MMPBSA.py: An Efficient Program for End-State Free Energy Calculations

Combined molecular mechanical and continuum solvent approach (MM-PBSA/GBSA) to predict ligand binding

Massova, I., & Kollman, P. A. (2000) · Perspectives in Drug Discovery and Design · doi:10.1023/a:1008763014207 · Cited by 1,015

Isolation of SARS-CoV-2-related coronavirus from Malayan pangolins

Xiao, K., Zhai, J., Feng, Y., Zhou, N., Zhang, X., Zou, J.-J., Li, N., Guo, Y., Li, X., Shen, X., et al. (2020) · Nature · doi:10.1038/s41586-020-2313-x · Cited by 728

Molecular basis for redox control by the human cystine/glutamate antiporter system xc−

Parker, J. L., Deme, J. C., Kolokouris, D., Kuteyi, G., Biggin, P. C., Lea, S. M., & Newstead, S. (2021) · Nature Communications · doi:10.1038/s41467-021-27414-1 · Cited by 272

Predicting Relative Protein Affinity of Novel Per- and Polyfluoroalkyl Substances (PFASs) by An Efficient Molecular Dynamics Approach

Cheng, W., & Ng, C. A. (2018) · Environmental Science & Technology · doi:10.1021/acs.est.8b01268 · Cited by 141

Real-time dynamic single-molecule protein sequencing on an integrated semiconductor device

(2022) · doi:10.1126/science.abo7651 · Cited by 134

Characterization of the binding of MRTX1133 as an avenue for the discovery of potential KRASG12D inhibitors for cancer therapy

Issahaku, A. R., Mukelabai, N., Agoni, C., Rudrapal, M., Aldosari, S. M., Almalki, S. G., & Khan, J. (2022) · Scientific Reports · doi:10.1038/s41598-022-22668-1 · Cited by 93

Different positron emission tomography tau tracers bind to multiple binding sites on the tau fibril: insight from computational modeling

Murugan, N. A., Nordberg, A., & Ågren, H. (2018) · ACS Chemical Neuroscience · doi:10.1021/acschemneuro.8b00093 · Cited by 92

Structural basis for the ligand-dependent activation of heterodimeric AHR-ARNT complex

Diao, X., Shang, Q., Guo, M., Huang, Y., Zhang, M., Chen, X., Liang, Y., Sun, X., Zhou, F., Zhuang, J., et al. (2025) · Nature communications · doi:10.1038/s41467-025-56574-7 · Cited by 72

In Silico Modeling and Scoring of PROTAC-Mediated Ternary Complex Poses

Liao, J., Nie, X., Unarta, I. C., Ericksen, S. S., & Tang, W. (2022) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.1c02155 · Cited by 62

BiPPred: Combined sequence‐ and structure‐based prediction of peptide binding to the Hsp70 chaperone BiP

Schneider, M., Rosam, M., Glaser, M., Patronov, A., Shah, H., Back, K. C., Daake, M. A., Buchner, J., & Antes, I. (2016) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.25084 · Cited by 51

Insights from incorporating quantum computing into drug design workflows

Lau, B., Emani, P. S., Chapman, J., Yao, L., Lam, T., Merrill, P., Warrell, J., Gerstein, M. B., & Lam, H. Y. K. (2023) · Bioinformatics · doi:10.1093/bioinformatics/btac789 · Cited by 54

Identification of oleoylethanolamide as an endogenous ligand for HIF-3α

Diao, X., Ye, F., Zhang, M., Ren, X., Tian, X., Lu, J., Sun, X., Hou, Z., Chen, X., Li, F., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-30338-z · Cited by 51

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

Cheng, W., Doering, J. A., LaLone, C., & Ng, C. (2021) · Toxicological Sciences · doi:10.1093/toxsci/kfab004 · Cited by 49

Deciphering Dimerization Modes of PAS Domains: Computational and Experimental Analyses of the AhR:ARNT Complex Reveal New Insights Into the Mechanisms of AhR Transformation

Corrada, D., Soshilov, A. A., Denison, M. S., & Bonati, L. (2016) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1004981 · Cited by 43

Molecular insights into human phosphatidylserine synthase 1 reveal its inhibition promotes LDL uptake

Long, T., Li, D., Vale, G., Jiang, Y., Schmiege, P., Yang, Z. J., McDonald, J. G., & Li, X. (2024) · Cell · doi:10.1016/j.cell.2024.08.004 · Cited by 31

Domino-like effect of C112R mutation on ApoE4 aggregation and its reduction by Alzheimer’s Disease drug candidate

Nemergut, M., Marques, S. M., Uhrik, L., Vanova, T., Nezvedova, M., Gadara, D. C., Jha, D., Tulis, J., Novakova, V., Planas-Iglesias, J., et al. (2023) · Molecular Neurodegeneration · doi:10.1186/s13024-023-00620-9 · Cited by 30

Free energy perturbation calculations of mutation effects on SARS-CoV-2 RBD::ACE2 binding affinity

Sergeeva, A. P., Katsamba, P. S., Liao, J., Sampson, J. M., Bahna, F., Mannepalli, S., Morano, N. C., Shapiro, L., Friesner, R. A., & Honig, B. (2023) · Journal of Molecular Biology · doi:10.1016/j.jmb.2023.168187 · Cited by 27

Allosterically Coupled Multisite Binding of Testosterone to Human Serum Albumin

Jayaraj, A., Schwanz, H. A., Spencer, D. J., Bhasin, S., Hamilton, J. A., Jayaram, B., Goldman, A. L., Krishna, M., Krishnan, M., Shah, A., et al. (2021) · Endocrinology · doi:10.1210/endocr/bqaa199 · Cited by 28

Computational DNA binding studies of (–)-epigallocatechin-3-gallate

Galindo-Murillo, R., & Cheatham, T. E. (2018) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2017.1389306 · Cited by 27

Structural modeling of the AhR:ARNT complex in the bHLH–PASA–PASB region elucidates the key determinants of dimerization

Corrada, D., Denison, M. S., & Bonati, L. (2017) · Molecular BioSystems · doi:10.1039/c7mb00005g · Cited by 24

Exploring alternate states and oligomerization preferences of coiled‐coils by de novo structure modeling

Rämisch, S., Lizatović, R., & André, I. (2015) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.24729 · Cited by 24

Harnessing artificial intelligence to identify Bufalin as a molecular glue degrader of estrogen receptor alpha

Jiang, S., Liu, K., Jiang, T., Li, H., Wei, X., Wan, X., Zhong, C., Gong, R., Chen, Z., Zou, C., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-62288-7 · Cited by 23

Computational analysis of antimicrobial peptides targeting key receptors in infection-related cardiovascular diseases: molecular docking and dynamics insights

Dermawan, D., & Alotaiq, N. (2025) · Scientific Reports · doi:10.1038/s41598-025-93683-1 · Cited by 19

Deep Conservation of Histone Variants in Thermococcales Archaea

Stevens, K. M., Hocher, A., & Warnecke, T. (2022) · Genome Biology and Evolution · doi:10.1093/gbe/evab274 · Cited by 13

CycleDesigner: Leveraging CycRFdiffusion and HighFold to Design Cyclic Peptide Binders for Specific Targets

Zhang, C., Xu, Z., Lin, K., Zhu, N., Zhang, C., Xu, W., Guo, J., Su, A., Li, C., & Duan, H. (2025) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.5c00227 · 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

Structural insight into the binding interactions of NTPs and nucleotide analogues to RNA dependent RNA polymerase of SARS-CoV-2

Koulgi, S., Jani, V., V N, M. U., Sonavane, U., & Joshi, R. (2022) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2021.1894985 · Cited by 12

HighPlay: Cyclic Peptide Sequence Design Based on Reinforcement Learning and Protein Structure Prediction

Lin, H., Zhu, C., Shang, T., Zhu, N., Lin, K., Zhang, C., Shao, X., Wang, X., & Duan, H. (2025) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.5c00896 · Cited by 10

Nuclear Receptor Interdomain Communication is Mediated by the Hinge with Ligand Specificity

Hazarika, S., Yu, T., Biswas, A., Dube, N., Villalona, P., & Okafor, C. D. (2024) · Journal of Molecular Biology · doi:10.1016/j.jmb.2024.168805 · Cited by 7

Unveiling the Catalytic Mechanism and Conformational Dynamics of Guinea Pig l -Asparaginase Type 1 for Leukemia Drug Design

Andjelkovic, M., Zinovjev, K., Ruiz-Pernía, J. J., & Tuñón, I. (2025) · ACS Catalysis · doi:10.1021/acscatal.4c07791 · Cited by 7

Hidden GPCR structural transitions addressed by multiple walker supervised molecular dynamics (mwSuMD)

Deganutti, G., Pipito, L., Rujan, R. M., Weizmann, T., Griffin, P., Ciancetta, A., Moro, S., & Reynolds, C. A. (2025) · eLife · doi:10.7554/elife.96513 · Cited by 7

Allosteric activation of the SPRTN protease by ubiquitin maintains genome stability

Dürauer, S., Kang, H.-S., Wiebeler, C., Machida, Y., Schnapka, D. S., Yaneva, D., Renz, C., Götz, M. J., Weickert, P., Major, A. C., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-61224-z · Cited by 6

Molecular insights into the role of Estrogen Receptor Beta in Ecdysterone Mediated Anabolic Activity

Tariq, S. S., Sardar, M., Shafiq, M., Heinz, H., Nur-e-Alam, M., Ahmed, A., & Ul-Haq, Z. (2025) · PLoS One · doi:10.1371/journal.pone.0320865 · Cited by 4

Rational design of monomeric IL37 variants guided by stability and dynamical analyses of IL37 dimers

Sardag, I., Duvenci, Z. S., Belkaya, S., & Timucin, E. (2024) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2024.04.037 · Cited by 4

BEGAN: Boltzmann-Reweighted Data Augmentation for Enhanced GAN-Based Molecule Design in Insect Pheromone Receptors

Dai, J., Zhang, Y., Shi, C., Liu, Y., Xiu, P., & Wang, Y. (2024) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.4c06729 · Cited by 3

AP2/ERF Transcription Factor Orthologs of the Desert Tree Prosopis cineraria Show Higher Copy Number and DNA-Binding Affinity than Drought-Sensitive Species

(2024) · doi:10.1007/s00344-024-11532-3 · Cited by 3

A Citrate Synthase Splice Variant Rewires the TCA Cycle to Promote Colorectal Cancer Progression

Cheung, J. C. T., Ng, L. W., Zhu, Z., Chen, B., Li, S., Xu, M., Ding, X., Pu, D., Hu, Y., Ren, Y., et al. (2025) · Cancer Research · doi:10.1158/0008-5472.can-24-2355 · Cited by 3

Mechanistic basis for the opposing effects of H2A and H2B ubiquitination on nucleosome stability and dynamics

Baweja, L., & Wereszczynski, J. (2025) · Epigenetics & Chromatin · doi:10.1186/s13072-025-00635-0 · Cited by 3

The Oncogenic EGFR–SHC1 Fusion Confers Insensitivity to EGFR-TKIs via Dual Activation of N-EGFR Kinase Domain and C-SHC1 Phosphorylation Sites in Lung Cancer

Zheng, J., Zhao, S., Zhan, J., Zhuang, W., Chen, M., Jiang, W., Huang, Y., He, J., Hu, L., Pang, L., et al. (2026) · Cancer Discovery · doi:10.1158/2159-8290.cd-25-1936 · Cited by 2

The flexible stalk domain of sTREM2 modulates its interactions with brain-based phospholipids

(2025) · doi:10.7554/elife.102269.3 · Cited by 2

Multiscale computational analysis reveals enhanced allosteric modulation of Nav1.5 by dual binding of dapagliflozin and ertugliflozin

Chattopadhyay, A., Fatehi, M., Mosa, F. E. S., Gruber, B., Light, P. E., & Barakat, K. (2025) · Scientific Reports · doi:10.1038/s41598-025-30298-6 · Cited by 2

The small molecule ML233 is a direct inhibitor of tyrosinase function

Menard, R., Baanannou, A., Halluin, C., Morse, D., Kuhn, S., Graber, J. H., Strickland, J., & Madelaine, R. (2025) · Communications Biology · doi:10.1038/s42003-025-07973-5 · Cited by 2

De novo protein–ligand design including protein flexibility and conformational adaptation

Agamia, J., & Zacharias, M. (2026) · Bioinformatics · doi:10.1093/bioinformatics/btag027 · Cited by 2

Exploring the Conformational Dynamics of RNA Dependent RNA Polymerase of SARS-CoV-2 in the Presence of Various Nucleotide Analogues

Koulgi, S., Jani, V., Uppuladinne V N, M., Sonavane, U., & Joshi, R. (2020) · doi:10.26434/chemrxiv.12886856