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 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
Elucidating the potential effects of point mutations on FGFR3 inhibitor resistance via combined molecular dynamics simulation and community network analysis	17
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
SpaceGrow: efficient shape-based virtual screening of billion-sized combinatorial fragment spaces	16
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
Artificial intelligence for prediction of biological activities and generation of molecular hits using stereochemical information	15
Benchmarking ANI potentials as a rescoring function and screening FDA drugs for SARS-CoV-2 Mpro	14
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Evolution of Support Vector Machine and Regression Modeling in Chemoinformatics and Drug Discovery	6
pH-dependent solubility prediction for optimized drug absorption and compound uptake by plants	6
Consensus scoring evaluated using the GPCR-Bench dataset: Reconsidering the role of MM/GBSA	6
Crystal polymorphism and spectroscopical properties of sulfonamides in solid state by means of First Principles calculations	6
Automated high throughput pKa and distribution coefficient measurements of pharmaceutical compounds for the SAMPL8 blind prediction challenge	6
Molecular dynamics simulations reveal the inhibition mechanism of Cdc42 by RhoGDI1	6
De novo drug design as GPT language modeling: large chemistry models with supervised and reinforcement learning	6
Insight into the mechanism of molecular recognition between human Integrin-Linked Kinase and Cpd22 and its implication at atomic level	6
In silico exploration of natural xanthone derivatives as potential inhibitors of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replication and cellular entry	6
Obtaining QM/MM binding free energies in the SAMPL8 drugs of abuse challenge: indirect approaches	6
Conformational energies of reference organic molecules: benchmarking of common efficient computational methods against coupled cluster theory	6
Stacking Gaussian processes to improve $$pK_a$$ predictions in the SAMPL7 challenge	6
A deep neural network: mechanistic hybrid model to predict pharmacokinetics in rat	6
Elucidating allosteric signal disruption in PBP2a: impact of N146K/E150K mutations on ceftaroline resistance in methicillin-resistant Staphylococcus aureus	6
Study of SQ109 analogs binding to mycobacterium MmpL3 transporter using MD simulations and alchemical relative binding free energy calculations	6
Computational investigation to identify multi-targeted anti-hyperglycemic potential of substituted 2-Mercaptobenzimidazole derivatives and synthesis of new α-glucosidase inhibitors	6
Fine tuning for success in structure-based virtual screening	6
A high quality, industrial data set for binding affinity prediction: performance comparison in different early drug discovery scenarios	6
Comparison of logP and logD correction models trained with public and proprietary data sets	6
Prot2Prot: a deep learning model for rapid, photorealistic macromolecular visualization	5

The in silico identification of novel broad-spectrum antidotes for poisoning by organophosphate anticholinesterases	5
Precise force-field-based calculations of octanol-water partition coefficients for the SAMPL7 molecules	5
Examining unsupervised ensemble learning using spectroscopy data of organic compounds	5
RDPSOVina: the random drift particle swarm optimization for protein–ligand docking	5
Identifying and characterising promising small molecule inhibitors of kinesin spindle protein using ligand-based virtual screening, molecular docking, molecular dynamics and MM‑GBSA calculations	5
Design of new imidazole derivatives with anti-HCMV activity: QSAR modeling, synthesis and biological testing	5
COSMO-RS blind prediction of distribution coefficients and aqueous pKa values from the SAMPL8 challenge	5
Integrated data-driven and experimental approaches to accelerate lead optimization targeting SARS-CoV-2 main protease	5
Inhibition mechanism of MRTX1133 on KRASG12D: a molecular dynamics simulation and Markov state model study	5
Identification of HPr kinase/phosphorylase inhibitors: novel antimicrobials against resistant Enterococcus faecalis	5
In silico identification and in vitro antiviral validation of potential inhibitors against Chikungunya virus	4
Binding affinity prediction for binary drug–target interactions using semi-supervised transfer learning	4
From UK-2A to florylpicoxamid: Active learning to identify a mimic of a macrocyclic natural product	4
Energy–entropy method using multiscale cell correlation to calculate binding free energies in the SAMPL8 host–guest challenge	4
Discovering promising drug candidates for Parkinson’s disease: integrating miRNA and DEG analysis with molecular dynamics and MMPBSA	4
Faster and more diverse de novo molecular optimization with double-loop reinforcement learning using augmented SMILES	4
Molecular dynamics simulations as a guide for modulating small molecule aggregation	4
Deciphering the molecular choreography of Janus kinase 2 inhibition via Gaussian accelerated molecular dynamics simulations: a dynamic odyssey	4
Understanding the relationship between preferential interactions of peptides in water-acetonitrile mixtures with protein-solvent contact surface area	4
TargIDe: a machine-learning workflow for target identification of molecules with antibiofilm activity against Pseudomonas aeruginosa	4
FitScore: a fast machine learning-based score for 3D virtual screening enrichment	4
The power of a mentor	4
Prediction of n-octanol/water partition coefficients and acidity constants (pKa) in the SAMPL7 blind challenge with the IEFPCM-MST model	4
Molecular dynamics study on micelle-small molecule interactions: developing a strategy for an extensive comparison	4
FastGrow: on-the-fly growing and its application to DYRK1A	4
Improved prediction and characterization of blood-brain barrier penetrating peptides using estimated propensity scores of dipeptides	3
Identification of a druggable site on GRP78 at the GRP78-SARS-CoV-2 interface and virtual screening of compounds to disrupt that interface	3
Binding site identification of G protein-coupled receptors through a 3D Zernike polynomials-based method: application to C. elegans olfactory receptors	3
SAMPL7 physical property prediction from EC-RISM theory	3
Data-informed reparameterization of modified RNA and the effect of explicit water models: application to pseudouridine and derivatives	3
Correction to: Conformational energies of reference organic molecules: benchmarking of common efficient computational methods against coupled cluster theory	3
Correction to: Assessing the performance of docking, FEP, and MM/GBSA methods on a series of KLK6 inhibitors	3
Predicting partition coefficients for the SAMPL7 physical property challenge using the ClassicalGSG method	3
Multi-targeted benzylpiperidine–isatin hybrids: Design, synthesis, biological and in silico evaluation as monoamine oxidases and acetylcholinesterase inhibitors for neurodegenerative disease therapies	3
Exploring the interaction mechanism between antagonist and the jasmonate receptor complex by molecular dynamics simulation	3
Hampering the early aggregation of PrP-E200K protein by charge-based inhibitors: a computational study	3
Exploring DrugCentral: from molecular structures to clinical effects	3
Unveiling the G4-PAMAM capacity to bind and protect Ang-(1-7) bioactive peptide by molecular dynamics simulations	3
Galileo: Three-dimensional searching in large combinatorial fragment spaces on the example of pharmacophores	3
From oncoproteins to spike proteins: the evaluation of intramolecular stability using hydropathic force field	3
Insight on the mechanism of hexameric Pseudin-4 against bacterial membrane-mimetic environment	3