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 2021-04-01 to 2025-04-01.)

Article	Citations
Computational workflow for discovering small molecular binders for shallow binding sites by integrating molecular dynamics simulation, pharmacophore modeling, and machine learning: STAT3 as case study	112
From closed to open: three dynamic states of membrane-bound cytochrome P450 3A4	58
Molecular docking, dynamics simulations, and in vivo studies of gallic acid in adenine-induced chronic kidney disease: targeting KIM-1 and NGAL	51
Discovery of novel IDO1 inhibitors via structure-based virtual screening and biological assays	42
On the NS-DSSB unidirectional estimates in the SAMPL6 SAMPLing challenge	38
Computational peptide discovery with a genetic programming approach	34
GPCRLigNet: rapid screening for GPCR active ligands using machine learning	22
Promoter recognition specificity of Corynebacterium glutamicum stress response sigma factors σD and σH deciphered using computer modeling and point mutagenesis	21
Energy-entropy prediction of octanol–water logP of SAMPL7 N-acyl sulfonamide bioisosters	20
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	17
On the relevance of query definition in the performance of 3D ligand-based virtual screening	17
Elucidating the potential effects of point mutations on FGFR3 inhibitor resistance via combined molecular dynamics simulation and community network analysis	17
Investigating the role of glycans in Omicron sub-lineages XBB.1.5 and XBB.1.16 binding to host receptor using molecular dynamics and binding free energy calculations	16
Extended continuous similarity indices: theory and application for QSAR descriptor selection	16
SpaceGrow: efficient shape-based virtual screening of billion-sized combinatorial fragment spaces	16
Artificial intelligence for prediction of biological activities and generation of molecular hits using stereochemical information	15
Explicit solvation thermodynamics in ionic solution: extending grid inhomogeneous solvation theory to solvation free energy of salt–water mixtures	14
Computational Identification and Illustrative Standard for Representation of Unimolecular G-Quadruplex Secondary Structures (CIIS-GQ)	14
Benchmarking ANI potentials as a rescoring function and screening FDA drugs for SARS-CoV-2 Mpro	14
Progress on open chemoinformatic tools for expanding and exploring the chemical space	13
Computational investigation of functional water molecules in GPCRs bound to G protein or arrestin	13
MolGraph: a Python package for the implementation of molecular graphs and graph neural networks with TensorFlow and Keras	13
Application of the alchemical transfer and potential of mean force methods to the SAMPL8 host-guest blinded challenge	13
Correlation of protein binding pocket properties with hits’ chemistries used in generation of ultra-large virtual libraries	13
Evaluation of log P, pKa, and log D predictions from the SAMPL7 blind challenge	12

Multitask machine learning models for predicting lipophilicity (logP) in the SAMPL7 challenge	12
Reliable gas-phase tautomer equilibria of drug-like molecule scaffolds and the issue of continuum solvation	11
Evaluation of interactions between the hepatitis C virus NS3/4A and sulfonamidobenzamide based molecules using molecular docking, molecular dynamics simulations and binding free energy calculations	11
Ligand binding: evaluating the contribution of the water molecules network using the Fragment Molecular Orbital method	11
OFraMP: a fragment-based tool to facilitate the parametrization of large molecules	11
Using diverse potentials and scoring functions for the development of improved machine-learned models for protein–ligand affinity and docking pose prediction	10
Enhancing sampling of water rehydration upon ligand binding using variants of grand canonical Monte Carlo	10
Comparing classification models—a practical tutorial	10
Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host–guest binding: I. Standard procedure	10
Molecular and thermodynamic insights into interfacial interactions between collagen and cellulose investigated by molecular dynamics simulation and umbrella sampling	10
Des3PI: a fragment-based approach to design cyclic peptides targeting protein–protein interactions	9
Molecular mechanism of thiamine pyrophosphate import into mitochondria: a molecular simulation study	9
DeepCubist: Molecular Generator for Designing Peptidomimetics based on Complex three-dimensional scaffolds	9
A combined ligand and target-based virtual screening strategy to repurpose drugs as putrescine uptake inhibitors with trypanocidal activity	9
Molecule auto-correction to facilitate molecular design	9
ChemFlow_py: a flexible toolkit for docking and rescoring	8
RestraintMaker: a graph-based approach to select distance restraints in free-energy calculations with dual topology	8
A replica exchange umbrella sampling (REUS) approach to predict host–guest binding free energies in SAMPL8 challenge	8
Structure-based virtual screening workflow to identify antivirals targeting HIV-1 capsid	8
Predicting octanol/water partition coefficients using molecular simulation for the SAMPL7 challenge: comparing the use of neat and water saturated 1-octanol	8
Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host–guest binding: II. regression and dielectric constant	8
Affinity prediction using deep learning based on SMILES input for D3R grand challenge 4	8
SAMPL7 blind challenge: quantum–mechanical prediction of partition coefficients and acid dissociation constants for small drug-like molecules	8
TeM-DTBA: time-efficient drug target binding affinity prediction using multiple modalities with Lasso feature selection	7
Encoding mu-opioid receptor biased agonism with interaction fingerprints	7
Reactivities of acrylamide warheads toward cysteine targets: a QM/ML approach to covalent inhibitor design	7
Role of water coordination at zinc binding site and its catalytic pathway of dizinc creatininase: insights from quantum cluster approach	7
PoseEdit: enhanced ligand binding mode communication by interactive 2D diagrams	7
Predicting octanol/water partition coefficients and pKa for the SAMPL7 challenge using the SM12, SM8 and SMD solvation models	7
QM assisted ML for 19F NMR chemical shift prediction	7