yusuke1997/dblp-id-title huggingface dataset:
Possible allosteric interactions of monoindazole-substituted P2 cyclic urea analogues with wild-type and mutant HIV-1 protease
Sampling conformational hyperspace: Techniques for improving completeness
Blinded predictions of standard binding free energies: lessons learned from the SAMPL6 challenge
Can topological indices transmit information on properties but not on structures?
A graph-theoretic approach to modeling metabolic pathways
PRO_LIGAND: An approach to de novo molecular design. 6. Flexible fitting in the design of peptides
Two-track virtual screening approach to identify both competitive and allosteric inhibitors of human small C-terminal domain phosphatase 1
Molecular Lipophilicity Potential, a tool in 3D QSAR: Method and applications
Sampling and convergence in free energy calculations of protein-ligand interactions: The binding of triphenoxypyridine derivatives to factor Xa and trypsin
Exploring privileged structures: the combinatorial synthesis of cyclic peptides
Orientational sampling and rigid-body minimization in molecular docking revisited: On-the-fly optimization and degeneracy removal
TargetNet: a web service for predicting potential drug-target interaction profiling via multi-target SAR models
Dissecting the molecular recognition of dual lapatinib derivatives for EGFR/HER2
Therapeutic potency of a developed optimized polyherbal formulation in ameliorating obesity induced inflammation and oxidative stress in Swiss albino mice by targeting PPARγ, insulin receptor and AMPK signalling pathway
SAMPL7 TrimerTrip host-guest binding poses and binding affinities from spherical-coordinates-biased simulations
Evaluation of a method for controlling molecular scaffold diversity in de novo ligand design
A D3R prospective evaluation of machine learning for protein-ligand scoring
A promising enantioselective Diels-Alder dienophile by computer-assisted rational design: 2, 5-diphenyl-1-vinyl-borolane
Discovery of a reversible ALDH1A3 inhibitor throwugh a consensus docking-based virtual screening study
Comparison of protein surfaces using a genetic algorithm
Blinded prediction of protein-ligand binding affinity using Amber thermodynamic integration for the 2018 D3R grand challenge 4
Molecular model of the neural dopamine transporter
Strategic approaches to drug design. I. An integrated software framework for molecular modelling
Alpha shock
Role of indirect readout mechanism in TATA box binding protein-DNA interaction
Computer simulation of the binding of amonfide and azonafide to DNA
Design of new secreted phospholipase A 2 inhibitors based on docking calculations by modifying the pharmacophore segments of the FPL67047XX inhibitor
μOR-ligand: target-aware view-based hybrid feature selection for μ-opioid receptor ligand functional classification
DREAM++: Flexible docking program for virtual combinatorial libraries
Combining fragment docking with graph theory to improve ligand docking for homology model structures
Distinct functional and conformational states of the human lymphoid tyrosine phosphatase catalytic domain can be targeted by choice of the inhibitor chemotype
Force-field parametrization of retro-inverso modified residues: Development of torsional and electrostatic parameters
Modeling & Informatics at Vertex Pharmaceuticals Incorporated: our philosophy for sustained impact
Benchmarking the performance of MM/PBSA in virtual screening enrichment using the GPCR-Bench dataset
Structure-reactivity modeling using mixture-based representation of chemical reactions
Semi-rigid analogues of the calcium antagonist verapamil: A molecular modelling study
Developing a predictive QSAR model for FGFR-1 inhibitors: integrating computational and experimental validation
Molecular simulation-based 3D structural construction of olfactory receptor with agonist binding
Human farnesyl pyrophosphate synthase inhibition by nitrogen bisphosphonates: a 3D-QSAR study
Machine learning-based QSAR and structure-based virtual screening guided discovery of novel mIDH1 inhibitors from natural products
AI-driven molecular modeling and design: from property prediction to drug generation
Quantitative structure-activity relationship analysis of canonical inhibitors of serine proteases
Using physics-based pose predictions and free energy perturbation calculations to predict binding poses and relative binding affinities for FXR ligands in the D3R Grand Challenge 2
On the force field optimisation of β-lactam cores using the force field Toolkit
Toward the identification of the cardiac cGMP inhibited-phosphodiesterase catalytic site
Ligand-biased ensemble receptor docking (LigBEnD): a hybrid ligand/receptor structure-based approach
Antifungal triazole alcohols: A comparative analysis of structure-activity, structure-teratogenicity and structure-therapeutic index relationships using the Multiple Computer-Automated Structure Evaluation (Multi-CASE) methodology
Protein-ligand docking with multiple flexible side chains
Molecular dynamics of Mycobacterium tuberculosis KasA: implications for inhibitor and substrate binding and consequences for drug design
Exploring therapeutic targets for cryptococcosis: in silico and in vitro testing for isocitrate lyase (ICL1) potential inhibitors
Combined QSAR and molecule docking studies on predicting P-glycoprotein inhibitors
A comparison of molecular representations for lipophilicity quantitative structure-property relationships with results from the SAMPL6 logP Prediction Challenge
Structural organization of G-protein-coupled receptors
Predicting absolute aqueous solubility by applying a machine learning model for an artificially liquid-state as proxy for the solid-state
Computer simulation of biological interactions and reactivity
Permuting input for more effective sampling of 3D conformer space
Comparative study of the prereactive protein kinase A Michaelis complex with Kemptide substrate
An inequality for 3D database searching and its use in evaluating the treatment of conformational flexibility
Structure-activity relationships of thiostrepton derivatives: implications for rational drug design
Molecular modelling and conformational analysis of a GABA B antagonist
Insights into the binding mode and mechanism of action of some atypical retinoids as ligands of the small heterodimer partner (SHP)
Differentiation of delta, µ, and kappa opioid receptor agonists based on pharmacophore development and computed physicochemical properties
Guiding effective decisions: an interview with Matthew Segall, CEO of Optibrium
Analysis and use of fragment-occurrence data in similarity-based virtual screening
Considerations on the recognition of the D1 receptor by agonists
DockingApp: a user friendly interface for facilitated docking simulations with AutoDock Vina
Computational identification of epitopes in the glycoproteins of novel bunyavirus (SFTS virus) recognized by a human monoclonal antibody (MAb 4-5)
Ligand design by a combinatorial approach based on modeling and experiment: application to HLA-DR4
5, 10-Methylene-5, 6, 7, 8-tetrahydrofolate conformational transitions upon binding to thymidylate synthase: molecular mechanics and continuum solvent studies
Effects of inductive bias on computational evaluations of ligand-based modeling and on drug discovery
An interview with Phil Bourne, associate director of the RCSB protein data bank
From data point timelines to a well curated data set, data mining of experimental data and chemical structure data from scientific articles, problems and possible solutions
MolAlign: an algorithm for aligning multiple small molecules
Prediction of free energies of hydration with COSMO-RS on the SAMPL3 data set
Structural changes by sulfoxidation of phenothiazine drugs
Absolute binding free energies for octa-acids and guests in SAMPL5 - Evaluating binding free energies for octa-acid and guest complexes in the SAMPL5 blind challenge
Predictive cartography of metal binders using generative topographic mapping
Computational prediction of kink properties of helices in membrane proteins
QSPR ensemble modelling of the 1: 1 and 1: 2 complexation of Co2+, Ni2+, and Cu2+ with organic ligands: relationships between stability constants
Correction: Complex peptide macrocycle optimization: combining NMR restraints with conformational analysis to guide structure-based and ligand-based design
CGEMA and VGAP: a Colour Graphics Editor for Multiple Alignment using a Variable GAP penalty. Application to the muscarinic acetylcholine receptor
Molecular modelling studies on the ORL1-receptor and ORL1-agonists
Extrapolative prediction using physically-based QSAR
Classification of protein disulphide-bridge topologies
A molecular mechanics study of the effect of substitution in position 1 on the conformational space of the oxytocin/vasopressin ring
Precise force-field-based calculations of octanol-water partition coefficients for the SAMPL7 molecules
3D-QSAR study of hallucinogenic phenylalkylamines by using CoMFA approach
The need for scientific software engineering in the pharmaceutical industry
Many InChIs and quite some feat
Managing bias in ROC curves
A novel method of aligning molecules by local surface shape similarity
Predicting binding affinities of host-guest systems in the SAMPL3 blind challenge: the performance of relative free energy calculations
ProSeg: a database of local structures of protein segments
A machine learning approach to computer-aided molecular design
Erratum to: Prediction of tautomer ratios by embedded-cluster integral equation theory
Computational analysis of EBNA1 "druggability" suggests novel insights for Epstein-Barr virus inhibitor design
Tautomeric equilibria in 8-oxopurines: Implications for mutagenicity
Proteochemometric model for predicting the inhibition of penicillin-binding proteins
Temperature effect on poly(dA).poly(dT): molecular dynamics simulation studies of polymeric and oligomeric constructs
Machine learning study for the prediction of transdermal peptide
Fine-tuning of a generative neural network for designing multi-target compounds
Chemoinformatics methods for systematic comparison of molecules from natural and synthetic sources and design of hybrid libraries
Collaboration, competition, validation and plans for the future - An interview with Gerard Kleywegt, Head of the Protein Data Bank in Europe
Machine learning of chemical reactivity from databases of organic reactions
Hydration in drug design. 3. Conserved water molecules at the ligand-binding sites of homologous proteins
Anti-inflammatory potential of Grewialin from Grewia optiva: insights from molecular docking, ADMET, DFT, and in-vitro studies
Possibilities for transfer of relevant data without revealing structural information
A comparative study of AutoDock and PMF scoring performances, and SAR of 2-substituted pyrazolotriazolopyrimidines and 4-substituted pyrazolopyrimidines as potent xanthine oxidase inhibitors
A knowledge-based approach to generating diverse but energetically representative ensembles of ligand conformers
Heterofullerenes: Structure and property predictions, possible uses and synthesis proposals
Euclidean chemical spaces from molecular fingerprints: Hamming distance and Hempel's ravens
Chemometric QSAR studies of antifungal azoxy compounds
Computational simulations of the conformational behaviour of the adhesive proteins RGDS fragment
"Heptadecanol" a phytochemical multi-target inhibitor of SMYD3 & GFPT2 proteins in non-small cell lung cancer: an in-silico & in-vitro investigation
Computer-aided molecular modeling and design of DNA-inserting molecules
Molecular modeling on pyruvate phosphate dikinase of Entamoeba histolytica and in silico virtual screening for novel inhibitors
Ligand expansion in ligand-based virtual screening using relevance feedback
In silico prediction of acyl glucuronide reactivity
Flexsim-R: A virtual affinity fingerprint descriptor to calculate similarities of functional groups
AI-driven protein pocket detection through integrating deep Q-networks for structural analysis
Automated site-directed drug design: Approaches to the formation of 3D molecular graphs
The discovery of novel auxin transport inhibitors by molecular modeling and three-dimensional pattern analysis
Calculate protein-ligand binding affinities with the extended linear interaction energy method: application on the Cathepsin S set in the D3R Grand Challenge 3
Rational molecular design of novel class-III peptidic antagonists to competitively disrupt human PPARδ self-binding peptide
ForceGen 3D structure and conformer generation: from small lead-like molecules to macrocyclic drugs
Co-operative intra-protein structural response due to protein-protein complexation revealed through thermodynamic quantification: study of MDM2-p53 binding
Computational Model of the Complex between GR113808 and the 5-HT4 Receptor Guided by Site-Directed Mutagenesis and the Crystal Structure of Rhodopsin
Druggability of methyl-lysine binding sites
Surflex-Dock 2.1: Robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search
A computational tool to optimize ligand selectivity between two similar biomacromolecular targets
Modeling chemical reactions for drug design
Elaborate ligand-based modeling reveal new submicromolar Rho kinase inhibitors
Impact of physical activity on the hypothalamic-pituitary-gonadal axis in older males: a comparative and AI-based predictive modeling study of demographic factors and stress markers
Modelling a 3D structure for EgDf1 from shape Echinococcus granulosus: putative epitopes, phosphorylation motifs and ligand
A fast empirical method for the calculation of molecular polarizability
Identifying potential binding modes and explaining partitioning behavior using flexible alignments and multidimensional scaling
Overview of the SAMPL6 pK a challenge: evaluating small molecule microscopic and macroscopic pK a predictions
Tools, techniques, organisation and culture of the CADD group at Sygnature Discovery
Consensus model for identification of novel PI3K inhibitors in large chemical library
Rapid discovery of inhibitors of Toxoplasma gondii using hybrid structure-based computational approach
Predicting allergic contact dermatitis: a hierarchical structure-activity relationship (SAR) approach to chemical classification using topological and quantum chemical descriptors
Homology modeling and metabolism prediction of human carboxylesterase-2 using docking analyses by GriDock : a parallelized tool based on AutoDock 4.0
3d electron cloud descriptors for enhanced QSAR modeling of anti-colorectal cancer compounds
In-silico guided discovery of novel CCR9 antagonists
Investigation of the metal binding site in methionine aminopeptidase by density functional theory
Is there a future for computational chemistry in drug research?
An integrated approach to knowledge-driven structure-based virtual screening
Structural explanation for the tunable substrate specificity of an E. coli nucleoside hydrolase: insights from molecular dynamics simulations
Estimating the domain of applicability for machine learning QSAR models: a study on aqueous solubility of drug discovery molecules
A comparison of heuristic search algorithms for molecular docking
Thermodynamic free energy map for the non-oxidative glycolysis pathways
Development of biologically active compounds by combining 3D QSAR and structure-based design methods
Variability in docking success rates due to dataset preparation
Insights into the preferential order of strand exchange in the Cre/loxP recombinase system: impact of the DNA spacer flanking sequence and flexibility
Extended solvent-contact model approach to blind SAMPL5 prediction challenge for the distribution coefficients of drug-like molecules
Bias, reporting, and sharing: computational evaluations of docking methods
Computational insights into the interaction mechanism of triazolyl substituted tetrahydrobenzofuran derivatives with H+, K+-ATPase at different pH
SAMPL6 host-guest challenge: binding free energies via a multistep approach
Ligand intramolecular motions in ligand-protein interaction: ALPHA, a novel dynamic descriptor and a QSAR study with extended steroid benchmark dataset
Mechanism of action of aspartic proteinases: Application of transition-state analogue theory
The good, the bad and the twisted: a survey of ligand geometry in protein crystal structures
Molecular dynamics simulation and linear interaction energy study of d-Glu-based inhibitors of the MurD ligase
Incorporating specificity into optimization: evaluation of SPA using CSAR 2014 and CASF 2013 benchmarks
Empirical estimation of the energetic contribution of individual interface residues in structures of protein-protein complexes
Structural comparison of NK 2 receptor agonists and antagonists
Multitarget neuroprotective effects of β-sitosterol in diabetes-associated neurodegeneration: a coupled experimental/computational study
Computational characterization and machine learning analysis of quantum optimized marine fungal metabolites targeting PD-L1 in cancer immunotherapy
Creating and virtually screening databases of fluorescently-labelled compounds for the discovery of target-specific molecular probes
Deciphering the sequence-dependent unfolding pathways of an RNA pseudoknot with steered molecular dynamics
Bioactive metabolites from Paeonia lactiflora protect against heat-induced male infertility in Drosophila melanogaster by modulating Vasa: integrating in vivo and computational analyses
Thermodynamic aspects of hydrophobicity and biological QSAR
Protein pocket and ligand shape comparison and its application in virtual screening
A systematic insight into glycycoumarin as potential IL-8/topo I inhibitor from natural products collected in Taibai mountain based on the combination of in silico and bioassay
Impact of domain knowledge on blinded predictions of binding energies by alchemical free energy calculations
Disrupting tuberculosis pathogenesis by targeting DprE1 in cell wall biosynthesis: a structural dynamics perspective
Design of dimerization inhibitors of HIV-1 aspartic proteinase: A computer-based combinatorial approach
Absolute and relative pK a predictions via a DFT approach applied to the SAMPL6 blind challenge
Identification of ligand efficient, fragment-like hits from an HTS library: structure-based virtual screening and docking investigations of 2H- and 3H-pyrazolo tautomers for Aurora kinase A selectivity
Structure-based virtual screening workflow to identify antivirals targeting HIV-1 capsid
Classification of a large anticancer data set by Adaptive Fuzzy Partition
Prediction of in vitro metabolic stability of calcitriol analogs by QSAR
PLASS: Protein-ligand affinity statistical score - a knowledge-based force-field model of interaction derived from the PDB
Comparative Molecular Similarity Index Analysis (CoMSIA) to study hydrogen-bonding properties and to score combinatorial libraries
Analysis of Fas-ligand interactions using a molecular model of the receptor-ligand interface
Box size effects are negligible for solvation free energies of neutral solutes
Quantitative prediction of imprinting factor of molecularly imprinted polymers by artificial neural network
A high quality, industrial data set for binding affinity prediction: performance comparison in different early drug discovery scenarios
Application of shape-based and pharmacophore-based in silico screens for identification of Type II protein kinase inhibitors
Reverse engineering chemical structures from molecular descriptors: how many solutions?
A common motif in G-protein-coupled seven transmembrane helix receptors
Tautomerism of xanthine and alloxanthine: A model for substrate recognition by xanthine oxidase
Is the parallel or antiparallel beta-sheet more stable? A semiempirical study
Enantioselectivity of epoxide hydrolase catalysed oxirane ring opening: a 3D QSAR Study
Structure-activity relationships of cannabinoids: A joint CoMFA and pseudoreceptor modelling study
Computer-aided drug design: the next 20 years
Encoding mu-opioid receptor biased agonism with interaction fingerprints
Erratum to: Close intramolecular sulfur-oxygen contacts: modified force field parameters for improved conformation generation
Predicting drug-target affinity through triple pre-activated random residual planet convolution coupled attention network and contact maps
Convex-PL: a novel knowledge-based potential for protein-ligand interactions deduced from structural databases using convex optimization
So you think you understand tautomerism?
D3R grand challenge 2015: Evaluation of protein-ligand pose and affinity predictions
Correction to: Conformational energies of reference organic molecules: benchmarking of common efficient computational methods against coupled cluster theory
Fragment-based strategy for structural optimization in combination with 3D-QSAR
A comparison of different functions for predicted protein model quality assessment
Performance of multiple docking and refinement methods in the pose prediction D3R prospective Grand Challenge 2016
What do we know and when do we know it?
Selective inhibition of 6-phosphogluconate dehydrogenase from Trypanosoma brucei
Knowing when to give up: early-rejection stratagems in ligand docking
Computational design and experimental confirmation of a disulfide-stapled YAP helix α1 -trap derived from TEAD4 helical hairpin to selectively capture YAP α1-helix with potent antitumor activity
Designing novel FAK inhibitors targeting gastric cancer: a combined approach using machine learning, docking analysis, molecular dynamics simulations, and experimental validation
Tuning of hydrogen bond strength using substituents on phenol and aniline: A possible ligand design strategy
In silico identification of noncompetitive inhibitors targeting an uncharacterized allosteric site of falcipain-2
Statistical analysis of EGFR structures' performance in virtual screening
Extensive benchmark of rDock as a peptide-protein docking tool
A comprehensive analysis of the thermodynamic events involved in ligand-receptor binding using CoRIA and its variants
Overview of the perspectives devoted to tautomerism in molecular design
Computational chemistry in pharmaceutical research: at the crossroads
Web application for studying the free energy of binding and protonation states of protein-ligand complexes based on HINT
Computational insights into ligand-induced G protein and β-arrestin signaling of the dopamine D1 receptor
Model of full-length HIV-1 integrase complexed with viral DNA as template for anti-HIV drug design
Modeling of protease I collagenolytic enzyme from the fiddler crab Uca pugilator
Understanding and modulating cyclin-dependent kinase inhibitor specificity: molecular modeling and biochemical evaluation of pyrazolopyrimidinones as CDK2/cyclin A and CDK4/cyclin D1 inhibitors
Energy-entropy method using multiscale cell correlation to calculate binding free energies in the SAMPL8 host-guest challenge
Symposium overview the Shell Conference on computer-aided molecular modelling
Selenoglycosides in silico: ab initio-derived reparameterization of MM4, conformational analysis using histo-blood group ABH antigens and lectin docking as indication for potential of bioactivity
COSMO-RS blind prediction of distribution coefficients and aqueous pKa values from the SAMPL8 challenge
Predicting octanol/water partition coefficients using molecular simulation for the SAMPL7 challenge: comparing the use of neat and water saturated 1-octanol
Structure-guided fragment-based in silico drug design of dengue protease inhibitors
A proposed bioactive conformation of Peptide T
Performance evaluation of molecular docking and free energy calculations protocols using the D3R Grand Challenge 4 dataset
Simulation of carbohydrate-protein interactions: Computer-aided design of a second generation GM1 mimic
Local elevation: A method for improving the searching properties of molecular dynamics simulation
Blinded predictions of distribution coefficients in the SAMPL5 challenge
Development of small molecules designed to modulate protein-protein interactions
Structural impacts of two disease-linked ADAR1 mutants: a molecular dynamics study
Modeling of enzyme-substrate complexes for the metalloproteases MMP-3, ADAM-9 and ADAM-10