OOIR: Observatory of International Research

Papers

(The median citation count of Journal of Computer-Aided Molecular Design is 3. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 250 papers]. The publications cover those that have been published in the past four years, i.e., from 2021-05-01 to 2025-05-01.)

Article	Citations
Energy-entropy prediction of octanol–water logP of SAMPL7 N-acyl sulfonamide bioisosters	120
Computational investigation of functional water molecules in GPCRs bound to G protein or arrestin	59
Computational peptide discovery with a genetic programming approach	53
GPCRLigNet: rapid screening for GPCR active ligands using machine learning	45
In silico exploration of natural xanthone derivatives as potential inhibitors of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replication and cellular entry	38
Enhancing sampling of water rehydration upon ligand binding using variants of grand canonical Monte Carlo	35
A high quality, industrial data set for binding affinity prediction: performance comparison in different early drug discovery scenarios	22
PoseEdit: enhanced ligand binding mode communication by interactive 2D diagrams	21
Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host–guest binding: II. regression and dielectric constant	21
QM assisted ML for 19F NMR chemical shift prediction	21
Obtaining QM/MM binding free energies in the SAMPL8 drugs of abuse challenge: indirect approaches	20
Evolution of Support Vector Machine and Regression Modeling in Chemoinformatics and Drug Discovery	18
COSMO-RS blind prediction of distribution coefficients and aqueous pKa values from the SAMPL8 challenge	17
FastGrow: on-the-fly growing and its application to DYRK1A	17
pH-dependent solubility prediction for optimized drug absorption and compound uptake by plants	16
Design of new imidazole derivatives with anti-HCMV activity: QSAR modeling, synthesis and biological testing	15
SAMPL7 physical property prediction from EC-RISM theory	14
Correction to: Conformational energies of reference organic molecules: benchmarking of common efficient computational methods against coupled cluster theory	14
Identification of potential inhibitors of Mycobacterium tuberculosis shikimate kinase: molecular docking, in silico toxicity and in vitro experiments	14
The FMO2 analysis of the ligand-receptor binding energy: the Biscarbene-Gold(I)/DNA G-Quadruplex case study	14
Computational design and experimental confirmation of a disulfide-stapled YAP helixα1-trap derived from TEAD4 helical hairpin to selectively capture YAP α1-helix with potent antitumor activity	14
Improving drug discovery with a hybrid deep generative model using reinforcement learning trained on a Bayesian docking approximation	13
An overview of the SAMPL8 host–guest binding challenge	13
De novo drug design through gradient-based regularized search in information-theoretically controlled latent space	13
Binding free energies for the SAMPL8 CB8 “Drugs of Abuse” challenge from umbrella sampling combined with Hamiltonian replica exchange	12

Insight into the sequence-specific elements leading to increased DNA bending and ligase-mediated circularization propensity by antitumor trabectedin	12
Imputation of sensory properties using deep learning	12
User-centric design of a 3D search interface for protein-ligand complexes	12
Improvement of multi-task learning by data enrichment: application for drug discovery	12
Improving virtual screening results with MM/GBSA and MM/PBSA rescoring	11
Development and interpretation of a QSAR model for in vitro breast cancer (MCF-7) cytotoxicity of 2-phenylacrylonitriles	11
Contact networks in RNA: a structural bioinformatics study with a new tool	11
Modeling receptor flexibility in the structure-based design of KRASG12C inhibitors	11
Fine-tuning of a generative neural network for designing multi-target compounds	11
Benchmarking ANI potentials as a rescoring function and screening FDA drugs for SARS-CoV-2 Mpro	10
On the NS-DSSB unidirectional estimates in the SAMPL6 SAMPLing challenge	10
Molecular docking, dynamics simulations, and in vivo studies of gallic acid in adenine-induced chronic kidney disease: targeting KIM-1 and NGAL	10
From closed to open: three dynamic states of membrane-bound cytochrome P450 3A4	10
DeepCubist: Molecular Generator for Designing Peptidomimetics based on Complex three-dimensional scaffolds	9
Extended continuous similarity indices: theory and application for QSAR descriptor selection	9
Comparing classification models—a practical tutorial	9
Molecular dynamics simulations reveal the inhibition mechanism of Cdc42 by RhoGDI1	9
Molecular and thermodynamic insights into interfacial interactions between collagen and cellulose investigated by molecular dynamics simulation and umbrella sampling	8
Prediction of n-octanol/water partition coefficients and acidity constants (pKa) in the SAMPL7 blind challenge with the IEFPCM-MST model	8
Comparative assessment of physics-based in silico methods to calculate relative solubilities	8
Steered molecular dynamics simulation as a post-process to optimize the iBRAB-designed Fab model	8
Development of human lactate dehydrogenase a inhibitors: high-throughput screening, molecular dynamics simulation and enzyme activity assay	8
Reliable gas-phase tautomer equilibria of drug-like molecule scaffolds and the issue of continuum solvation	8
Exploring DrugCentral: from molecular structures to clinical effects	8
In silico design of dehydrophenylalanine containing peptide activators of glucokinase using pharmacophore modelling, molecular dynamics and machine learning: implications in type 2 diabetes	8
Combining crystallographic and binding affinity data towards a novel dataset of small molecule overlays	8
Comparison of logP and logD correction models trained with public and proprietary data sets	8
MDFit: automated molecular simulations workflow enables high throughput assessment of ligands-protein dynamics	8
Exploring the anti-diabetic potential of the Vigna sesquipedalis using in vitro, in vivo and computational models	8
Ligand-based and structure-based studies to develop predictive models for SARS-CoV-2 main protease inhibitors through the 3d-qsar.com portal	8
Turbo prediction: a new approach for bioactivity prediction	7
Holistic in silico developability assessment of novel classes of small proteins using publicly available sequence-based predictors	7
Correction to: Computational workflow for discovering small molecular binders for shallow binding sites by integrating molecular dynamics simulation, pharmacophore modeling, and machine learning: STAT	7
Structural impacts of two disease-linked ADAR1 mutants: a molecular dynamics study	7
Predicting absolute aqueous solubility by applying a machine learning model for an artificially liquid-state as proxy for the solid-state	7
From mundane to surprising nonadditivity: drivers and impact on ML models	7
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	6
Simplified, interpretable graph convolutional neural networks for small molecule activity prediction	6
Structure-based pose prediction: Non-cognate docking extended to macrocyclic ligands	6
Using diverse potentials and scoring functions for the development of improved machine-learned models for protein–ligand affinity and docking pose prediction	6
Reactivities of acrylamide warheads toward cysteine targets: a QM/ML approach to covalent inhibitor design	6
TeM-DTBA: time-efficient drug target binding affinity prediction using multiple modalities with Lasso feature selection	6
Enabling data-limited chemical bioactivity predictions through deep neural network transfer learning	6
Enhancement by pyrazolones of colistin efficacy against mcr-1-expressing E. coli: an in silico and in vitro investigation	6
The AI-driven Drug Design (AIDD) platform: an interactive multi-parameter optimization system integrating molecular evolution with physiologically based pharmacokinetic simulations	6
Molecular mechanism of thiamine pyrophosphate import into mitochondria: a molecular simulation study	6
Automated high throughput pKa and distribution coefficient measurements of pharmaceutical compounds for the SAMPL8 blind prediction challenge	6
On the construction of LIECE models for the serotonin receptor 5-HT$$_{\text {2A}}$$R	6
Exploring aromatic cage flexibility of the histone methyllysine reader protein Spindlin1 and its impact on binding mode prediction: an in silico study	6
Insights into the coordination chemistry of antineoplastic doxorubicin with 3d-transition metal ions Zn2+, Cu2+, and VO2+: a study using well-calibrated thermodynamic cycles and chemical interaction q	6

Application of the alchemical transfer and potential of mean force methods to the SAMPL8 host-guest blinded challenge	6
Crystal polymorphism and spectroscopical properties of sulfonamides in solid state by means of First Principles calculations	6
Structure-based virtual screening workflow to identify antivirals targeting HIV-1 capsid	6
Identification of HPr kinase/phosphorylase inhibitors: novel antimicrobials against resistant Enterococcus faecalis	5
The in silico identification of novel broad-spectrum antidotes for poisoning by organophosphate anticholinesterases	5
Synthesis, TD-DFT calculations, molecular docking and ADME studies of new spiro-oxindole derivatives containing 5(4H)-oxazolone as anti-viral and anti-bacterial agents	5
TargIDe: a machine-learning workflow for target identification of molecules with antibiofilm activity against Pseudomonas aeruginosa	5
Correction: Exploring DrugCentral: from molecular structures to clinical effects	5
Is there a common allosteric binding site for G-protein coupled receptors?	5
Molecular dynamics study on micelle-small molecule interactions: developing a strategy for an extensive comparison	5
Prot2Prot: a deep learning model for rapid, photorealistic macromolecular visualization	5
Best practices for repurposing studies	5
In silico identification and in vitro antiviral validation of potential inhibitors against Chikungunya virus	5
A least-squares-fitting procedure for an efficient preclinical ranking of passive transport across the blood–brain barrier endothelium	4
On the force field optimisation of $$\beta$$-lactam cores using the force field Toolkit	4
Identifying signatures of proteolytic stability and monomeric propensity in O-glycosylated insulin using molecular simulation	4
Binding of small molecule inhibitors to RNA polymerase-Spt5 complex impacts RNA and DNA stability	4
Promoter recognition specificity of Corynebacterium glutamicum stress response sigma factors σD and σH deciphered using computer modeling and point mutagenesis	4
OPTUNA optimization for predicting chemical respiratory toxicity using ML models	4
Convolidine as potent BACE1 inhibitor for Alzheimer’s disease; in-silico coupled with in-vitro assessment	4
Rethinking the applicability domain analysis in QSAR models	4
Elucidating the potential effects of point mutations on FGFR3 inhibitor resistance via combined molecular dynamics simulation and community network analysis	4
Artificial intelligence for prediction of biological activities and generation of molecular hits using stereochemical information	4
StackHCV: a web-based integrative machine-learning framework for large-scale identification of hepatitis C virus NS5B inhibitors	4
ADis-QSAR: a machine learning model based on biological activity differences of compounds	4
Quantum simulations of SARS-CoV-2 main protease Mpro enable high-quality scoring of diverse ligands	4
Deciphering the sequence-dependent unfolding pathways of an RNA pseudoknot with steered molecular dynamics	4
Investigating the role of glycans in Omicron sub-lineages XBB.1.5 and XBB.1.16 binding to host receptor using molecular dynamics and binding free energy calculations	4
Correction: Complex peptide macrocycle optimization: combining NMR restraints with conformational analysis to guide structure-based and ligand-based design	4
ChemFlow_py: a flexible toolkit for docking and rescoring	3
SAMPL7 blind challenge: quantum–mechanical prediction of partition coefficients and acid dissociation constants for small drug-like molecules	3
Precise force-field-based calculations of octanol-water partition coefficients for the SAMPL7 molecules	3
Binding site identification of G protein-coupled receptors through a 3D Zernike polynomials-based method: application to C. elegans olfactory receptors	3
Fine tuning for success in structure-based virtual screening	3
Computational investigation to identify multi-targeted anti-hyperglycemic potential of substituted 2-Mercaptobenzimidazole derivatives and synthesis of new α-glucosidase inhibitors	3
Des3PI: a fragment-based approach to design cyclic peptides targeting protein–protein interactions	3
Identifying and characterising promising small molecule inhibitors of kinesin spindle protein using ligand-based virtual screening, molecular docking, molecular dynamics and MM‑GBSA calculations	3
A deep neural network: mechanistic hybrid model to predict pharmacokinetics in rat	3
Molecular dynamics simulations as a guide for modulating small molecule aggregation	3
OFraMP: a fragment-based tool to facilitate the parametrization of large molecules	3
A combined ligand and target-based virtual screening strategy to repurpose drugs as putrescine uptake inhibitors with trypanocidal activity	3
Consensus scoring evaluated using the GPCR-Bench dataset: Reconsidering the role of MM/GBSA	3
The power of a mentor	3
Identification of a druggable site on GRP78 at the GRP78-SARS-CoV-2 interface and virtual screening of compounds to disrupt that interface	3
On the relevance of query definition in the performance of 3D ligand-based virtual screening	3