring approaches: A comparative study based on MMP3 inhibitors
GALAHAD: 1. Pharmacophore identification by hypermolecular alignment of ligands in 3D
A QM/MM study of the binding of RAPTA ligands to cathepsin B
Predicting drug-induced liver injury in human with Naïve Bayes classifier approach
D3R Grand Challenge 4: prospective pose prediction of BACE1 ligands with AutoDock-GPU
High-affinity interactions of ligands at recombinant Guinea pig 5HT7 receptors
Free energy force field (FEFF) 3D-QSAR analysis of a set of Plasmodium falciparum dihydrofolate reductase inhibitors
A fast and efficient method for 2D and 3D molecular shape description
Influence of gauche effect on uncharged oxime reactivators for the reactivation of tabun-inhibited AChE: quantum chemical and steered molecular dynamics studies
Constitutional, configurational and conformational analysis of transition metal coordination complexes
Elucidating the potential effects of point mutations on FGFR3 inhibitor resistance via combined molecular dynamics simulation and community network analysis
Visualization of multi-property landscapes for compound selection and optimization
AFAL: a web service for profiling amino acids surrounding ligands in proteins
Geometries of functional group interactions in enzyme-ligand complexes: Guides for receptor modelling
Mechanism of falcipain-2 inhibition by α, β-unsaturated benzo[1, 4]diazepin-2-one methyl ester
Charge calculations in molecular mechanics. IX. * A general parameterisation of the scheme for saturated halogen, oxygen and nitrogen compounds
Filtering databases and chemical libraries
Computational study of pH-dependent oligomerization and ligand binding in Alt a 1, a highly allergenic protein with a unique fold
Toward better QSAR/QSPR modeling: simultaneous outlier detection and variable selection using distribution of model features
Free-energy perturbation and quantum mechanical study of SAMPL4 octa-acid host-guest binding energies
Investigation of substituent effect of 1-(3, 3-diphenylpropyl)-piperidinyl phenylacetamides on CCR5 binding affinity using QSAR and virtual screening techniques
Deciphering the molecular choreography of Janus kinase 2 inhibition via Gaussian accelerated molecular dynamics simulations: a dynamic odyssey
Unveiling a novel ellagic acid derivative as a potent lipoxygenase (LOX) inhibitor: integration of computational modeling and experimental validation
Cheminformatics aspects of high throughput screening: from robots to models: symposium summary
A fast new approach to pharmacophore mapping and its application to dopaminergic and benzodiazepine agonists
Machine learning-accelerated quantum mechanics-based atomistic simulations for industrial applications
Prediction of the three-dimensional structure of the human Fas receptor by comparative molecular modeling
Multi-scale in-silico modelling to unveil structural requirements for DNA-PK inhibitors as radiosensitizers and MolSHAP based design of novel ligands
A computational analysis of the binding mode of closantel as inhibitor of the Onchocerca volvulus chitinase: insights on macrofilaricidal drug design
Neural network-based QSAR and insecticide discovery: spinetoram
Identification of novel inhibitors for Pim-1 kinase using pharmacophore modeling based on a novel method for selecting pharmacophore generation subsets
Identifying conformational changes of the beta 2 adrenoceptor that enable accurate prediction of ligand/receptor interactions and screening for GPCR modulators
Upperbound procedures for the identification of similar three-dimensional chemical structures
Substructural fragments: an universal language to encode reactions, molecular and supramolecular structures
Evaluation of log P, pK a , and log D predictions from the SAMPL7 blind challenge
Camdas: An automated conformational analysis system using molecular dynamics
Boosted leave-many-out cross-validation: the effect of training and test set diversity on PLS statistics
SAMPL7 TrimerTrip host-guest binding affinities from extensive alchemical and end-point free energy calculations
Comparison of commercially available genetic algorithms: GAs as variable selection tool
Automated molecule editing in molecular design
Unsupervised guided docking of covalently bound ligands
Boosted feature selectors: a case study on prediction P-gp inhibitors and substrates
Knowledge-guided docking: accurate prospective prediction of bound configurations of novel ligands using Surflex-Dock
RestraintMaker: a graph-based approach to select distance restraints in free-energy calculations with dual topology
Data sharing matters
Enabling the hypothesis-driven prioritization of ligand candidates in big databases: Screenlamp and its application to GPCR inhibitor discovery for invasive species control
Ligand and structure-based toxicological assessment of (thio)semicarbazones on cholinesterases
Prediction of trypsin/molecular fragment binding affinities by free energy decomposition and empirical scores
Drug search for leishmaniasis: a virtual screening approach by grid computing
An Effective Simulation of Aqueous Micellar Aggregates by Computational Models
Conformation of receptor-associated PGI2: An investigation by molecular modeling
The role of human in the loop: lessons from D3R challenge 4
Protonation-induced stereoisomerism in nicotine: Conformational studies using classical (AMBER) and ab initio (Car-Parrinello) molecular dynamics
Identification of ligands for RNA targets via structure-based virtual screening: HIV-1 TAR
Evaluation of Protein-Ligand binding interactions of alkaline phosphatase inhibitors by Quantum-Mechanical methods
Maximum common substructure-based Tversky index: an asymmetric hybrid similarity measure
Reflections on the past 25 years
Multiple protein structures and multiple ligands: effects on the apparent goodness of virtual screening results
Effects of variable selection on CoMFA coefficient contour maps in a set of triazines inhibiting DHFR
Ligand binding to domain-3 of human serum albumin: a chemometric analysis
Prediction of n-octanol/water partition coefficients and acidity constants (pK a ) in the SAMPL7 blind challenge with the IEFPCM-MST model
Shaping suvorexant: application of experimental and theoretical methods for driving synthetic designs
Improving quantitative structure-activity relationship models using Artificial Neural Networks trained with dropout
NMR-assisted computational studies of peptidomimetic inhibitors bound in the hydrophobic pocket of HIV-1 glycoprotein 41
Calculating distribution coefficients based on multi-scale free energy simulations: an evaluation of MM and QM/MM explicit solvent simulations of water-cyclohexane transfer in the SAMPL5 challenge
In silico identification of novel ligands for G-quadruplex in the c-MYC promoter
Octanol-water partition coefficient measurements for the SAMPL6 blind prediction challenge
The sequence homologies of cytochromes P-450 and active-site geometries
Current perspective of information technologies in drug discovery
SAMPL5: 3D-RISM partition coefficient calculations with partial molar volume corrections and solute conformational sampling
Exploring the stability of ligand binding modes to proteins by molecular dynamics simulations
BRADSHAW: a system for automated molecular design
Limiting assumptions in structure-based design: binding entropy
Exploring sets of molecules from patents and relationships to other active compounds in chemical space networks
Prediction of hydration free energies for aliphatic and aromatic chloro derivatives using molecular dynamics simulations with the OPLS-AA force field
GridMol: a grid application for molecular modeling and visualization
Faster and more diverse de novo molecular optimization with double-loop reinforcement learning using augmented SMILES
IRC-Fuse: improved and robust prediction of redox-sensitive cysteine by fusing of multiple feature representations
On the activation and deactivation pathways of the Lck kinase domain: a computational study
Protein farnesyltransferase: Flexible docking studies on inhibitors using computational modeling
A simple, fast and convenient new method for predicting the stability of nitro compounds
A new topological index to elucidate apolar hydrocarbons
Toward Mycobacterium tuberculosis DXR inhibitor design: homology modeling and molecular dynamics simulations
Using a staged multi-objective optimization approach to find selective pharmacophore models
Discovery of new multifunctional selective acetylcholinesterase inhibitors: structure-based virtual screening and biological evaluation
Sensitivity of molecular docking to induced fit effects in influenza virus neuraminidase
Prediction of partition and distribution coefficients in various solvent pairs with COSMO-RS
Surrogate docking: structure-based virtual screening at high throughput speed
Pyrimidin-4-bromobenzenesulfonamide/-4-nitrobenzenesulfonamide hybrids as potential BRAFV600E inhibitors: experimental, computational and biological evaluations