OOIR: Observatory of International Research

Papers

(The median citation count of Journal of Computer-Aided Molecular Design is 4. 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 2020-03-01 to 2024-03-01.)

Article	Citations
Interpretation of machine learning models using shapley values: application to compound potency and multi-target activity predictions	240
Artificial intelligence in chemistry and drug design	76
Meta-iPVP: a sequence-based meta-predictor for improving the prediction of phage virion proteins using effective feature representation	49
TargetCPP: accurate prediction of cell-penetrating peptides from optimized multi-scale features using gradient boost decision tree	43
SAMPL7 Host–Guest Challenge Overview: assessing the reliability of polarizable and non-polarizable methods for binding free energy calculations	43
Evaluation of log P, pKa, and log D predictions from the SAMPL7 blind challenge	40
Evolution of Support Vector Machine and Regression Modeling in Chemoinformatics and Drug Discovery	39
Supervised molecular dynamics for exploring the druggability of the SARS-CoV-2 spike protein	38
Improving virtual screening results with MM/GBSA and MM/PBSA rescoring	35
ProIn-Fuse: improved and robust prediction of proinflammatory peptides by fusing of multiple feature representations	33
Revealing cytotoxic substructures in molecules using deep learning	33
Exploring the inhibitory activity of valproic acid against the HDAC family using an MMGBSA approach	30
Machine learning-accelerated quantum mechanics-based atomistic simulations for industrial applications	29
Mutation-mediated influences on binding of anaplastic lymphoma kinase to crizotinib decoded by multiple replica Gaussian accelerated molecular dynamics	25
SAMPL7 TrimerTrip host–guest binding affinities from extensive alchemical and end-point free energy calculations	25
Progress on open chemoinformatic tools for expanding and exploring the chemical space	25
Towards a converged strategy for including microsolvation in reaction mechanism calculations	23
Overview of the SAMPL6 pKa challenge: evaluating small molecule microscopic and macroscopic pKa predictions	23
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
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	20
SAMPL7 TrimerTrip host–guest binding poses and binding affinities from spherical-coordinates-biased simulations	20
AMOEBA binding free energies for the SAMPL7 TrimerTrip host–guest challenge	20
Predictive potential of eigenvalue-based topological molecular descriptors	19

Advances in exploring activity cliffs	18
Computational exploration and experimental validation to identify a dual inhibitor of cholinesterase and amyloid-beta for the treatment of Alzheimer’s disease	18
Large-scale evaluation of cytochrome P450 2C9 mediated drug interaction potential with machine learning-based consensus modeling	17
An overview of the SAMPL8 host–guest binding challenge	16
SAMPL7 blind predictions using nonequilibrium alchemical approaches	16
ReSCoSS: a flexible quantum chemistry workflow identifying relevant solution conformers of drug-like molecules	15
The critical role of QM/MM X-ray refinement and accurate tautomer/protomer determination in structure-based drug design	15
Characterization of PD-L1 binding sites by a combined FMO/GRID-DRY approach	15
Improving the binding affinity estimations of protein–ligand complexes using machine-learning facilitated force field method	14
Multitask machine learning models for predicting lipophilicity (logP) in the SAMPL7 challenge	13
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
StackHCV: a web-based integrative machine-learning framework for large-scale identification of hepatitis C virus NS5B inhibitors	12
COSMO-RS predictions of logP in the SAMPL7 blind challenge	11
Application of target repositioning and in silico screening to exploit fatty acid binding proteins (FABPs) from Echinococcus multilocularis as possible drug targets	11
Comparing predictive ability of QSAR/QSPR models using 2D and 3D molecular representations	11
QSAR and molecular docking for the search of AOX inhibitors: a rational drug discovery approach	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
Improving small molecule force fields by identifying and characterizing small molecules with inconsistent parameters	11
Evaluation of multi-target deep neural network models for compound potency prediction under increasingly challenging test conditions	10
Energy–entropy method using multiscale cell correlation to calculate binding free energies in the SAMPL8 host–guest challenge	10
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
Prediction of n-octanol/water partition coefficients and acidity constants (pKa) in the SAMPL7 blind challenge with the IEFPCM-MST model	10
Relative free-energy calculations for scaffold hopping-type transformations with an automated RE-EDS sampling procedure	9
Binding thermodynamics and interaction patterns of human purine nucleoside phosphorylase-inhibitor complexes from extensive free energy calculations	9
Computational insights into the molecular mechanisms of differentiated allosteric modulation at the mu opioid receptor by structurally similar bitopic modulators	9
SAMPL7: Host–guest binding prediction by molecular dynamics and quantum mechanics	9
Quantum–mechanical property prediction of solvated drug molecules: what have we learned from a decade of SAMPL blind prediction challenges?	9
Comparison of logP and logD correction models trained with public and proprietary data sets	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
Ligand binding: evaluating the contribution of the water molecules network using the Fragment Molecular Orbital method	8
Addressing free fatty acid receptor 1 (FFAR1) activation using supervised molecular dynamics	8
Fine-tuning of a generative neural network for designing multi-target compounds	8
Design of new imidazole derivatives with anti-HCMV activity: QSAR modeling, synthesis and biological testing	8
Explicit solvation thermodynamics in ionic solution: extending grid inhomogeneous solvation theory to solvation free energy of salt–water mixtures	8
Simplified, interpretable graph convolutional neural networks for small molecule activity prediction	8
Binding free energy predictions in host-guest systems using Autodock4. A retrospective analysis on SAMPL6, SAMPL7 and SAMPL8 challenges	8
Binding site identification of G protein-coupled receptors through a 3D Zernike polynomials-based method: application to C. elegans olfactory receptors	8
Covalent docking in CDOCKER	7
Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host–guest binding: II. regression and dielectric constant	7
DeepCOMO: from structure-activity relationship diagnostics to generative molecular design using the compound optimization monitor methodology	7
Benchmarking the performance of MM/PBSA in virtual screening enrichment using the GPCR-Bench dataset	7
Development and interpretation of a QSAR model for in vitro breast cancer (MCF-7) cytotoxicity of 2-phenylacrylonitriles	7
Covalent inhibitor reactivity prediction by the electrophilicity index—in and out of scope	7
A high quality, industrial data set for binding affinity prediction: performance comparison in different early drug discovery scenarios	7
Application of the alchemical transfer and potential of mean force methods to the SAMPL8 host-guest blinded challenge	7

An online repository of solvation thermodynamic and structural maps of SARS-CoV-2 targets	7
Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host–guest binding: I. Standard procedure	7
Enhancing sampling of water rehydration upon ligand binding using variants of grand canonical Monte Carlo	7
Extended continuous similarity indices: theory and application for QSAR descriptor selection	7
Comparing classification models—a practical tutorial	6
Structure-based virtual screening workflow to identify antivirals targeting HIV-1 capsid	6
The slow but steady rise of binding free energy calculations in drug discovery	6
Multiple linear regression models for predicting the n‑octanol/water partition coefficients in the SAMPL7 blind challenge	6
Testing automatic methods to predict free binding energy of host–guest complexes in SAMPL7 challenge	6
In silico and in vitro anti-AChE activity investigations of constituents from Mytragyna speciosa for Alzheimer’s disease treatment	6
Experimental characterization of the association of β-cyclodextrin and eight novel cyclodextrin derivatives with two guest compounds	6
Predicting PAMPA permeability using the 3D-RISM-KH theory: are we there yet?	6
PoseEdit: enhanced ligand binding mode communication by interactive 2D diagrams	6
Imputation of sensory properties using deep learning	6
Physicochemical QSAR analysis of hERG inhibition revisited: towards a quantitative potency prediction	5
IRC-Fuse: improved and robust prediction of redox-sensitive cysteine by fusing of multiple feature representations	5
Best practices for repurposing studies	5
FastGrow: on-the-fly growing and its application to DYRK1A	5
Role of water coordination at zinc binding site and its catalytic pathway of dizinc creatininase: insights from quantum cluster approach	5
RestraintMaker: a graph-based approach to select distance restraints in free-energy calculations with dual topology	5
Modeling receptor flexibility in the structure-based design of KRASG12C inhibitors	5
SAMPL7 physical property prediction from EC-RISM theory	5
Adapting the DeepSARM approach for dual-target ligand design	5
Precise force-field-based calculations of octanol-water partition coefficients for the SAMPL7 molecules	5
A replica exchange umbrella sampling (REUS) approach to predict host–guest binding free energies in SAMPL8 challenge	5
Des3PI: a fragment-based approach to design cyclic peptides targeting protein–protein interactions	5
In silico identification of noncompetitive inhibitors targeting an uncharacterized allosteric site of falcipain-2	5
Design and tests of prospective property predictions for novel antimalarial 2-aminopropylaminoquinolones	5
Druggable hot spots in trypanothione reductase: novel insights and opportunities for drug discovery revealed by DRUGpy	5
Galileo: Three-dimensional searching in large combinatorial fragment spaces on the example of pharmacophores	5
Automated high throughput pKa and distribution coefficient measurements of pharmaceutical compounds for the SAMPL8 blind prediction challenge	5
Predicting octanol/water partition coefficients using molecular simulation for the SAMPL7 challenge: comparing the use of neat and water saturated 1-octanol	5
High-throughput virtual screening and preclinical analysis identifies CB-1, a novel potent dual B-Raf/c-Raf inhibitor, effective against wild and mutant variants of B-Raf expression in colorectal carc	5
Target identification for repurposed drugs active against SARS-CoV-2 via high-throughput inverse docking	4
A binding mode hypothesis for prothioconazole binding to CYP51 derived from first principles quantum chemistry	4
Combining fragment docking with graph theory to improve ligand docking for homology model structures	4
Outliers in SAR and QSAR: 3. Importance of considering the role of water molecules in protein–ligand interactions and quantitative structure–activity relationship studies	4
The FMO2 analysis of the ligand-receptor binding energy: the Biscarbene-Gold(I)/DNA G-Quadruplex case study	4
Improved prediction and characterization of blood-brain barrier penetrating peptides using estimated propensity scores of dipeptides	4
Identification of novel EED-EZH2 PPI inhibitors using an in silico fragment mapping method	4
On the NS-DSSB unidirectional estimates in the SAMPL6 SAMPLing challenge	4
Multi-task convolutional neural networks for predicting in vitro clearance endpoints from molecular images	4
Peptide nucleic acid Hoogsteen strand linker design for major groove recognition of DNA thymine bases	4
Exploiting activity cliffs for building pharmacophore models and comparison with other pharmacophore generation methods: sphingosine kinase 1 as case study	4
Resveratrol as a nontoxic excipient stabilizes insulin in a bioactive hexameric form	4
Data-informed reparameterization of modified RNA and the effect of explicit water models: application to pseudouridine and derivatives	4
Predicting partition coefficients for the SAMPL7 physical property challenge using the ClassicalGSG method	4
Obtaining QM/MM binding free energies in the SAMPL8 drugs of abuse challenge: indirect approaches	4
A remark on the efficiency of the double-system/single-box nonequilibrium approach in the SAMPL6 SAMPLing challenge	4
Ligand-based and structure-based studies to develop predictive models for SARS-CoV-2 main protease inhibitors through the 3d-qsar.com portal	4
An activity prediction model for steroidal and triterpenoidal inhibitors of Acetylcholinesterase enzyme	4
Exploring the interaction mechanism between antagonist and the jasmonate receptor complex by molecular dynamics simulation	4
Hampering the early aggregation of PrP-E200K protein by charge-based inhibitors: a computational study	4
Predicting octanol/water partition coefficients and pKa for the SAMPL7 challenge using the SM12, SM8 and SMD solvation models	4
Novel phosphatidylinositol 4-kinases III beta (PI4KIIIβ) inhibitors discovered by virtual screening using free energy models	4