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Design and Immunological Evaluation of a Hybrid Peptide as a Potent TLR2 Agonist by Structure-Based Virtual Screening

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Computational Evaluation of Phytocompounds From Selective Medicinal Plants as Potential Antidiabetic Agents

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CH−π interactions confer orientational flexibility in protein–carbohydrate binding sites

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Incorporation of the TIP4P water model into a continuum solvent for computing solvation free energy

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Incorporating the excluded solvent volume and surface charges for computing solvation free energy

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Insights into the interaction mechanisms of estrogen-related receptor alpha (ERRα) with ligands via molecular dynamics simulations

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Cumulative Submillisecond All-Atom Simulations of the Temperature-Induced Coil-to-Globule Transition of Poly(N-vinylcaprolactam) in Aqueous Solution

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Discovery of novel inhibitors of CDK2 using docking and physics‐based binding free energy calculation

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Potential effects of metal ion induced two-state allostery on the regulatory mechanism of add adenine riboswitch

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Alanine substitution in cellobiohydrolase provides new insights into substrate threading

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Ligand‐Driven Conformational Dynamics Influences Selectivity of UbiX

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Insights into the synergistic mechanism of target resistance: A case study of N. lugens RDL-GABA receptors and fipronil

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Mammalian-like steroidogenesis in plants gives rise to endocrine-mimetic cardenolides

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Strategy using three layers of surface charge for computing solvation free energy of ions

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Inhibitory mechanism of peptides with a repeating hydrophobic and hydrophilic residue pattern on interleukin-10

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Computer-assisted identification of novel small molecule inhibitors targeting GLUT1

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Venetoclax analogs as promising anticancer therapeutics via targeting Bcl-2 protein: in-silico drug discovery study

Almansour, N. M., Allemailem, K. S., Aty, A. A. A. E., Boussoufa, D., Ismail, E. I. F., & Ibrahim, M. A. A. (2023) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2023.2180668 · Cited by 6

Revealing the intricate mechanism governing the pH-dependent activity of a quintessential representative of flavoproteins, glucose oxidase

Tu, T., Zhang, Y., Yan, Y., Li, L., Liu, X., Hakulinen, N., Zhang, W., Mu, Y., Luo, H., Yao, B., et al. (2024) · Fundamental Research · doi:10.1016/j.fmre.2024.04.009 · Cited by 6

Discovery of novel PRMT1 inhibitors: a combined approach using AI classification model and traditional virtual screening

Zhang, J., Ren, Y., Teng, Y., Wu, H., Xue, J., Chen, L., Song, X., Li, Y., Zhou, Y., Pang, Z., et al. (2025) · Frontiers in Chemistry · doi:10.3389/fchem.2025.1548812 · Cited by 6

In silicoscreening of small molecule modulators and their binding studies against human sirtuin-6 protein

Jos, S., Aouti, S., Unni, S., Haridass, V., Gogoi, H., Deshmukh, P. H., Padmanabhan, B., & Padavattan, S. (2021) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2021.1938229 · Cited by 6

Ligands‐induced open‐close conformational change during DapE catalysis: Insights from molecular dynamics simulations

Muduli, S., & Mishra, S. (2023) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.26466 · Cited by 6

An in silico approach to develop potential therapies against Middle East Respiratory Syndrome Coronavirus (MERS-CoV)

Biswas, S., Mita, M. A., Afrose, S., Hasan, M. R., Shimu, M. S. S., Zaman, S., & Saleh, M. A. (2024) · Heliyon · doi:10.1016/j.heliyon.2024.e25837 · Cited by 6

GraphEGFR : Multi‐task and transfer learning based on molecular graph attention mechanism and fingerprints improving inhibitor bioactivity prediction for EGFR family proteins on data scarcity

Boonyarit, B., Yamprasert, N., Kaewnuratchadasorn, P., Kinchagawat, J., Prommin, C., Rungrotmongkol, T., & Nutanong, S. Y. (2024) · Journal of Computational Chemistry · doi:10.1002/jcc.27388 · Cited by 8

Repurposing of drug candidates against Epstein–Barr virus: Virtual screening, docking computations, molecular dynamics, and quantum mechanical study

Ibrahim, M. A. A., Hassan, A. M. A., Mohamed, E. A. R., Mekhemer, G. A. H., Sidhom, P. A., El‐Tayeb, M. A., Khan, S., Shoeib, T., Soliman, M. E. S., & Abdelrahman, A. H. M. (2024) · PLoS ONE · doi:10.1371/journal.pone.0312100 · Cited by 6

Gallic Acid: A Potent Metabolite Targeting Shikimate Kinase in Acinetobacter baumannii

Alturki, M. S., Khzem, A. H. A., Gomaa, M. S., Tawfeeq, N., Alhamadah, M. H., Alshehri, F. M., Alzahrani, R. R., Alghamdi, H., Rants’o, T. A., Ayil, K. A. G., et al. (2024) · Metabolites · doi:10.3390/metabo14120727 · Cited by 6

Potential P-glycoprotein (P-gp) inhibitors from SuperDRUG2 database toward reversing multidrug resistance in cancer treatment: Database mining, molecular dynamics, and binding energy estimations

Abdeljawaad, K. A. A., Abdelrahman, A. H. M., Sidhom, P. A., Tallima, H., Shoeib, T., Mekhemer, G. A. H., Sayed, S. R. M., El‐Tayeb, M. A., Hegazy, M. F., & Ibrahim, M. A. A. (2025) · Journal of Molecular Graphics and Modelling · doi:10.1016/j.jmgm.2025.108997 · Cited by 6

Binding free energy calculations of adenosine deaminase inhibitors

Coi, A., Tonelli, M., Ganadu, M. L., & Bianucci, A. M. (2006) · Bioorganic & Medicinal Chemistry · doi:10.1016/j.bmc.2005.11.047 · Cited by 6

Molecular modeling of the inhibition of protein–protein interactions with small molecules: The IL2–IL2Rα case

Pieraccini, S., Gonda, R. D., & Sironi, M. (2011) · Chemical Physics Letters · doi:10.1016/j.cplett.2011.10.044 · Cited by 6

Design, synthesis and biological evaluation of bisabolangelone oxime derivatives as potassium-competitive acid blockers (P-CABs)

Huang, N., Wang, W.-B., Chen, L., Luo, H., Wang, J., Deng, W., & Zou, K. (2016) · Bioorganic & Medicinal Chemistry Letters · doi:10.1016/j.bmcl.2016.03.051 · Cited by 6

VP40 of the Ebola Virus as a Target for EboV Therapy: Comprehensive Conformational and Inhibitor Binding Landscape from Accelerated Molecular Dynamics

Balmith, M., & Soliman, M. E. S. (2017) · Cell Biochemistry and Biophysics · doi:10.1007/s12013-017-0783-8 · Cited by 6

Comparative Modeling and Evaluation of Leukotriene B4 Receptors for Selective Drug Discovery Towards the Treatment of Inflammatory Diseases

Ibrahim, M. A. A., & Hassan, A. M. A. (2018) · The Protein Journal · doi:10.1007/s10930-018-9797-3 · Cited by 6

Computational Evaluation of Selectivity of Inhibition of Muscarinic Receptors M1-M4

Mikurova, A. V., Skvortsov, V. S., & Raevsky, O. A. (2018) · Biomedical Chemistry Research and Methods · doi:10.18097/bmcrm00072 · Cited by 6

Molecular mechanisms of inhibitor bindings to A-FABP deciphered by using molecular dynamics simulations and calculations of MM-GBSA

Yin, Y., Zhao, J., Zhang, L. L., Xu, X., & Liu, J.-E. (2021) · SAR and QSAR in environmental research · doi:10.1080/1062936x.2021.1891966 · Cited by 5

Theoretical investigations on the effects of mutations in important residues of NS1B on its RNA-binding using molecular dynamics simulations

Xu, D., & Zheng, Q. (2022) · Computers in Biology and Medicine · doi:10.1016/j.compbiomed.2022.105412 · Cited by 6

Computational investigation on the role of C-Terminal of human albumin on the dimerization of Aβ1-42 peptide

(2020) · Biointerface Research in Applied Chemistry · doi:10.33263/briac101.944955 · Cited by 6

Molecular Dynamics Simulation of the Antigen–Antibody Complex Formation Process between Hen Egg-White Lysozyme and HyHEL-10

Takamatsu, Y., Hamakubo, T., & Yamashita, T. (2022) · Bulletin of the Chemical Society of Japan · doi:10.1246/bcsj.20220239 · Cited by 6

In silico Mutagenesis and Modeling of Decoy Peptides Targeting CIB1 to Obscure its Role in Triple-negative Breast Cancer Progression

Shahab, M., Liang, C., Duan, X., Wadood, A., Junaid, M., Almuqri, E. A., & Zheng, G. (2023) · Current Pharmaceutical Design · doi:10.2174/1381612829666230327162852 · Cited by 6

Tuning the Solvation Term in the MM-PBSA/GBSA Binding Affinity Predictions

Maffucci, I. (2015) · BENTHAM SCIENCE PUBLISHERS eBooks · Cited by 1

Assessment of Computational Methods for Ligand Binding

Mikulskis, P. (2015) · Lund University Publications (Lund University)

The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities

Genheden, S., & Ryde, U. (2015) · Expert Opinion on Drug Discovery · doi:10.1517/17460441.2015.1032936 · Cited by 5,769

Case-specific performance of MM-PBSA, MM-GBSA, and SIE in virtual screening

Virtanen, S. I., Niinivehmas, S. P., & Pentikäinen, O. T. (2015) · Journal of Molecular Graphics and Modelling · doi:10.1016/j.jmgm.2015.10.012 · Cited by 68

MM-GB(PB)SA Calculations of Protein-Ligand Binding Free Energies

Hayes, J., & Archontis, G. (2012) · InTech eBooks · doi:10.5772/37107 · Cited by 142