AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading

Particle swarm optimization

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A new optimizer using particle swarm theory

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Further development and validation of empirical scoring functions for structure-based binding affinity prediction

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Discovery of High-Affinity Noncovalent Allosteric KRAS Inhibitors That Disrupt Effector Binding

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De Novo Molecule Design Through the Molecular Generative Model Conditioned by 3D Information of Protein Binding Sites

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Perfluoroalkyl Substances (PFASs) Are Substrates of the Renal Human Organic Anion Transporter 4 (OAT4)

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Artificial intelligence for drug discovery and development in Alzheimer's disease

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Simultaneous Targeting of NPC1 and VDAC1 by Itraconazole Leads to Synergistic Inhibition of mTOR Signaling and Angiogenesis

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Heme and hemoglobin utilization by Mycobacterium tuberculosis

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Uni-Mol: A Universal 3D Molecular Representation Learning Framework

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Comparison of structure- and ligand-based scoring functions for deep generative models: a GPCR case study

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Identification of the nicotinamide salvage pathway as a new toxification route for antimetabolites

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BACE1 molecular docking and anti-Alzheimer’s disease activities of ginsenosides

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Probing the interaction of Rivastigmine Tartrate, an important Alzheimer’s drug, with serum albumin: Attempting treatment of Alzheimer’s disease

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Hybrid Multifunctional Modulators Inhibit Multifaceted Aβ Toxicity and Prevent Mitochondrial Damage

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Artificial Intelligence Technologies for COVID-19 De Novo Drug Design

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Explainable Deep Relational Networks for Predicting Compound-Protein Affinities and Contacts

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Cross-docking study on InhA inhibitors: a combination of Autodock Vina and PM6-DH2 simulations to retrieve bio-active conformations

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In-vitro molecular docking analysis of microalgae extracted phycocyanin as an anti-diabetic candidate

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Directed Evolution of Flavin-Dependent Halogenases for Site- and Atroposelective Halogenation of 3-Aryl-4(3 H )-Quinazolinones via Kinetic or Dynamic Kinetic Resolution

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Identification of Compounds for Butyrylcholinesterase Inhibition

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Chitosan-based magnetic adsorbent for removal of water-soluble anionic dye: Artificial neural network modeling and molecular docking insights

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Identification of FDA approved drugs and nucleoside analogues as potential SARS-CoV-2 A1pp domain inhibitor: An in silico study

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In-Vitro and In-Silico Assessment of Per- and Polyfluoroalkyl Substances (PFAS) in Aqueous Film-Forming Foam (AFFF) Binding to Human Serum Albumin

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Insights from incorporating quantum computing into drug design workflows

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Phytochemicals present in Indian ginseng possess potential to inhibit SARS-CoV-2 virulence: A molecular docking and MD simulation study

Kushwaha, P. P., Singh, A. K., Prajapati, K. S., Shuaib, M., Gupta, S., & Kumar, S. (2021) · Microbial Pathogenesis · doi:10.1016/j.micpath.2021.104954 · Cited by 53

The CDK12 inhibitor SR-4835 functions as a molecular glue that promotes cyclin K degradation in melanoma

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Evolutionary origin of the mitochondrial cholesterol transport machinery reveals a universal mechanism of steroid hormone biosynthesis in animals

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Editor’s Highlight: Microbial-Derived 1,4-Dihydroxy-2-naphthoic Acid and Related Compounds as Aryl Hydrocarbon Receptor Agonists/Antagonists: Structure–Activity Relationships and Receptor Modeling

Cheng, Y., Jin, U.-H., Davidson, L. A., Chapkin, R. S., Jayaraman, A., Tamamis, P., Orr, A., Allred, C., Denison, M. S., Soshilov, A., et al. (2017) · Toxicological Sciences · doi:10.1093/toxsci/kfw230 · Cited by 48

Integrative Computational Approaches to Inform Relative Bioaccumulation Potential of Per- and Polyfluoroalkyl Substances Across Species

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On-the-fly QM/MM docking with attracting cavities.

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Characterization and effects of binding of food-derived bioactive phycocyanobilin to bovine serum albumin

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Predicting Potential SARS-COV-2 Drugs—In Depth Drug Database Screening Using Deep Neural Network Framework SSnet, Classical Virtual Screening and Docking

Karki, N., Verma, N., Trozzi, F., Tao, P., Kraka, E., & Zoltowski, B. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22041573 · Cited by 43

Guanosine monophosphate reductase 1 is a potential therapeutic target for Alzheimer’s disease

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A new paradigm for applying deep learning to protein–ligand interaction prediction

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Are HFPO-TA and HFPO-DA safe substitutes for PFOA? A comprehensive toxicity study using zebrafish (Danio rerio) embryos and adults

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Identification of binding sites contributing to volatile anesthetic effects on GABA type A receptors

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The Interaction of Antipsychotic Drugs with Lipids and Subsequent Lipid Reorganization Investigated Using Biophysical Methods

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Systematic characterization of multi-omics landscape between gut microbial metabolites and GPCRome in Alzheimer’s disease

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FINDSITEcomb2.0: A New Approach for Virtual Ligand Screening of Proteins and Virtual Target Screening of Biomolecules

Zhou, H., Cao, H., & Skolnick, J. (2018) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.8b00309 · Cited by 39

Reactivity of Diphenylpropynone Derivatives Toward Metal-Associated Amyloid-β Species

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Protein representations: Encoding biological information for machine learning in biocatalysis

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Digested protein from chia seed (Salvia hispanica L.) prevents obesity and associated inflammation of adipose tissue in mice fed a high-fat diet

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Ranking power of the SQM/COSMO scoring function on carbonic anhydrase II-inhibitor complexes.

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A Novel N-Methyltransferase in Arabidopsis Appears to Feed a Conserved Pathway for Nicotinate Detoxification among Land Plants and Is Associated with Lignin Biosynthesis

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FRAGSITE: A Fragment-Based Approach for Virtual Ligand Screening

Zhou, H., Cao, H., & Skolnick, J. (2021) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.0c01160 · Cited by 32

Assessment of Antibiofilm Potencies of Nervonic and Oleic Acid against Acinetobacter baumannii Using In Vitro and Computational Approaches

Khadke, S. K., Lee, J.-H., Kim, Y.-G., Raj, V., & Lee, J. (2021) · Biomedicines · doi:10.3390/biomedicines9091133 · Cited by 33

Inhibition of ergosterol synthesis in Candida albicans by novel eugenol tosylate congeners targeting sterol 14α-demethylase (CYP51) enzyme

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Decoding the Foodome: Molecular Networks Connecting Diet and Health

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Inhibitory Effect of Berberine on Broiler P-glycoprotein Expression and Function: In Situ and In Vitro Studies

Zhang, Y., Guo, L., Huang, J., Sun, Y., He, F., Zloh, M., & Wang, L. (2019) · International Journal of Molecular Sciences · doi:10.3390/ijms20081966 · Cited by 30

Tuning Reactivity of Diphenylpropynone Derivatives with Metal-Associated Amyloid-β Species via Structural Modifications

Liu, Y., Kochi, A., Pithadia, A. S., Lee, S., Nam, Y., Beck, M. W., He, X., Lee, D., & Lim, M. H. (2013) · Inorganic Chemistry · doi:10.1021/ic400851w · Cited by 30

Antioxidant activity of the main phenolics found in red fruits: An in vitro and in silico study

Gonçalves, A. C., Falcão, A., Alves, G., Silva, L. R., & Flores-Félix, J. D. (2024) · Food Chemistry · doi:10.1016/j.foodchem.2024.139459 · Cited by 28

Ketamine Metabolite (2 R,6 R)-Hydroxynorketamine Interacts with μ and κ Opioid Receptors

Joseph, T. T., Bu, W., Lin, W., Zoubak, L., Yeliseev, A., Liu, R., Eckenhoff, R. G., & Brannigan, G. (2021) · ACS Chemical Neuroscience · doi:10.1021/acschemneuro.0c00741 · Cited by 28

Allosteric potentiation of a ligand-gated ion channel is mediated by access to a deep membrane-facing cavity

Heusser, S. A., Lycksell, M., Wang, X., McComas, S. E., Howard, R. J., & Lindahl, E. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1809650115 · Cited by 23

An allosteric propofol-binding site in kinesin disrupts kinesin-mediated processive movement on microtubules

Woll, K. A., Guzik-Lendrum, S., Bensel, B. M., Bhanu, N. V., Dailey, W. P., Garcia, B. A., Gilbert, S. P., & Eckenhoff, R. G. (2018) · Journal of Biological Chemistry · doi:10.1074/jbc.ra118.002182 · Cited by 23

Involvement of the GABAA receptor α subunit in the mode of action of etifoxine

Mattei, C., Taly, A., Soualah, Z., Saulais, O., Henrion, D., Guérineau, N. C., Verleye, M., & Legros, C. (2019) · Pharmacological Research · doi:10.1016/j.phrs.2019.04.034 · Cited by 26

Design, synthesis, and in vitro and in vivo characterization of new memantine analogs for Alzheimer’s disease

Turcu, A. L., Companys-Alemany, J., Phillips, M. B., Patel, D. S., Griñán-Ferré, C., Loza, M. I., Brea, J. M., Pérez, B., Soto, D., Sureda, F. X., et al. (2022) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2022.114354 · Cited by 27

Functions of Essential Genes and a Scale-Free Protein Interaction Network Revealed by Structure-Based Function and Interaction Prediction for a Minimal Genome

Zhang, C., Zheng, W., Cheng, M., Omenn, G. S., Freddolino, P. L., & Zhang, Y. (2021) · Journal of Proteome Research · doi:10.1021/acs.jproteome.0c00359 · Cited by 27

Retro Drug Design: From Target Properties to Molecular Structures

Wang, Y., Michael, S., Yang, S.-M., Huang, R., Cruz-Gutierrez, K., Zhang, Y., Zhao, J., Xia, M., Shinn, P., & Sun, H. (2022) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.2c00123 · Cited by 24

Synthetic bovine lactoferrin peptide Lfampin kills Entamoeba histolytica trophozoites by necrosis and resolves amoebic intracecal infection in mice

Díaz-Godínez, C., González-Galindo, X., Meza-Menchaca, T., Bobes, R. J., de la Garza, M., León-Sicairos, N., Laclette, J. P., & Carrero, J. C. (2019) · Bioscience Reports · doi:10.1042/bsr20180850 · Cited by 23

Production and Purification of Novel Hypocholesterolemic Peptides from Lactic Fermented Spirulina platensis through High Hydrostatic Pressure-Assisted Protease Hydrolysis

Chen, G.-W., & Yang, M.-H. (2021) · Catalysts · doi:10.3390/catal11080873 · Cited by 23

Evaluating generalization in protein–ligand cofolding methods

Škrinjar, P., Eberhardt, J., Studer, G., Tauriello, G., Schwede, T., & Durairaj, J. (2026) · Nature Structural & Molecular Biology · doi:10.1038/s41594-026-01797-5 · Cited by 22

Investigating Potential GLP-1 Receptor Agonists in Cyclopeptides from Pseudostellaria heterophylla, Linum usitatissimum, and Drymaria diandra, and Peptides Derived from Heterophyllin B for the Treatment of Type 2 Diabetes: An In Silico Study

Liao, H.-J., & Tzen, J. T. C. (2022) · Metabolites · doi:10.3390/metabo12060549 · Cited by 21

Docking simulations suggest that all-trans retinoic acid could bind to retinoid X receptors

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Structural Re-arrangement and Peroxidase Activation of Cytochrome c by Anionic Analogues of Vitamin E, Tocopherol Succinate and Tocopherol Phosphate

Yanamala, N., Kapralov, A. A., Djukic, M., Peterson, J., Mao, G., Klein-Seetharaman, J., Stoyanovsky, D. A., Stursa, J., Neuzil, J., & Kagan, V. E. (2014) · Journal of Biological Chemistry · doi:10.1074/jbc.m114.601377 · Cited by 19

Aromatic Residues in the Substrate Cleft of RPE65 Protein Govern Retinol Isomerization and Modulate Its Progression

Chander, P., Gentleman, S., Poliakov, E., & Redmond, T. M. (2012) · Journal of Biological Chemistry · doi:10.1074/jbc.m112.364596 · Cited by 19

Cyclophilin A Inhibition: Targeting Transition-State-Bound Enzyme Conformations for Structure-Based Drug Design

Nagaraju, M., McGowan, L. C., & Hamelberg, D. (2013) · Journal of Chemical Information and Modeling · doi:10.1021/ci300432w · Cited by 18

Cryo-EM structure of the Rous sarcoma virus octameric cleaved synaptic complex intasome

Pandey, K. K., Bera, S., Shi, K., Rau, M. J., Oleru, A. V., Fitzpatrick, J. A. J., Engelman, A. N., Aihara, H., & Grandgenett, D. P. (2021) · Communications Biology · doi:10.1038/s42003-021-01855-2 · Cited by 14

Diosmetin attenuates oxidative stress-induced damage to lens epithelial cells via the mitogen-activated protein kinase (MAPK) pathway

Guo, G., & Dong, J. (2022) · Bioengineered · doi:10.1080/21655979.2022.2068755 · Cited by 17

Ecdysterone prevents negative effect of acute immobilization stress on energy metabolism of rat liver mitochondria

Baev, A. Y., Charishnikova, O. S., Khasanov, F. A., Nebesnaya, K. S., Makhmudov, A. R., Rakhmedova, M. T., Khushbaktova, Z. A., Syrov, V. N., & Levitskaya, Y. V. (2022) · The Journal of Steroid Biochemistry and Molecular Biology · doi:10.1016/j.jsbmb.2022.106066 · Cited by 16

Combined Physics- and Machine-Learning-Based Method to Identify Druggable Binding Sites Using SILCS-Hotspots

Nordquist, E. B., Zhao, M., Kumar, A., & MacKerell, A. D. (2024) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.4c01189 · Cited by 15

Aminoalcoholate-driven tetracopper(II) cores as dual acetyl and butyrylcholinesterase inhibitors: Experimental and theoretical elucidation of mechanism of action

Bondžić, A. M., Senćanski, M. V., Vujačić Nikezić, A. V., Kirillova, M. V., André, V., Kirillov, A. M., & Bondžić, B. P. (2020) · Journal of Inorganic Biochemistry · doi:10.1016/j.jinorgbio.2019.110990 · Cited by 14

Protein-inhibitor interaction studies using NMR

Ishima, R. (2015) · Applications of NMR Spectroscopy · doi:10.2174/9781608059621115010007 · Cited by 13

Structural insights into pink-eyed dilution protein (Oca2)

Mesdaghi, S., Murphy, D. L., Simpkin, A. J., & Rigden, D. J. (2023) · Bioscience Reports · doi:10.1042/bsr20230060 · Cited by 13

A Putative Binding Model of Nitazene Derivatives at the μ-Opioid Receptor

Clayton, J., Shi, L., Robertson, M. J., Skiniotis, G., Michaelides, M., Stavitskaya, L., & Shen, J. (2025) · Neuropharmacology · doi:10.1016/j.neuropharm.2025.110437 · Cited by 12

Specificity and mechanism of TonB-dependent ferric catecholate uptake by Fiu

Yang, T., Zou, Y., Ng, H. L., Kumar, A., Newton, S. M., & Klebba, P. E. (2024) · Frontiers in Microbiology · doi:10.3389/fmicb.2024.1355253 · Cited by 11

TextGrad: Automatic "Differentiation" via Text

Yuksekgonul, M., Bianchi, F., Boen, J., Liu, S., Huang, Z., Guestrin, C., & Zou, J. (2024) · arXiv · doi:10.48550/arxiv.2406.07496 · Cited by 12

Fisetin as a Blueprint for Senotherapeutic Agents – Elucidating Geroprotective and Senolytic Properties with Molecular Modeling

Spiegel, M. (2025) · Chemistry – A European Journal · doi:10.1002/chem.202403755 · Cited by 12

Phytoecdysteroids and Anabolic Effect of Atriplex dimorphostegia: UPLC-PDA-MS/MS Profiling, In Silico and In Vivo Models

Zaghloul, E., Handousa, H., Singab, A. N. B., Elmazar, M. M., Ayoub, I. M., & Swilam, N. (2023) · Plants · doi:10.3390/plants12010206 · Cited by 11

Assessing the binding properties of CASP14 targets and models

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Recognition of galactose by a scaffold protein recruits a transcriptional activator for the GAL regulon induction in Candida albicans

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