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 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
Comparing predictive ability of QSAR/QSPR models using 2D and 3D molecular representations	14
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
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
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
Prediction of n-octanol/water partition coefficients and acidity constants (pKa) in the SAMPL7 blind challenge with the IEFPCM-MST model	12
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
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
Imputation of sensory properties using deep learning	8
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
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
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
Structure-based virtual screening workflow to identify antivirals targeting HIV-1 capsid	6
In silico identification of noncompetitive inhibitors targeting an uncharacterized allosteric site of falcipain-2	6
Computational insights into ligand–induced G protein and β-arrestin signaling of the dopamine D1 receptor	6
Druggable hot spots in trypanothione reductase: novel insights and opportunities for drug discovery revealed by DRUGpy	6
Identification of novel EED-EZH2 PPI inhibitors using an in silico fragment mapping method	6
Modeling receptor flexibility in the structure-based design of KRASG12C inhibitors	6
IRC-Fuse: improved and robust prediction of redox-sensitive cysteine by fusing of multiple feature representations	6
Exploring the interaction mechanism between antagonist and the jasmonate receptor complex by molecular dynamics simulation	6
Predicting octanol/water partition coefficients using molecular simulation for the SAMPL7 challenge: comparing the use of neat and water saturated 1-octanol	6
Multiple linear regression models for predicting the n‑octanol/water partition coefficients in the SAMPL7 blind challenge	6
Ligand-based and structure-based studies to develop predictive models for SARS-CoV-2 main protease inhibitors through the 3d-qsar.com portal	6
Best practices for repurposing studies	6
Molecular and thermodynamic insights into interfacial interactions between collagen and cellulose investigated by molecular dynamics simulation and umbrella sampling	6
Deciphering the conformational transitions of LIMK2 active and inactive states to ponder specific druggable states through microsecond scale molecular dynamics simulation	5
Binding affinity prediction for binary drug–target interactions using semi-supervised transfer learning	5

Reliable gas-phase tautomer equilibria of drug-like molecule scaffolds and the issue of continuum solvation	5
Crystal polymorphism and spectroscopical properties of sulfonamides in solid state by means of First Principles calculations	5
On the NS-DSSB unidirectional estimates in the SAMPL6 SAMPLing challenge	5
Improvement of multi-task learning by data enrichment: application for drug discovery	5
The FMO2 analysis of the ligand-receptor binding energy: the Biscarbene-Gold(I)/DNA G-Quadruplex case study	5
SAMPL7 physical property prediction from EC-RISM theory	5
TargIDe: a machine-learning workflow for target identification of molecules with antibiofilm activity against Pseudomonas aeruginosa	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
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
MM/GBSA prediction of relative binding affinities of carbonic anhydrase inhibitors: effect of atomic charges and comparison with Autodock4Zn	5
Adapting the DeepSARM approach for dual-target ligand design	5
Faster and more diverse de novo molecular optimization with double-loop reinforcement learning using augmented SMILES	5
Predicting octanol/water partition coefficients and pKa for the SAMPL7 challenge using the SM12, SM8 and SMD solvation models	5
Des3PI: a fragment-based approach to design cyclic peptides targeting protein–protein interactions	5
A replica exchange umbrella sampling (REUS) approach to predict host–guest binding free energies in SAMPL8 challenge	5
Exploiting activity cliffs for building pharmacophore models and comparison with other pharmacophore generation methods: sphingosine kinase 1 as case study	5
Target identification for repurposed drugs active against SARS-CoV-2 via high-throughput inverse docking	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
From oncoproteins to spike proteins: the evaluation of intramolecular stability using hydropathic force field	4
Predicting partition coefficients for the SAMPL7 physical property challenge using the ClassicalGSG method	4
Discovery of novel IDO1 inhibitors via structure-based virtual screening and biological assays	4
Protocol for iterative optimization of modified peptides bound to protein targets	4
Peptide nucleic acid Hoogsteen strand linker design for major groove recognition of DNA thymine bases	4
Data-informed reparameterization of modified RNA and the effect of explicit water models: application to pseudouridine and derivatives	4
A deep neural network: mechanistic hybrid model to predict pharmacokinetics in rat	4
Computational investigation of functional water molecules in GPCRs bound to G protein or arrestin	4
The role of zinc finger linkers in zinc finger protein binding to DNA	4
Complex peptide macrocycle optimization: combining NMR restraints with conformational analysis to guide structure-based and ligand-based design	4
Identification of potential inhibitors of Mycobacterium tuberculosis shikimate kinase: molecular docking, in silico toxicity and in vitro experiments	4
Hampering the early aggregation of PrP-E200K protein by charge-based inhibitors: a computational study	4
OFraMP: a fragment-based tool to facilitate the parametrization of large molecules	4
GPCRLigNet: rapid screening for GPCR active ligands using machine learning	4
In silico identification and in vitro antiviral validation of potential inhibitors against Chikungunya virus	3
RDPSOVina: the random drift particle swarm optimization for protein–ligand docking	3
Fine tuning for success in structure-based virtual screening	3
Conformational energies of reference organic molecules: benchmarking of common efficient computational methods against coupled cluster theory	3
Contact networks in RNA: a structural bioinformatics study with a new tool	3
Unveiling the G4-PAMAM capacity to bind and protect Ang-(1-7) bioactive peptide by molecular dynamics simulations	3
Study of SQ109 analogs binding to mycobacterium MmpL3 transporter using MD simulations and alchemical relative binding free energy calculations	3
Identification of HPr kinase/phosphorylase inhibitors: novel antimicrobials against resistant Enterococcus faecalis	3
Using diverse potentials and scoring functions for the development of improved machine-learned models for protein–ligand affinity and docking pose prediction	3
Energy-entropy prediction of octanol–water logP of SAMPL7 N-acyl sulfonamide bioisosters	3
Structural mechanism of Fab domain dissociation as a measure of interface stability	3
Molecular dynamics simulations as a guide for modulating small molecule aggregation	3
Insight into the mechanism of molecular recognition between human Integrin-Linked Kinase and Cpd22 and its implication at atomic level	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
Enabling data-limited chemical bioactivity predictions through deep neural network transfer learning	3