OOIR: Observatory of International Research

Papers

(The TQCC of Journal of Computer-Aided Molecular Design is 7. 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 2021-06-01 to 2025-06-01.)

Article	Citations
Energy-entropy prediction of octanol–water logP of SAMPL7 N-acyl sulfonamide bioisosters	124
Computational investigation of functional water molecules in GPCRs bound to G protein or arrestin	60
Computational peptide discovery with a genetic programming approach	49
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
GPCRLigNet: rapid screening for GPCR active ligands using machine learning	38
Enhancing sampling of water rehydration upon ligand binding using variants of grand canonical Monte Carlo	23
A high quality, industrial data set for binding affinity prediction: performance comparison in different early drug discovery scenarios	22
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	18
Evolution of Support Vector Machine and Regression Modeling in Chemoinformatics and Drug Discovery	17
PoseEdit: enhanced ligand binding mode communication by interactive 2D diagrams	17
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	16
pH-dependent solubility prediction for optimized drug absorption and compound uptake by plants	15
Design of new imidazole derivatives with anti-HCMV activity: QSAR modeling, synthesis and biological testing	15
The FMO2 analysis of the ligand-receptor binding energy: the Biscarbene-Gold(I)/DNA G-Quadruplex case study	14
Correction to: Conformational energies of reference organic molecules: benchmarking of common efficient computational methods against coupled cluster theory	14
SAMPL7 physical property prediction from EC-RISM theory	14
Identification of potential inhibitors of Mycobacterium tuberculosis shikimate kinase: molecular docking, in silico toxicity and in vitro experiments	14
Improving drug discovery with a hybrid deep generative model using reinforcement learning trained on a Bayesian docking approximation	13
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	13
Imputation of sensory properties using deep learning	13
An overview of the SAMPL8 host–guest binding challenge	13
Improvement of multi-task learning by data enrichment: application for drug discovery	12

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	11
User-centric design of a 3D search interface for protein-ligand complexes	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
De novo drug design through gradient-based regularized search in information-theoretically controlled latent space	11
From closed to open: three dynamic states of membrane-bound cytochrome P450 3A4	10
Molecular docking, dynamics simulations, and in vivo studies of gallic acid in adenine-induced chronic kidney disease: targeting KIM-1 and NGAL	10
On the NS-DSSB unidirectional estimates in the SAMPL6 SAMPLing challenge	10
DeepCubist: Molecular Generator for Designing Peptidomimetics based on Complex three-dimensional scaffolds	9
Benchmarking ANI potentials as a rescoring function and screening FDA drugs for SARS-CoV-2 Mpro	9
Reliable gas-phase tautomer equilibria of drug-like molecule scaffolds and the issue of continuum solvation	9
Comparing classification models—a practical tutorial	9
Molecular and thermodynamic insights into interfacial interactions between collagen and cellulose investigated by molecular dynamics simulation and umbrella sampling	9
Extended continuous similarity indices: theory and application for QSAR descriptor selection	9
MDFit: automated molecular simulations workflow enables high throughput assessment of ligands-protein dynamics	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
Comparative assessment of physics-based in silico methods to calculate relative solubilities	8
Exploring DrugCentral: from molecular structures to clinical effects	8
Multi-Omics Analysis of the virulence factors and designing of next-generation multi-epitopes Vaccines against Rickettsia prowazekii: a computer-aided vaccine designing approach	8
Steered molecular dynamics simulation as a post-process to optimize the iBRAB-designed Fab model	8
Comparison of logP and logD correction models trained with public and proprietary data sets	8
Prediction of n-octanol/water partition coefficients and acidity constants (pKa) in the SAMPL7 blind challenge with the IEFPCM-MST model	8
Exploring the anti-diabetic potential of the Vigna sesquipedalis using in vitro, in vivo and computational models	8
Combining crystallographic and binding affinity data towards a novel dataset of small molecule overlays	8
Molecular dynamics simulations reveal the inhibition mechanism of Cdc42 by RhoGDI1	8
Ligand-based and structure-based studies to develop predictive models for SARS-CoV-2 main protease inhibitors through the 3d-qsar.com portal	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
Development of human lactate dehydrogenase a inhibitors: high-throughput screening, molecular dynamics simulation and enzyme activity assay	7
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
Predicting absolute aqueous solubility by applying a machine learning model for an artificially liquid-state as proxy for the solid-state	7