OOIR: Observatory of International Research

Papers

(The TQCC of Journal of Computer-Aided Molecular Design is 6. 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 2021-02-01 to 2025-02-01.)

Article	Citations
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	93
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	52
Elucidating the potential effects of point mutations on FGFR3 inhibitor resistance via combined molecular dynamics simulation and community network analysis	48
Artificial intelligence for prediction of biological activities and generation of molecular hits using stereochemical information	37
Binding thermodynamics and interaction patterns of human purine nucleoside phosphorylase-inhibitor complexes from extensive free energy calculations	31
GPCRLigNet: rapid screening for GPCR active ligands using machine learning	27
Application of the alchemical transfer and potential of mean force methods to the SAMPL8 host-guest blinded challenge	18
On the NS-DSSB unidirectional estimates in the SAMPL6 SAMPLing challenge	16
Multitask machine learning models for predicting lipophilicity (logP) in the SAMPL7 challenge	15
Explicit solvation thermodynamics in ionic solution: extending grid inhomogeneous solvation theory to solvation free energy of salt–water mixtures	15
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	14
Computational investigation of functional water molecules in GPCRs bound to G protein or arrestin	14
Discovery of novel IDO1 inhibitors via structure-based virtual screening and biological assays	14
Progress on open chemoinformatic tools for expanding and exploring the chemical space	13
Energy-entropy prediction of octanol–water logP of SAMPL7 N-acyl sulfonamide bioisosters	13
Extended continuous similarity indices: theory and application for QSAR descriptor selection	13
OFraMP: a fragment-based tool to facilitate the parametrization of large molecules	13
Evaluation of log P, pKa, and log D predictions from the SAMPL7 blind challenge	13
SpaceGrow: efficient shape-based virtual screening of billion-sized combinatorial fragment spaces	12
Computational peptide discovery with a genetic programming approach	12
On the relevance of query definition in the performance of 3D ligand-based virtual screening	11
Computational Identification and Illustrative Standard for Representation of Unimolecular G-Quadruplex Secondary Structures (CIIS-GQ)	11
Benchmarking ANI potentials as a rescoring function and screening FDA drugs for SARS-CoV-2 Mpro	11
Correlation of protein binding pocket properties with hits’ chemistries used in generation of ultra-large virtual libraries	11
A replica exchange umbrella sampling (REUS) approach to predict host–guest binding free energies in SAMPL8 challenge	10

Promoter recognition specificity of Corynebacterium glutamicum stress response sigma factors σD and σH deciphered using computer modeling and point mutagenesis	10
MolGraph: a Python package for the implementation of molecular graphs and graph neural networks with TensorFlow and Keras	10
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	10
Structure-based virtual screening workflow to identify antivirals targeting HIV-1 capsid	9
Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host–guest binding: II. regression and dielectric constant	9
Affinity prediction using deep learning based on SMILES input for D3R grand challenge 4	9
Encoding mu-opioid receptor biased agonism with interaction fingerprints	9
Obtaining QM/MM binding free energies in the SAMPL8 drugs of abuse challenge: indirect approaches	8
Identification of novel EED-EZH2 PPI inhibitors using an in silico fragment mapping method	8
Using diverse potentials and scoring functions for the development of improved machine-learned models for protein–ligand affinity and docking pose prediction	8
Molecular mechanism of thiamine pyrophosphate import into mitochondria: a molecular simulation study	8
Consensus scoring evaluated using the GPCR-Bench dataset: Reconsidering the role of MM/GBSA	8
Predicting octanol/water partition coefficients using molecular simulation for the SAMPL7 challenge: comparing the use of neat and water saturated 1-octanol	8
Enhancing sampling of water rehydration upon ligand binding using variants of grand canonical Monte Carlo	8
Molecular dynamics simulations reveal the inhibition mechanism of Cdc42 by RhoGDI1	8
RestraintMaker: a graph-based approach to select distance restraints in free-energy calculations with dual topology	7
Structure-based identification of inhibitors disrupting the CD2–CD58 interactions	7
SAMPL7 blind challenge: quantum–mechanical prediction of partition coefficients and acid dissociation constants for small drug-like molecules	7
Des3PI: a fragment-based approach to design cyclic peptides targeting protein–protein interactions	7
Editorial special issue on “Quantum Mechanics in Industry”	7
Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host–guest binding: I. Standard procedure	7
PoseEdit: enhanced ligand binding mode communication by interactive 2D diagrams	6
Role of water coordination at zinc binding site and its catalytic pathway of dizinc creatininase: insights from quantum cluster approach	6
Reliable gas-phase tautomer equilibria of drug-like molecule scaffolds and the issue of continuum solvation	6
Crystal polymorphism and spectroscopical properties of sulfonamides in solid state by means of First Principles calculations	6
A combined ligand and target-based virtual screening strategy to repurpose drugs as putrescine uptake inhibitors with trypanocidal activity	6
Stacking Gaussian processes to improve $$pK_a$$ predictions in the SAMPL7 challenge	6
DeepCubist: Molecular Generator for Designing Peptidomimetics based on Complex three-dimensional scaffolds	6
Ligand binding: evaluating the contribution of the water molecules network using the Fragment Molecular Orbital method	6
Comparing classification models—a practical tutorial	6
Fine tuning for success in structure-based virtual screening	6
ChemFlow_py: a flexible toolkit for docking and rescoring	6
Comparison of logP and logD correction models trained with public and proprietary data sets	6
A high quality, industrial data set for binding affinity prediction: performance comparison in different early drug discovery scenarios	6