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 2020-11-01 to 2024-11-01.)

Article	Citations
Evolution of Support Vector Machine and Regression Modeling in Chemoinformatics and Drug Discovery	72
Evaluation of log P, pKa, and log D predictions from the SAMPL7 blind challenge	52
SAMPL7 Host–Guest Challenge Overview: assessing the reliability of polarizable and non-polarizable methods for binding free energy calculations	52
Improving virtual screening results with MM/GBSA and MM/PBSA rescoring	43
PoseEdit: enhanced ligand binding mode communication by interactive 2D diagrams	32
Progress on open chemoinformatic tools for expanding and exploring the chemical space	31
Overview of the SAMPL6 pKa challenge: evaluating small molecule microscopic and macroscopic pKa predictions	30
An overview of the SAMPL8 host–guest binding challenge	27
Towards a converged strategy for including microsolvation in reaction mechanism calculations	25
AMOEBA binding free energies for the SAMPL7 TrimerTrip host–guest challenge	22
Non-equilibrium approach for binding free energies in cyclodextrins in SAMPL7: force fields and software	22
WIDOCK: a reactive docking protocol for virtual screening of covalent inhibitors	22
StackHCV: a web-based integrative machine-learning framework for large-scale identification of hepatitis C virus NS5B inhibitors	18
SAMPL7 blind predictions using nonequilibrium alchemical approaches	18
Extended continuous similarity indices: theory and application for QSAR descriptor selection	16
CAVIAR: a method for automatic cavity detection, description and decomposition into subcavities	15
A high quality, industrial data set for binding affinity prediction: performance comparison in different early drug discovery scenarios	15
Simplified, interpretable graph convolutional neural networks for small molecule activity prediction	14
QSAR and molecular docking for the search of AOX inhibitors: a rational drug discovery approach	14
Quantum simulations of SARS-CoV-2 main protease Mpro enable high-quality scoring of diverse ligands	14
Multitask machine learning models for predicting lipophilicity (logP) in the SAMPL7 challenge	14
Comparing predictive ability of QSAR/QSPR models using 2D and 3D molecular representations	14
COSMO-RS predictions of logP in the SAMPL7 blind challenge	13
Prediction of activity cliffs on the basis of images using convolutional neural networks	13
Relative free-energy calculations for scaffold hopping-type transformations with an automated RE-EDS sampling procedure	13

Comparison of logP and logD correction models trained with public and proprietary data sets	13
Binding site identification of G protein-coupled receptors through a 3D Zernike polynomials-based method: application to C. elegans olfactory receptors	12
Improving small molecule force fields by identifying and characterizing small molecules with inconsistent parameters	12
Prediction of n-octanol/water partition coefficients and acidity constants (pKa) in the SAMPL7 blind challenge with the IEFPCM-MST model	12
Binding free energy predictions in host-guest systems using Autodock4. A retrospective analysis on SAMPL6, SAMPL7 and SAMPL8 challenges	11
SAMPL7 blind challenge: quantum–mechanical prediction of partition coefficients and acid dissociation constants for small drug-like molecules	11
SAMPL7 protein-ligand challenge: A community-wide evaluation of computational methods against fragment screening and pose-prediction	11
SAMPL7: Host–guest binding prediction by molecular dynamics and quantum mechanics	11
Energy–entropy method using multiscale cell correlation to calculate binding free energies in the SAMPL8 host–guest challenge	11
Evaluation of multi-target deep neural network models for compound potency prediction under increasingly challenging test conditions	10
Physicochemical QSAR analysis of hERG inhibition revisited: towards a quantitative potency prediction	10
Covalent docking in CDOCKER	10
Fine-tuning of a generative neural network for designing multi-target compounds	10
Galileo: Three-dimensional searching in large combinatorial fragment spaces on the example of pharmacophores	10
Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host–guest binding: I. Standard procedure	9
Binding thermodynamics and interaction patterns of human purine nucleoside phosphorylase-inhibitor complexes from extensive free energy calculations	9
Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host–guest binding: II. regression and dielectric constant	9
Testing automatic methods to predict free binding energy of host–guest complexes in SAMPL7 challenge	9
Application of the alchemical transfer and potential of mean force methods to the SAMPL8 host-guest blinded challenge	9
Improved prediction and characterization of blood-brain barrier penetrating peptides using estimated propensity scores of dipeptides	8
Comparing classification models—a practical tutorial	8
FastGrow: on-the-fly growing and its application to DYRK1A	8
Automated high throughput pKa and distribution coefficient measurements of pharmaceutical compounds for the SAMPL8 blind prediction challenge	8
Explicit solvation thermodynamics in ionic solution: extending grid inhomogeneous solvation theory to solvation free energy of salt–water mixtures	8
Design of new imidazole derivatives with anti-HCMV activity: QSAR modeling, synthesis and biological testing	8
Ligand binding: evaluating the contribution of the water molecules network using the Fragment Molecular Orbital method	8
Imputation of sensory properties using deep learning	8
The slow but steady rise of binding free energy calculations in drug discovery	7
Predicting PAMPA permeability using the 3D-RISM-KH theory: are we there yet?	7
Enhancing sampling of water rehydration upon ligand binding using variants of grand canonical Monte Carlo	7
Multi-task convolutional neural networks for predicting in vitro clearance endpoints from molecular images	7
Precise force-field-based calculations of octanol-water partition coefficients for the SAMPL7 molecules	7
Obtaining QM/MM binding free energies in the SAMPL8 drugs of abuse challenge: indirect approaches	7
Development and interpretation of a QSAR model for in vitro breast cancer (MCF-7) cytotoxicity of 2-phenylacrylonitriles	7
In silico and in vitro anti-AChE activity investigations of constituents from Mytragyna speciosa for Alzheimer’s disease treatment	7