yusuke1997/dblp-id-title huggingface dataset:
A fragment-based approach to the SAMPL3 Challenge
Assessment of uncertainty in chemical models by Bayesian probabilities: Why, when, how?
Design, synthesis, and integrated in silico analysis of novel difluoroboron curcumin analogues as potent inhibitors of the K562 leukemia cell line
Dihydrofolate reductase: A potential drug target in trypanosomes and leishmania
Insight into the mechanism of molecular recognition between human Integrin-Linked Kinase and Cpd22 and its implication at atomic level
Predicting DPP-IV inhibitors with machine learning approaches
Structural requirements of Na + -dependent antidopaminergic agents: Tropapride, Piquindone, Zetidoline, and Metoclopramide Comparison with Na + -independent ligands
A combined ligand and target-based virtual screening strategy to repurpose drugs as putrescine uptake inhibitors with trypanocidal activity
Multitask machine learning models for predicting lipophilicity (logP) in the SAMPL7 challenge
Confidence limits, error bars and method comparison in molecular modeling. Part 2: comparing methods
Statistical relationships among docking scores for different protein binding sites
MEPSIM: A computational package for analysis and comparison of molecular electrostatic potentials
Experimental design based 3-D QSAR analysis of steroid-protein interactions: Application to human CBG complexes
Ab initio computational modeling of long loops in G-protein coupled receptors
An improved scoring function for suboptimal polar ligand complexes
Convolutional neural network scoring and minimization in the D3R 2017 community challenge
Discovery of novel and potent InhA direct inhibitors by ensemble docking-based virtual screening and biological assays
A DFT-based investigation of chitin-to-chitosan transition: effects of N-acetylation on structure and reactivity
If we designed airplanes like we design drugs..
Approaching the 5-HT3 receptor heterogeneity by computational studies of the transmembrane and intracellular domains
Benzimidazole derivatives. 4. The recognition of the voluminous substituent attached to the basic amino group of 5-HT4 receptor antagonists
Adapting the DeepSARM approach for dual-target ligand design
VSDMIP: virtual screening data management on an integrated platform
Academic librarians at play in the field of cheminformatics: building the case for chemistry research data management
Structural modeling of glucanase-substrate complexes suggests a conserved tyrosine is involved in carbohydrate recognition in plant 1, 3-1, 4-β-d-glucanases
On the representation of electrostatic fields around ab initio charge distributions
Molecular insight on the non-covalent interactions between carbapenems and l, d-transpeptidase 2 from Mycobacterium tuberculosis: ONIOM study
GalaxyDock BP2 score: a hybrid scoring function for accurate protein-ligand docking
IADE: a system for intelligent automatic design of bioisosteric analogs
Bond-based linear indices in QSAR: computational discovery of novel anti-trichomonal compounds
Protein Alpha Shape (PAS) Dock: A new gaussian-based score function suitable for docking in homology modelled protein structures
Classification of HIV protease inhibitors on the basis of their antiviral potency using radial basis function neural networks
PRO_LIGAND: An approach to de novo molecular design. 3. A genetic algorithm for structure refinement
A new method for estimating the importance of hydrogen-bonding groups in the binding site of a protein
An efficient synthesis of a rationally designed 1, 5 disubstituted imidazole AT 1 Angiotensin II receptor antagonist: reorientation of imidazole pharmacophore groups in losartan reserves high receptor affinity and confirms docking studies
Structural insight into the role of Gln293Met mutation on the Peloruside A/Laulimalide association with αβ-tubulin from molecular dynamics simulations, binding free energy calculations and weak interactions analysis
Pseudoreceptor model for ryanodine derivatives at calcium release channels
DeepTargetClass: a web-based platform for predicting protein target classes of small molecules
On the electrostatic and steric similarity of lactam compounds and the natural substrate for bacterial cell-wall biosynthesis
ChemFlow_py: a flexible toolkit for docking and rescoring
Quantum mechanical polar surface area
Molecular mechanics calculations on deaminooxytocin and on deamino-arginine-vasopressin and its analogues
Computational assessment of synthetic procedures
DeepCubist: Molecular Generator for Designing Peptidomimetics based on Complex three-dimensional scaffolds
TeM-DTBA: time-efficient drug target binding affinity prediction using multiple modalities with Lasso feature selection
Comparison of structure fingerprint and molecular interaction field based methods in explaining biological similarity of small molecules in cell-based screens
Theoretical studies of the mechanism of the action of the neurohypophyseal hormones. I. Molecular electrostatic potential (MEP) and molecular electrostatic field (MEF) maps of some vasopressin analogues
MCASE study of the multidrug resistance reversal activity of propafenone analogs
Binding of carboxylate and trimethylammonium salts to octa-acid and TEMOA deep-cavity cavitands
Lead optimization mapper: automating free energy calculations for lead optimization
Characterization of β 3 -adrenergic receptor: determination of pharmacophore and 3D QSAR model for β 3 adrenergic receptor agonism
Computational models to predict blood-brain barrier permeation and CNS activity
Computer-aided design of novel antibacterial 3-hydroxypyridine-4-ones: application of QSAR methods based on the MOLMAP approach
Discovery of small molecule inhibitors of ubiquitin-like poxvirus proteinase I7L using homology modeling and covalent docking approaches
Ligand binding: evaluating the contribution of the water molecules network using the Fragment Molecular Orbital method
Statistical variation in progressive scrambling
Quantitative structure-activity relationship analysis of β-amyloid aggregation inhibitors
Needle-in-a-haystack approach: rapid screening of PDE1C inhibitors through the combination of machine learning, molecular docking, molecular dynamics simulations and experimental validation
Ensemble pharmacophore meets ensemble docking: a novel screening strategy for the identification of RIPK1 inhibitors
Characterization of PDZ domain-peptide interactions using an integrated protocol of QM/MM, PB/SA, and CFEA analyses
The SAMPL6 challenge on predicting aqueous pK a values from EC-RISM theory
Introducing the 'active search' method for iterative virtual screening
Enhancement of chemical rules for predicting compound reactivity towards protein thiol groups
Structure-based drug design, synthesis and biological assays of P. falciparum Atg3-Atg8 protein-protein interaction inhibitors
Targeting neurodegeneration: three machine learning methods for G9a inhibitors discovery using PubChem and scikit-learn
Multiple ligand-binding modes in bacterial R67 dihydrofolate reductase
Flexibility of a biotinylated ligand in artificial metalloenzymes based on streptavidin - an insight from molecular dynamics simulations with classical and ab initio force fields
Evaluation of interactions between the hepatitis C virus NS3/4A and sulfonamidobenzamide based molecules using molecular docking, molecular dynamics simulations and binding free energy calculations
Evaluation of multi-target deep neural network models for compound potency prediction under increasingly challenging test conditions
Confidence limits, error bars and method comparison in molecular modeling. Part 1: The calculation of confidence intervals
Discovery of a nanomolar inhibitor of the human glyoxalase-I enzyme using structure-based poly-pharmacophore modelling and molecular docking
The inclusion of electrostatic hydration energies in molecular mechanics calculations
Structure-activity relationships for apomorphine congeners. Conformational energies vs. biological activities
Determination of receptor-bound drug conformations by QSAR using flexible fitting to derive a molecular similarity index
De novo design by pharmacophore-based searches in fragment spaces
DemQSAR: predicting human volume of distribution and clearance of drugs
Construction of 4D-QSAR Models for Use in the Design of Novel p38-MAPK Inhibitors
SAMPL2 and continuum modeling
Design of potential angiogenin inhibitors
CCDC well groomed: an interview with Colin Groom, Executive Director, Cambridge Crystallographic Data Centre, and Frank Allen, Emeritus Fellow
Identification of the quinolinedione inhibitor binding site in Cdc25 phosphatase B through docking and molecular dynamics simulations
Phenolic-based allosteric inhibition of PTP1B: unlocking new therapeutic potential for metabolic disorders
Comparison of the X-ray structure of baboon α-lactalbumin and the tertiary predicted computer models of human α-lactalbumin
Improved pose and affinity predictions using different protocols tailored on the basis of data availability
A 3D QSAR approach to the search for geometrical similarity in a series of nonpeptide angiotensin II receptor antagonists
Three dimensional model of severe acute respiratory syndrome coronavirus helicase ATPase catalytic domain and molecular design of severe acute respiratory syndrome coronavirus helicase inhibitors
Optimal strategies for virtual screening of induced-fit and flexible target in the 2015 D3R Grand Challenge
A comparative molecular field analysis of cytochrome P450 2A5 and 2A6 inhibitors
Fractional description of free energies of solvation
Conformational analysis of the ΜΒΡ83-99 (Phe91) and ΜΒΡ83-99 (Tyr91) peptide analogues and study of their interactions with the HLA-DR2 and human TCR receptors by using Molecular Dynamics
A quantum mechanics/molecular mechanics study on the hydrolysis mechanism of New Delhi metallo-β-lactamase-1
Conformational analysis of thioglycoside derivatives of histo-blood group ABH antigens using an ab initio-derived reparameterization of MM4: implications for design of non-hydrolysable mimetics
Comprehensive model of wild-type and mutant HIV-1 reverse transciptases
Substrate binding to mammalian 15-lipoxygenase
Investigation of the role of microtubule on the activity of the mitotic kinesin EG5 using multiscale modelling: unravelling molecular mechanisms
Structure-activity relationships for a new family of sulfonylurea herbicides
A critical cross-validation of high throughput structural binding prediction methods for pMHC
Improved mapping of protein binding sites
Structure-affinity relationships for the binding of actinomycin D to DNA
A comparative study of family-specific protein-ligand complex affinity prediction based on random forest approach
Experimental characterization of the association of β-cyclodextrin and eight novel cyclodextrin derivatives with two guest compounds
A giant's shoulders: a Perspective from Professor Norman L. Allinger
Investigations on the E/Z-isomerism of neonicotinoids
Quantum algorithm for protein-ligand docking sites identification in the interaction space
LASSO - ligand activity by surface similarity order: a new tool for ligand based virtual screening
Receptor model for the molecular basis of tissue selectivity of 1, 4-dihydropyridine calcium channel drugs
Identification of novel peroxisome proliferator-activated receptor-gamma (PPARγ) agonists using molecular modeling method
Solvation of the active site of cytochrome P450-cam
Predicting protein-ligand binding modes for CELPP and GC3: workflows and insight
Prediction of the tissue/blood partition coefficients of organic compounds based on the molecular structure using least-squares support vector machines
An automated method for predicting the positions of hydrogen-bonding atoms in binding sites
Conformational analyses on histamine H2-receptor antagonists
The 1988 Oholo Conference
Comparative molecular field analysis and molecular modeling studies of 20-(S)- camptothecin analogs as inhibitors of DNA topoisomerase I and anticancer/antitumor agents
Quantitative structure-activity relationship studies of mushroom tyrosinase inhibitors
The atom assignment problem in automated de novo drug design. 3. Algorithms for optimization of fragment placement onto 3D molecular graphs
The great descriptor melting pot: mixing descriptors for the common good of QSAR models
Validation tools for variable subset regression
To buy or not to buy?
Multiple ligand docking by Glide: implications for virtual second-site screening
Could the presence of sodium ion influence the accuracy and precision of the ligand-posing in the human A2A adenosine receptor orthosteric binding site using a molecular docking approach? Insights from Dockbench
Ligand-receptor docking with the Mining Minima optimizer
Unravelling the covalent binding of zampanolide and taccalonolide AJ to a minimalist representation of a human microtubule
Prediction of CB[8] host-guest binding free energies in SAMPL6 using the double-decoupling method
In silico fragment-mapping method: a new tool for fragment-based/structure-based drug discovery
Pattern-free generation and quantum mechanical scoring of ring-chain tautomers
Applicability of a thermodynamic cycle approach for a force field parametrization targeting non-aqueous solvation free energies
Homology modelling of the human adenosine A 2B receptor based on X-ray structures of bovine rhodopsin, the beta 2 -adrenergic receptor and the human adenosine A 2A receptor
Representation, searching and discovery of patterns of bases in complex RNA structures
Computational photochemistry of retinal proteins
Parameterization of a coarse-grained model of cholesterol with point-dipole electrostatics
Of possible cheminformatics futures
Computer-aided molecular design under the SWOTlight
New molecular shape descriptors: Application in database screening
Charge calculations in molecular mechanics 7: Application to polar π systems incorporating nitro, cyano, amino, C=S and thio substituents
WIZARD: AI in conformational analysis
Multi-task convolutional neural networks for predicting in vitro clearance endpoints from molecular images
Theoretical insights into the optoelectronic and charge-transfer characteristics of 5-(1H-1,2,4-triazol-1-yl)-2-thiophenecarboxylic acid
3D hydrogen bond thermodynamics (HYBOT) potentials in molecular modelling
Chemical space sampling by different scoring functions and crystal structures
Binding of novel fullerene inhibitors to HIV-1 protease: insight through molecular dynamics and molecular mechanics Poisson-Boltzmann surface area calculations
On the use of isovalued surfaces to determine molecule shape and reaction pathways
GRIND-derived pharmacophore model for a series of α-tropanyl derivative ligands of the sigma-2 receptor *
Inactive and active states and supramolecular organization of GPCRs: insights from computational modeling
Computational study on the molecular inclusion of andrographolide by cyclodextrin
Prospective virtual screening for novel p53-MDM2 inhibitors using ultrafast shape recognition
ReSCoSS: a flexible quantum chemistry workflow identifying relevant solution conformers of drug-like molecules
Structure-activity relationship between the 3D distribution of the electrophilicity of sugar derivatives and their cytotoxic and antiviral properties
Toward the discovery of inhibitors of babesipain-1, a Babesia bigemina cysteine protease: in vitro evaluation, homology modeling and molecular docking studies
A preliminary 3D model for cytochrome P450 2D6 constructed by homology model building
Drug Design Data Resource, Grand Challenge 4, second of two issues
IA, database of known ligands of aminoacyl-tRNA synthetases
A Taxicab geometry quantification system to evaluate the performance of in silico methods: a case study on adenosine receptors ligands
Unveiling structural dynamics and allosteric vulnerabilities in Klebsiella pneumoniae KPHS_11890: an integrated DRKG-MD study
Computational and biophysical approaches to protein-protein interaction inhibition of Plasmodium falciparum AMA1/RON2 complex
Discovery and evaluation of novel Mycobacterium tuberculosis ketol-acid reductoisomerase inhibitors as therapeutic drug leads
Binding thermodynamics and interaction patterns of human purine nucleoside phosphorylase-inhibitor complexes from extensive free energy calculations
Hampering the early aggregation of PrP-E200K protein by charge-based inhibitors: a computational study
BUNDLE: A program for building the transmembrane domains of G-protein-coupled receptors
Constrained search of conformational hyperspace
Synergy of advanced machine learning and deep neural networks with consensus molecular docking for virtual screening of anaplastic lymphoma kinase inhibitors
Homology modeling of 5-lipoxygenase and hints for better inhibitor design
Performance of HADDOCK and a simple contact-based protein-ligand binding affinity predictor in the D3R Grand Challenge 2
The conformational preferences of γ-lactam and its role in constraining peptide structure
Testing the semi-explicit assembly solvation model in the SAMPL3 community blind test
Design of a Fragment Library that maximally represents available chemical space
SAMPL7 blind challenge: quantum-mechanical prediction of partition coefficients and acid dissociation constants for small drug-like molecules
Inhibitor screening identifies Entecavir as a promising candidate targeting human eIF4E to block cap-dependent translation in cancer: an integrated in silico and in vitro study
A critical assessment of finite element modeling approach for protein dynamics
Analysis methods for identifying coordinated movements during ligand unbinding
Making priors a priority
Predicting hydration free energies of polychlorinated aromatic compounds from the SAMPL-3 data set with FiSH and LIE models
Sampling and refinement protocols for template-based macrocycle docking: 2018 D3R Grand Challenge 4
Open-ComBind: harnessing unlabeled data for improved binding pose prediction
Automatic superposition of drug molecules based on their common receptor site
The SAMPL5 challenge for embedded-cluster integral equation theory: solvation free energies, aqueous p K a , and cyclohexane-water log D
Opening mechanism of adenylate kinase can vary according to selected molecular dynamics force field
Assessing the lipophilicity of fragments and early hits
Docking study of the precursor peptide of matoparan onto its putative processing enzyme, dipeptidyl peptidase IV: a revisit to molecular ticketing
Combining molecular dynamics simulation and ligand-receptor contacts analysis as a new approach for pharmacophore modeling: beta-secretase 1 and check point kinase 1 as case studies
Data quality in drug discovery: the role of analytical performance in ligand binding assays
Lessons for fragment library design: analysis of output from multiple screening campaigns
Combining docking-based comparative intermolecular contacts analysis and k-nearest neighbor correlation for the discovery of new check point kinase 1 inhibitors
A CoMFA analysis with conformational propensity: An attempt to analyze the SAR of a set of molecules with different conformational flexibility using a 3D-QSAR method
Herman Skolnik award symposium honoring Yvonne Martin
Conformational analysis of methylphenidate: comparison of molecular orbital and molecular mechanics methods
Molecular dynamics simulation study of PTP1B with allosteric inhibitor and its application in receptor based pharmacophore modeling
Refinement of modelled structures by knowledge-based energy profiles and secondary structure prediction: Application to the human procarboxypeptidase A2
Different approaches toward an automatic structural alignment of drug moleculars: Applications to sterol mimics, thrombin and thermolysin inhibitors
Calibrating the gap: a user-friendly aqueous pK a prediction protocol for organic acids, alcohols, and amines
Statistics in molecular modeling: a summary
COSMIC(90): An improved molecular mechanics treatment of hydrocarbons and conjugated systems
Molecular similarity: The introduction of flexible fitting
Development and testing of a de novo drug-design algorithm
Molecular docking performance evaluated on the D3R Grand Challenge 2015 drug-like ligand datasets
Blowing a breath of fresh share on data
The sensitivity of the results of molecular docking to induced fit effects: Application to thrombin, thermolysin and neuraminidase
Insight into the modified Ibalizumab-human CD4 receptor interactions: using a computational binding free energy approach
Tripos Rediscovered - An Interview with Jim Hopkins, CEO of Tripos Discovery Informatics
Computational design of d-peptide inhibitors of hepatitis delta antigen dimerization
Modern drug design: the implication of using artificial neuronal networks and multiple molecular dynamic simulations
Efficient screening of protein-ligand complexes in lipid bilayers using LoCoMock score
Efficient molecular mechanics simulations of the folding, orientation, and assembly of peptides in lipid bilayers using an implicit atomic solvation model
Prediction of peptide binding to a major histocompatibility complex class I molecule based on docking simulation
Improving the accuracy of the FMO binding affinity prediction of ligand-receptor complexes containing metals
Similarity searching in large combinatorial chemistry spaces
Computational insights into the selectivity mechanism of APP-IP over matrix metalloproteinases
Slate: A method for the superposition of flexible ligands
Comparative virtual screening and novelty detection for NMDA-Glycine B antagonists
Tomocomd-Cardd, a novel approach for computer-aided ' rational' drug design: I. Theoretical and experimental assessment of a promising method for computational screening and in silico design of new anthelmintic compounds
Conformational analysis of six- and twelve-membered ring compounds by molecular dynamics
Role of protein flexibility in the design of Bcl-X L targeting agents: insight from molecular dynamics
D3R Grand Challenge 3: blind prediction of protein-ligand poses and affinity rankings
Reaction mechanisms in peptide synthesis. Part 2. Tautomerism of the peptide bond
Seeking potential anticonvulsant agents that target GABAA receptors using experimental and theoretical procedures
Enabling data-limited chemical bioactivity predictions through deep neural network transfer learning
Improving database enrichment through ensemble docking
Combining crystallographic and binding affinity data towards a novel dataset of small molecule overlays
Discovery of novel inhibitors for Leishmania nucleoside diphosphatase kinase (NDK) based on its structural and functional characterization
Urgency and austerity as drivers of success
Collaborating to improve the use of free-energy and other quantitative methods in drug discovery
Preface to the special issue in memory of Phil Magee
Structural pairwise comparisons of HLM stability of phenyl derivatives: Introduction of the Pfizer metabolism index (PMI) and metabolism-lipophilicity efficiency (MLE)
Aspects of the mechanism of catalysis of glucose oxidase: A docking, molecular mechanics and quantum chemical study
Identification of cylin-dependent kinase 1 inhibitors of a new chemical type by structure-based design and database searching
QSAR study and VolSurf characterization of anti-HIV quinolone library
Structure-based 3D QSAR and design of novel acetylcholinesterase inhibitors
Interactions between cycloguanil derivatives and wild type and resistance-associated mutant Plasmodium falciparum dihydrofolate reductases
Three-dimensional modelling of human cytochrome P450 1A2 and its interaction with caffeine and MeIQ
A fast and efficient method to generate biologically relevant conformations
TrixX: structure-based molecule indexing for large-scale virtual screening in sublinear time
Developing a high-quality scoring function for membrane protein structures based on specific inter-residue interactions
A molecular modeling study on binding of drugs to calmodulin
A molecular model for the active site of S-adenosyl-l-homocysteine hydrolase
Chemical and protein structural basis for biological crosstalk between PPARα and COX enzymes
The big problems don't go away by themselves
Computational investigation of the binding mode of bis(hydroxylphenyl)arenes in 17β-HSD1: molecular dynamics simulations, MM-PBSA free energy calculations, and molecular electrostatic potential maps