The HDOCK server for integrated protein–protein docking

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302

The Amber biomolecular simulation programs

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The I-TASSER Suite: protein structure and function prediction

Yang, J., Yan, R., Roy, A., Xu, D., Poisson, J., & Zhang, Y. (2015) · Nature Methods · doi:10.1038/nmeth.3213 · Cited by 5,596

HADDOCK: A Protein−Protein Docking Approach Based on Biochemical or Biophysical Information

Dominguez, C., Boelens, R., & Bonvin, A. M. J. J. (2003) · Journal of the American Chemical Society · doi:10.1021/ja026939x · Cited by 3,187

Comparative Protein Structure Modeling of Genes and Genomes

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HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment

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How significant is a protein structure similarity with TM-score = 0.5?

Xu, J., & Zhang, Y. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq066 · Cited by 1,142

CAPRI: A Critical Assessment of PRedicted Interactions

Janin, J., Henrick, K., Moult, J., Eyck, L. T., Sternberg, M. J. E., Vajda, S., Vakser, I., & Wodak, S. J. (2003) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.10381 · Cited by 703

Sequence co-evolution gives 3D contacts and structures of protein complexes

Hopf, T. A., Schärfe, C. P. I., Rodrigues, J. P. G. L. M., Green, A. G., Kohlbacher, O., Sander, C., Bonvin, A. M. J. J., & Marks, D. S. (2014) · eLife · doi:10.7554/elife.03430 · Cited by 515

NGL viewer: web-based molecular graphics for large complexes

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Enhancing alphafold-multimer-based protein complex structure prediction with MULTICOM in CASP15

Liu, J., Guo, Z., Wu, T., Roy, R. S., Quadir, F., Chen, C., & Cheng, J. (2023) · Communications Biology · doi:10.1038/s42003-023-05525-3 · Cited by 86

SARS-CoV-2 Variants Show a Gradual Declining Pathogenicity and Pro-Inflammatory Cytokine Stimulation, an Increasing Antigenic and Anti-Inflammatory Cytokine Induction, and Rising Structural Protein Instability: A Minimal Number Genome-Based Approach

Barh, D., Tiwari, S., Rodrigues Gomes, L. G., Ramalho Pinto, C. H., Andrade, B. S., Ahmad, S., Aljabali, A. A. A., Alzahrani, K. J., Banjer, H. J., Hassan, S. S., et al. (2023) · Inflammation · doi:10.1007/s10753-022-01734-w · Cited by 50

Improved Antibody‐Specific Epitope Prediction Using AlphaFold and AbAdapt**

(2022) · doi:10.1002/cbic.202200303 · Cited by 36

An in-silico study of the mutation-associated effects on the spike protein of SARS-CoV-2, Omicron variant

(2022) · doi:10.1371/journal.pone.0266844 · Cited by 28

Arf GTPase activates the WAVE regulatory complex through a distinct binding site

Yang, S., Tang, Y., Liu, Y., Brown, A. J., Schaks, M., Ding, B., Kramer, D. A., Mietkowska, M., Ding, L., Alekhina, O., et al. (2022) · Science Advances · doi:10.1126/sciadv.add1412 · Cited by 24

Non-Canonical TERT Activity Initiates Osteogenesis in Calcific Aortic Valve Disease

Cuevas, R. A., Hortells, L., Chu, C. C., Wong, R., Crane, A., Boufford, C. K., Regan, C., Moorhead, W. J., Bashline, M. J., Parwal, A., et al. (2025) · Circulation Research · doi:10.1161/circresaha.122.321889 · Cited by 11

AF3Score: A Score-Only Adaptation of AlphaFold3 for Biomolecular Structure Evaluation

Liu, Y., Yu, Q., Wang, D., & Chen, M. (2025) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.5c00653 · Cited by 9

Insights into electron transfer and bifurcation of the Synechocystis sp. PCC6803 hydrogenase reductase module

(2024) · doi:10.1016/j.bbabio.2024.149508 · Cited by 8

Borrelia burgdorferi PlzA is a cyclic‐di‐GMP dependent DNA and RNA binding protein

Jusufovic, N., Krusenstjerna, A. C., Savage, C. R., Saylor, T. C., Brissette, C. A., Zückert, W. R., Schlax, P. J., Motaleb, M. A., & Stevenson, B. (2024) · Molecular Microbiology · doi:10.1111/mmi.15254 · Cited by 7

Targeting Dysregulated Ion Channels in Liver Tumors with Venom Peptides

Achimba, F., Faezov, B., Cohen, B., Dunbrack, R., & Holford, M. (2024) · Molecular Cancer Therapeutics · doi:10.1158/1535-7163.mct-23-0256 · Cited by 6

Sampling and Ranking of Protein Conformations Using Machine Learning Techniques Do Not Improve the Quality of Rigid Protein–Protein Docking

Stratiichuk, R., Kyrylenko, R., Koleiev, I., Savchenko, I., Voitsitskyi, T., Husak, V., Yesylevskyy, S., Starosyla, S., & Nafiiev, A. (2025) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.5c01765 · Cited by 6

Inhibition of SARS-CoV-2 3CL protease by the anti-viral chimeric protein RetroMAD1

Chan, L.-C., Mat Yassim, A. S., Ahmad Fuaad, A. A. H., Leow, T. C., Sabri, S., Radin Yahaya, R. S., & Abu Bakar, A. M. S. (2023) · Scientific Reports · doi:10.1038/s41598-023-47511-z · Cited by 5

An in-silico study of the mutation-associated effects on the spike protein of SARS-CoV-2, Omicron variant

Shishir, T. A., Jannat, T., & Naser, I. B. (2022) · doi:10.1101/2022.02.21.481269 · Cited by 5

Pan-cancer analyses suggest kindlin-associated global mechanochemical alterations

Chowdhury, D., Mistry, A., Maity, D., Bhatia, R., Priyadarshi, S., Wadan, S., Chakraborty, S., & Haldar, S. (2024) · Communications Biology · doi:10.1038/s42003-024-06044-5 · Cited by 5

Improved antibody-specific epitope prediction using AlphaFold and AbAdapt

Xu, Z., Davila, A., Wiamowski, J., Teraguchi, S., & Standley, D. M. (2022) · doi:10.1101/2022.05.21.492907 · Cited by 4

DeepAssembly2: A Web Server for Protein Complex Structure Assembly Based on Domain-Domain Interactions

Xia, Y., Pu, Y., Wang, S., Zhuang, J., Liu, D., Hou, M., & Zhang, G. (2025) · Journal of Molecular Biology · doi:10.1016/j.jmb.2025.169128 · Cited by 2

YAP1 and QSER1 are key modulators of embryonic signaling pathways in the mammalian epiblast

Abraham, E., Roule, T., Douglas, A., Megill, E., Pericak, O. M., Howe, J. E., Choya-Foces, C., Garbincius, J. F., Cohen, H. M., Roig-Flórez, P., et al. (2026) · EMBO Reports · doi:10.1038/s44319-026-00746-z · Cited by 1

Accurate protein-protein interactions modeling through physics-informed geometric invariant learning

(2026) · doi:10.1038/s42003-026-09809-2 · Cited by 1

Integrated multiomics analysis identifies potential biomarkers and therapeutic targets for autophagy associated AKI to CKD transition

Wang, Y., & Li, Q. (2025) · Scientific Reports · doi:10.1038/s41598-025-97269-9 · Cited by 1

Narrow funnel-like interaction energy distribution is an indicator of specific protein interaction partner

Choi, J. (2023) · iScience · doi:10.1016/j.isci.2023.106911 · Cited by 1

Inactive β1-integrin acts as a junctional scaffold for angiopoietin/TIE2/FOXO1 signaling

Sipilä, T., Ponna, S. K., Venkatesha Murthy, A., Pink, A., Enkavi, G., Bohra, S. K., Lewna, K., Ganesh, K., Liu, Q., Korhonen, M., et al. (2026) · Journal of Clinical Investigation · doi:10.1172/jci190552