OOIR: Observatory of International Research

Papers

(The TQCC of Journal of Computer-Aided Molecular Design is 8. 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 2020-05-01 to 2024-05-01.)

Article	Citations
Interpretation of machine learning models using shapley values: application to compound potency and multi-target activity predictions	258
Artificial intelligence in chemistry and drug design	77
Evolution of Support Vector Machine and Regression Modeling in Chemoinformatics and Drug Discovery	50
Meta-iPVP: a sequence-based meta-predictor for improving the prediction of phage virion proteins using effective feature representation	49
SAMPL7 Host–Guest Challenge Overview: assessing the reliability of polarizable and non-polarizable methods for binding free energy calculations	45
Evaluation of log P, pKa, and log D predictions from the SAMPL7 blind challenge	41
Supervised molecular dynamics for exploring the druggability of the SARS-CoV-2 spike protein	39
Improving virtual screening results with MM/GBSA and MM/PBSA rescoring	37
ProIn-Fuse: improved and robust prediction of proinflammatory peptides by fusing of multiple feature representations	33
Machine learning-accelerated quantum mechanics-based atomistic simulations for industrial applications	32
Progress on open chemoinformatic tools for expanding and exploring the chemical space	26
SAMPL7 TrimerTrip host–guest binding affinities from extensive alchemical and end-point free energy calculations	25
Mutation-mediated influences on binding of anaplastic lymphoma kinase to crizotinib decoded by multiple replica Gaussian accelerated molecular dynamics	25
Towards a converged strategy for including microsolvation in reaction mechanism calculations	24
Overview of the SAMPL6 pKa challenge: evaluating small molecule microscopic and macroscopic pKa predictions	23
Enhancing water sampling of buried binding sites using nonequilibrium candidate Monte Carlo	21
Interactions of GF-17 derived from LL-37 antimicrobial peptide with bacterial membranes: a molecular dynamics simulation study	21
Non-equilibrium approach for binding free energies in cyclodextrins in SAMPL7: force fields and software	21
WIDOCK: a reactive docking protocol for virtual screening of covalent inhibitors	21
AMOEBA binding free energies for the SAMPL7 TrimerTrip host–guest challenge	20
Predictive potential of eigenvalue-based topological molecular descriptors	20
Computational exploration and experimental validation to identify a dual inhibitor of cholinesterase and amyloid-beta for the treatment of Alzheimer’s disease	20
SAMPL7 TrimerTrip host–guest binding poses and binding affinities from spherical-coordinates-biased simulations	20
Advances in exploring activity cliffs	20
An overview of the SAMPL8 host–guest binding challenge	19

SAMPL7 blind predictions using nonequilibrium alchemical approaches	17
ReSCoSS: a flexible quantum chemistry workflow identifying relevant solution conformers of drug-like molecules	16
The critical role of QM/MM X-ray refinement and accurate tautomer/protomer determination in structure-based drug design	16
StackHCV: a web-based integrative machine-learning framework for large-scale identification of hepatitis C virus NS5B inhibitors	14
Multitask machine learning models for predicting lipophilicity (logP) in the SAMPL7 challenge	14
Quantum simulations of SARS-CoV-2 main protease Mpro enable high-quality scoring of diverse ligands	13
Prediction of ligand binding mode among multiple cross-docking poses by molecular dynamics simulations	13
Predicting reactivity to drug metabolism: beyond P450s—modelling FMOs and UGTs	13
QSAR and molecular docking for the search of AOX inhibitors: a rational drug discovery approach	13
PoseEdit: enhanced ligand binding mode communication by interactive 2D diagrams	12
Simplified, interpretable graph convolutional neural networks for small molecule activity prediction	12
Application of target repositioning and in silico screening to exploit fatty acid binding proteins (FABPs) from Echinococcus multilocularis as possible drug targets	12
Comparing predictive ability of QSAR/QSPR models using 2D and 3D molecular representations	12
Improving small molecule force fields by identifying and characterizing small molecules with inconsistent parameters	12
COSMO-RS predictions of logP in the SAMPL7 blind challenge	11
Extended continuous similarity indices: theory and application for QSAR descriptor selection	11
Energy–entropy method using multiscale cell correlation to calculate binding free energies in the SAMPL8 host–guest challenge	11
CAVIAR: a method for automatic cavity detection, description and decomposition into subcavities	11
Prediction of activity cliffs on the basis of images using convolutional neural networks	11
SAMPL7 protein-ligand challenge: A community-wide evaluation of computational methods against fragment screening and pose-prediction	10
SAMPL7 blind challenge: quantum–mechanical prediction of partition coefficients and acid dissociation constants for small drug-like molecules	10
Evaluation of multi-target deep neural network models for compound potency prediction under increasingly challenging test conditions	10
Prediction of n-octanol/water partition coefficients and acidity constants (pKa) in the SAMPL7 blind challenge with the IEFPCM-MST model	10
SAMPL7: Host–guest binding prediction by molecular dynamics and quantum mechanics	10
Relative free-energy calculations for scaffold hopping-type transformations with an automated RE-EDS sampling procedure	10
Comparison of logP and logD correction models trained with public and proprietary data sets	10
Quantum–mechanical property prediction of solvated drug molecules: what have we learned from a decade of SAMPL blind prediction challenges?	9
A high quality, industrial data set for binding affinity prediction: performance comparison in different early drug discovery scenarios	9
Fine-tuning of a generative neural network for designing multi-target compounds	9
An online repository of solvation thermodynamic and structural maps of SARS-CoV-2 targets	9
Application of the alchemical transfer and potential of mean force methods to the SAMPL8 host-guest blinded challenge	9
Binding free energy predictions in host-guest systems using Autodock4. A retrospective analysis on SAMPL6, SAMPL7 and SAMPL8 challenges	9
Binding site identification of G protein-coupled receptors through a 3D Zernike polynomials-based method: application to C. elegans olfactory receptors	9
Binding thermodynamics and interaction patterns of human purine nucleoside phosphorylase-inhibitor complexes from extensive free energy calculations	9
Flexi-pharma: a molecule-ranking strategy for virtual screening using pharmacophores from ligand-free conformational ensembles	8
Distinct binding of cetirizine enantiomers to human serum albumin and the human histamine receptor H1	8
Explicit solvation thermodynamics in ionic solution: extending grid inhomogeneous solvation theory to solvation free energy of salt–water mixtures	8
Covalent docking in CDOCKER	8
Covalent inhibitor reactivity prediction by the electrophilicity index—in and out of scope	8
Addressing free fatty acid receptor 1 (FFAR1) activation using supervised molecular dynamics	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