yusuke1997/dblp-id-title huggingface dataset:
Structure-based design of oxygen-linked macrocyclic kinase inhibitors: discovery of SB1518 and SB1578, potent inhibitors of Janus kinase 2 (JAK2) and Fms-like tyrosine kinase-3 (FLT3)
Predicting octanol/water partition coefficients and pKa for the SAMPL7 challenge using the SM12, SM8 and SMD solvation models
Molecular simulation assisted identification of Ca2+ binding residues in TMEM16A
Predicted 3D structures of olfactory receptors with details of odorant binding to OR1G1
Synergistic approach utilizing bioinformatics, machine learning, and traditional screening for the identification of novel CSK inhibitors targeting hepatocellular carcinoma
Application of a simple quantum chemical approach to ligand fragment scoring for Trypanosoma brucei pteridine reductase 1 inhibition
Synthesis, characterization, docking, MD simulation, and evaluation of antiproliferative effectiveness of new 4-aminobenzophenone derivatives
Use of surface area computations to describe atom-atom interactions
Binding free energies in the SAMPL6 octa-acid host-guest challenge calculated with MM and QM methods
Impact of graphene-based nanomaterials (GBNMs) on the structural and functional conformations of hepcidin peptide
Enhancement of the solubilities of polycyclic aromatic hydrocarbons by weak hydrogen bonds with water
A probabilistic method to report predictions from a human liver microsomes stability QSAR model: a practical tool for drug discovery
Structural prediction of a novel chitinase from the psychrophilic Glaciozyma antarctica PI12 and an analysis of its structural properties and function
On the fly estimation of host-guest binding free energies using the movable type method: participation in the SAMPL5 blind challenge
ChemGPS-NP Web : chemical space navigation online
A novel scoring function for molecular docking
Des3PI: a fragment-based approach to design cyclic peptides targeting protein-protein interactions
Novel insight into CFTR gene's single nucleotide variants classification via in-silico analysis of a conserved site
Comparison of cyclic delta-opioid peptides with non-peptide delta-agonist spiroindanyloxymorphone (SIOM) using the message-address concept: A molecular modeling study
Nonlinear dependence in comparative molecular field analysis
Computation of relative binding free energy for an inhibitor and its analogs binding with Erk kinase using thermodynamic integration MD simulation
Rational design of hirulog-type inhibitors of thrombin
Ligand-guided optimization of CXCR4 homology models for virtual screening using a multiple chemotype approach
Considerations and recent advances in QSAR models for cytochrome P450-mediated drug metabolism prediction
Atomistic lattice simulation of high T c oxides
Quantum chemical study on the interaction of some bisphosphonates and Ca 2+ : The role of molecular electrostatic potentials in the prediction of binding geometry
Molecular and structural determinants of adamantyl susceptibility to HLA-DRs allelic variants: an in silico approach to understand the mechanism of MLEs
Molecular and thermodynamic insights into interfacial interactions between collagen and cellulose investigated by molecular dynamics simulation and umbrella sampling
Chiral chromatography and multivariate quantitative structure-property relationships of benzimidazole sulphoxides
Exhaustive docking and solvated interaction energy scoring: lessons learned from the SAMPL4 challenge
An improved nicotinic pharmacophore and a stereoselective CoMFA-model for nicotinic agonists acting at the central nicotinic acetylcholine receptors labelled by [3H]-N-methylcarbamylcholine
Hydration of beta-cyclodextrin: A molecular dynamics simulation study
Dynamics and structural determinants of ligand recognition of the 5-HT6 receptor
HEPT derivatives as non-nucleoside inhibitors of HIV-1 reverse transcriptase: QSAR studies agree with the crystal structures
Looking forward into the next 25 years: the 25th anniversary issue of the Journal of Computer-Aided Molecular Design
Conformational studies on the four stereoisomers of the novel anticholinergic 4-(dimethylamino)-2-phenyl-2-(2-pyridyl)pentanamide
A proposal for the molecular basis of μ and δ opiate receptor differentiation based on modeling of two types of cyclic enkephalins and a narcotic alkaloid
Kideraspa: designing variants of staphylococcal protein a based on a diffusion model with kidera factors
Identifying signatures of proteolytic stability and monomeric propensity in O-glycosylated insulin using molecular simulation
ROCS-derived features for virtual screening
Evaluation of proposed modes of binding of (2S)-2-[4-[[(3S)-1-acetimidoyl-3-pyrrolidinyl]oxy]phenyl]-3-(7-amidino-2-naphthyl)propanoic acid hydrochloride and some analogs to Factor Xa using a comparative molecular field analysis
Discovering new PI3Kα inhibitors with a strategy of combining ligand-based and structure-based virtual screening
From oncoproteins to spike proteins: the evaluation of intramolecular stability using hydropathic force field
Encouraging data citation and discovery with the Data Citation Index
The power of a mentor
Visualisation and integration of G protein-coupled receptor related information help the modelling: Description and applications of the Viseur program
Three-dimensional quantitative structure-activity relationships of steroid aromatase inhibitors
LFER and CoMFA studies on optical resolution of alpha-alkyl alpha-aryloxy acetic acid methl esters on DACH-DNB chiral stationary phase
Congestion game scheduling for virtual drug screening optimization
Comparison of 3D quantitative structure-activity relationship methods: Analysis of the in vitro antimalarial activity of 154 artemisinin analogues by hypothetical active-site lattice and comparative molecular field analysis
Calculation of hydrophobic parameters directly from three-dimensional structures using comparative molecular field analysis
PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules
Cyclodextrin knowledgebase a web-based service managing CD-ligand complexation data
The atom assignment problem in automated de novo drug design. 2. A method for molecular graph and fragment perception
New insight in the structural features of haloadaptation in α-amylases from halophilic Archaea following homology modeling strategy: folded and stable conformation maintained through low hydrophobicity and highly negative charged surface
Drude polarizable force field for aliphatic ketones and aldehydes, and their associated acyclic carbohydrates
Virtual screening of integrase inhibitors by large scale binding free energy calculations: the SAMPL4 challenge
3-D QSAR analysis of steroid/protein interactions: The use of difference maps
Flexible matching of test ligands to a 3D pharmacophore using a molecular superposition force field: Comparison of predicted and experimental conformations of inhibitors of three enzymes
Development of a unique 3D interaction model of endogenous and synthetic peripheral benzodiazepine receptor ligands
Conformational energy downward driver (CEDD): Characterization and calibration of the method
Trainable structure-activity relationship model for virtual screening of CYP3A4 inhibition
Progress on open chemoinformatic tools for expanding and exploring the chemical space
Mutation effects of neuraminidases and their docking with ligands: a molecular dynamics and free energy calculation study
Weighted voting-based consensus clustering for chemical structure databases
A combined ligand-based and target-based drug design approach for G-protein coupled receptors: application to salvinorin A, a selective kappa opioid receptor agonist
Benchmarking GPCR homology model template selection in combination with de novo loop generation
Conformational analysis. Part 16 Conformational free energies in substituted piperidines and piperidinium salts
FRED and HYBRID docking performance on standardized datasets
Identification of family-specific residue packing motifs and their use for structure-based protein function prediction: I. Method development
SAMPL6 blind predictions of water-octanol partition coefficients using nonequilibrium alchemical approaches
Comparative receptor mapping of serotoninergic 5-HT3 and 5-HT4 binding sites
Identification of novel inhibitors of mitogen-activated protein kinase phosphatase-1 with structure-based virtual screening
Outliers in SAR and QSAR: 2. Is a flexible binding site a possible source of outliers?
Virtual and experimental high-throughput screening (HTS) in search of novel inosine 5′-monophosphate dehydrogenase II (IMPDH II) inhibitors
Complex macrocycle exploration: parallel, heuristic, and constraint-based conformer generation using ForceGen
Rational design of novel neurotensin mimetics: Discovery of a pharmacologically unprecedented agent exhibiting concentration-dependent dual effects as antagonist and full agonist
pK a based protonation states and microspecies for protein-ligand docking
SAMPL6 challenge results from a predictions based on a general Gaussian process model
ProteinShop: A tool for interactive protein manipulation and steering
Discovery of novel natural product-derived EGFR inhibitors using multiple linear regression, stacked ensemble regression, and fingerprinting approaches
Fragment-guided approach to incorporating structural information into a CoMFA study: BACE-1 as an example
Molecular graph convolutions: moving beyond fingerprints
Molecular modeling study of tubulosine and other related ipecac alkaloids
Flexible docking under pharmacophore type constraints
What induces pocket openings on protein surface patches involved in protein-protein interactions?
AMOEBA binding free energies for the SAMPL7 TrimerTrip host-guest challenge
Design, synthesis, evaluation and molecular modeling of quinazoline derivatives bearing amino acids as small-molecule PD-L1 inhibitors
Integrated data-driven and experimental approaches to accelerate lead optimization targeting SARS-CoV-2 main protease
ADAAPT: Amgen's data access, analysis, and prediction tools
Large scale free energy calculations for blind predictions of protein-ligand binding: the D3R Grand Challenge 2015
Modelling steric effects in DNA-binding platinum(II)-am(m)ine complexes
A method for fast energy estimation and visualization of protein-ligand interaction
Avalanche for shape and feature-based virtual screening with 3D alignment
Combining fragment homology modeling with molecular dynamics aims at prediction of Ca 2+ binding sites in CaBPs
Evaluating the performance of MM/PBSA for binding affinity prediction using class A GPCR crystal structures
The multi-copy simultaneous search methodology: a fundamental tool for structure-based drug design
How medicinal chemists learned about log P
Rational design of an enzyme mutant for anti-cocaine therapeutics
Modelling of the binding site of the human m1 muscarinic receptor: Experimental validation and refinement
Inhibition of protein interactions: co-crystalized protein-protein interfaces are nearly as good as holo proteins in rigid-body ligand docking
A 3 adenosine receptor activation mechanisms: molecular dynamics analysis of inactive, active, and fully active states
WIDOCK: a reactive docking protocol for virtual screening of covalent inhibitors
Simultaneous prediction of binding free energy and specificity for PDZ domain-peptide interactions
Novel anti-Plasmodial hits identified by virtual screening of the ZINC database
Structure-based drug design of small molecule AKT1 inhibitors to treat glioma
Multiple linear regression models for predicting the n‑octanol/water partition coefficients in the SAMPL7 blind challenge
A molecular-field-based similarity study of non-nucleoside HIV-1 reverse transcriptase inhibitors. 2. The relationship between alignment solutions obtained from conformationally rigid and flexible matching
Small molecule correctors of F508del-CFTR discovered by structure-based virtual screening
Evaluation of the EVA descriptor for QSAR studies: 3. The use of a genetic algorithm to search for models with enhanced predictive properties (EVA_GA)
Comparative molecular field analysis (CoMFA) study of epothilones - tubulin depolymerization inhibitors: Pharmacophore development using 3D QSAR methods
Modeling the evolution of drug resistance in malaria
Simple knowledge-based descriptors to predict protein-ligand interactions. Methodology and validation
Relative binding orientations of adenosine A 1 receptor ligands - A test case for Distributed Multipole Analysis in medicinal chemistry
Exploring the inhibitory activity of valproic acid against the HDAC family using an MMGBSA approach
Catalytic residues in hydrolases: analysis of methods designed for ligand-binding site prediction
An investigation into the construction of molecular models by the template joining method
Application of directed message-passing neural network to predict human oral bioavailability of pharmaceuticals
Rescoring of docking poses under Occam's Razor: are there simpler solutions?
Kinetic barriers in the isomerization of substituted ureas: implications for computer-aided drug design
SAMPL7: Host-guest binding prediction by molecular dynamics and quantum mechanics
Design of Ligand Binding to an Engineered Protein Cavity Using Virtual Screening and Thermal Up-shift Evaluation
Comparison of a homology model and the crystallographic structure of human 11β-hydroxysteroid dehydrogenase type 1 (11βHSD1) in a structure-based identification of inhibitors
Automated high throughput pK a and distribution coefficient measurements of pharmaceutical compounds for the SAMPL8 blind prediction challenge
Deep neural network affinity model for BACE inhibitors in D3R Grand Challenge 4
Let's get honest about sampling
Surface comparisons of some odour molecules: Conformational calculations on sandalwood odour V
TRAJELIX: A Computational Tool for the Geometric Characterization of Protein Helices During Molecular Dynamics Simulations
Covalent docking in CDOCKER
Can we really do computer-aided drug design?
Prospects for the structure‒function evolution of SARS-CoV-2 main protease inhibitors
Best practices for repurposing studies
Real value prediction of protein folding rate change upon point mutation
QSAR and classification models of a novel series of COX-2 selective inhibitors: 1, 5-diarylimidazoles based on support vector machines
Mechanism of inhibition of human secretory phospholipase A2 by flavonoids: rationale for lead design
Druggable hot spots in trypanothione reductase: novel insights and opportunities for drug discovery revealed by DRUGpy
Steered molecular dynamics simulation as a post-process to optimize the iBRAB-designed Fab model
Drug design for ever, from hype to hope
Targeting the deSUMOylase Ulp2 in Candida glabrata for antifungal therapies: in silico identification of silymarin and honokiol as potential inhibitors
Rational Design, synthesis and biological evaluation of novel triazole derivatives as potent and selective PRMT5 inhibitors with antitumor activity
Three-dimensional quantitative structure-activity and structure-selectivity relationships of dihydrofolate reductase inhibitors
A branch-and-bound method for optimal atom-type assignment in de novo ligand design
Relative binding affinity prediction of farnesoid X receptor in the D3R Grand Challenge 2 using FEP+
Biased retrieval of chemical series in receptor-based virtual screening
The challenges of making decisions using uncertain data
Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments
Integrated computational and experimental evaluation of grossamide as a natural product scaffold for dual carbohydrase inhibition in diabetes
Lions and tigers and bears, oh my! Three barriers to progress in computer-aided molecular design
Extraction and validation of substructure profiles for enriching compound libraries
A computationally efficient alternative to the Buckingham potential for molecular mechanics calculations
Predicting binding poses and affinity ranking in D3R Grand Challenge using PL-PatchSurfer2.0
Flexi-pharma: a molecule-ranking strategy for virtual screening using pharmacophores from ligand-free conformational ensembles
Development of human lactate dehydrogenase a inhibitors: high-throughput screening, molecular dynamics simulation and enzyme activity assay
Insights into the coordination chemistry of antineoplastic doxorubicin with 3d-transition metal ions Zn 2+ , Cu 2+ , and VO 2+ : a study using well-calibrated thermodynamic cycles and chemical interaction quantum chemistry models
A combined Fisher and Laplacian score for feature selection in QSAR based drug design using compounds with known and unknown activities
Computer Automated Structure Evaluation (CASE) of the teratogenicity of retinoids with the aid of a novel geometry index
Utilizing high throughput screening data for predictive toxicology models: protocols and application to MLSCN assays
Evaluation of extended parameter sets for the 3D-QSAR technique MaP: Implications for interpretability and model quality exemplified by antimalarially active naphthylisoquinoline alkaloids
Exploring the toxicity of fluoxastrobin: a combined computational and experimental approach
Editorial: Special Issue on "Evaluation of Computational Methods"
Challenges in the determination of the binding modes of non-standard ligands in X-ray crystal complexes
Size-intensive descriptors
A grand vision for configurable science and minimizing the loss model
Predicting anti-HIV activity: computational approach using a novel topological descriptor
A genetic algorithm for the automated generation of small organic molecules: Drug design using an evolutionary algorithm
Customizing scoring functions for docking
Similarity-based descriptors (SIBAR) - A tool for safe exchange of chemical information?
Docking-undocking combination applied to the D3R Grand Challenge 2015
Structure-based identification and clustering of protein families and superfamilies
Fragment-based lead generation: identification of seed fragments by a highly efficient fragment screening technology
A computational workflow for the design of irreversible inhibitors of protein kinases
A Three-dimensional Model of the Human Immunodeficiency Virus Type 1 Integration Complex
Development and NMR validation of minimal pharmacophore hypotheses for the generation of fragment libraries enriched in heparanase inhibitors
Molecular dynamics simulations reveal mechanistic insights into aptamer-induced structural rearrangements in viral capsid proteins
Molecular dynamics simulations and structure-based network analysis reveal structural and functional aspects of G-protein coupled receptor dimer interactions
The modelling of nucleophilic and electrophilic additions to organometallic complexes using molecular graphics techniques
Contact networks in RNA: a structural bioinformatics study with a new tool
Discovery of non-peptidic small molecule inhibitors of cyclophilin D as neuroprotective agents in Aβ-induced mitochondrial dysfunction
De novo drug design as GPT language modeling: large chemistry models with supervised and reinforcement learning
Conformational energy penalties of protein-bound ligands
A computer-aided approach to identify novel Leishmania major protein disulfide isomerase inhibitors for treatment of leishmaniasis
A comparative docking study and the design of potentially selective MMP inhibitors
Biomacromolecular quantitative structure-activity relationship (BioQSAR): a proof-of-concept study on the modeling, prediction and interpretation of protein-protein binding affinity
Localization and quantification of hydrophobicity: The molecular free energy density (MolFESD) concept and its application to sweetness recognition
Design, synthesis, pharmacological evaluation and computational modeling of 4-formyl-2-nitrophenyl quinoline-8-sulfonate derived thiosemicarbazones as antidiabetic agents
Ab initio study on the noncovalent adsorption of camptothecin anticancer drug onto graphene, defect modified graphene and graphene oxide
Docking-based CoMFA and CoMSIA studies of non-nucleoside reverse transcriptase inhibitors of the pyridinone derivative type
Calculation of distribution coefficients in the SAMPL5 challenge from atomic solvation parameters and surface areas
Addressing free fatty acid receptor 1 (FFAR1) activation using supervised molecular dynamics
Modeling the pharmacodynamics of passive membrane permeability
Predicting bioactive conformations and binding modes of macrocycles
Artificial neural network study on organ-targeting peptides
On the construction of LIECE models for the serotonin receptor 5-HT 2A R
An integrated suite of modeling tools that empower scientists in structure- and property-based drug design
Exploring the anti-diabetic potential of the Vigna sesquipedalis using in vitro, in vivo and computational models
Holistic in silico developability assessment of novel classes of small proteins using publicly available sequence-based predictors
DataCite and DOI names for research data
A novel approach to molecular similarity
Large-scale evaluation of cytochrome P450 2C9 mediated drug interaction potential with machine learning-based consensus modeling
Antitumor evaluation of novel alizarin-based derivatives through biological and computational approaches
Modeling error in experimental assays using the bootstrap principle: understanding discrepancies between assays using different dispensing technologies
New methods in predictive metabolism
Binding of small molecule inhibitors to RNA polymerase-Spt5 complex impacts RNA and DNA stability
Molecular modeling of interactions of the non-peptide antagonist YM087 with the human vasopressin V1a, V2 receptors and with oxytocin receptors
Open3DALIGN: an open-source software aimed at unsupervised ligand alignment
Call for papers: Symposium on Tautomers and Biology, American Chemical Society National Meeting, Boston, MA, USA August 2010
Transferable scoring function based on semiempirical quantum mechanical PM6-DH2 method: CDK2 with 15 structurally diverse inhibitors
Oxygen-containing fragments in natural products
Discovery of novel IDO1 inhibitors via structure-based virtual screening and biological assays
The Gold Rush of '89
Design and synthesis of type-III mimetics of ShK toxin
PRO_LIGAND: An approach to de novo molecular design. 1. Application to the design of organic molecules
Computational chemistry and cheminformatics: an essay on the future
Design and evaluation of novel thiazolidinedione-oxadiazole derivatives as potent α-amylase inhibitors for antidiabetic therapy
Combined use of pharmacophoric models together with drug metabolism and genotoxicity "in silico" studies in the hit finding process
ToGo-WF: prediction of RNA tertiary structures and RNA-RNA/protein interactions using the KNIME workflow
Combining in silico and in cerebro approaches for virtual screening and pose prediction in SAMPL4
Metal complexes of chiral pentaazacrowns as conformational templates for beta-turn recognition
Simulation analysis of formycin 5'-monophosphate analog substrates in the ricin A-chain active site
A structural and energetics analysis of the binding of a series of N -acetylneuraminic-acid-based inhibitors to influenza virus sialidase
Conformational preferences of the potent dopamine reuptake blocker BTCP and its analogs and their incorporation into a pharmacophore model
Active-site-directed 3D database searching: Pharmacophore extraction and validation of hits
Mycobacterium tuberculosis serine/threonine protein kinases: structural information for the design of their specific ATP-competitive inhibitors
Flexible ligand docking using a genetic algorithm
Predicting the relative binding affinity of mineralocorticoid receptor antagonists by density functional methods
Density functional and molecular docking studies towards investigating the role of single-wall carbon nanotubes as nanocarrier for loading and delivery of pyrazinamide antitubercular drug onto pncA protein
Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes
Molecular docking and QSAR of aplyronine A and analogues: potent inhibitors of actin