Comparative Protein Structure Modeling Using Modeller

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

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PROCHECK: a program to check the stereochemical quality of protein structures

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A general method applicable to the search for similarities in the amino acid sequence of two proteins

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ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins

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AQUA and PROCHECK-NMR: Programs for checking the quality of protein structures solved by NMR

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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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A new approach to protein fold recognition

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Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction

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Comparison of systematic search and database methods for constructing segments of protein structure

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Pre-fusion structure of a human coronavirus spike protein

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Zc3h12a is an RNase essential for controlling immune responses by regulating mRNA decay

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SARS-CoV-2 Disrupts Splicing, Translation, and Protein Trafficking to Suppress Host Defenses

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The cohesin ring concatenates sister DNA molecules

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A practical guide to large-scale docking

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The Molecular Basis of CRL4DDB2/CSA Ubiquitin Ligase Architecture, Targeting, and Activation

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Expanding functional protein sequence spaces using generative adversarial networks

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Structure of the membrane domain of respiratory complex I

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Identifying Recent Adaptations in Large-Scale Genomic Data

Grossman, S. R., Andersen, K. G., Shlyakhter, I., Tabrizi, S., Winnicki, S., Yen, A., Park, D. J., Griesemer, D., Karlsson, E. K., Wong, S. H., et al. (2013) · Cell · doi:10.1016/j.cell.2013.01.035 · Cited by 368

Structure of hepcidin-bound ferroportin reveals iron homeostatic mechanisms

Billesbølle, C. B., Azumaya, C. M., Kretsch, R. C., Powers, A. S., Gonen, S., Schneider, S., Arvedson, T., Dror, R. O., Cheng, Y., & Manglik, A. (2020) · Nature · doi:10.1038/s41586-020-2668-z · Cited by 344

SARM1 is a metabolic sensor activated by an increased NMN/NAD+ ratio to trigger axon degeneration

Figley, M. D., Gu, W., Nanson, J. D., Shi, Y., Sasaki, Y., Cunnea, K., Malde, A. K., Jia, X., Luo, Z., Saikot, F. K., et al. (2021) · Neuron · doi:10.1016/j.neuron.2021.02.009 · Cited by 324

Allosteric ligands for the pharmacologically dark receptors GPR68 and GPR65

Huang, X.-P., Karpiak, J., Kroeze, W. K., Zhu, H., Chen, X., Moy, S. S., Saddoris, K. A., Nikolova, V. D., Farrell, M. S., Wang, S., et al. (2015) · Nature · doi:10.1038/nature15699 · Cited by 284

In-cell architecture of an actively transcribing-translating expressome

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Interaction with Suv39H1 is critical for Snail-mediated E-cadherin repression in breast cancer

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Integrating diverse data for structure determination of macromolecular assemblies

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The SARS-CoV-2 Spike variant D614G favors an open conformational state

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Deep learning extends de novo protein modelling coverage of genomes using iteratively predicted structural constraints

Greener, J. G., Kandathil, S. M., & Jones, D. T. (2019) · Nature Communications · doi:10.1038/s41467-019-11994-0 · Cited by 178

YY1 haploinsufficiency causes an intellectual disability syndrome featuring transcriptional and chromatin dysfunction

Gabriele, M., Vulto-van Silfhout, A. T., Germain, P.-L., Vitriolo, A., Kumar, R., Douglas, E., Haan, E., Kosaki, K., Takenouchi, T., Rauch, A., et al. (2017) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2017.05.006 · Cited by 163

Structural basis of TFIIH activation for nucleotide excision repair

Kokic, G., Chernev, A., Tegunov, D., Dienemann, C., Urlaub, H., & Cramer, P. (2019) · Nature Communications · doi:10.1038/s41467-019-10745-5 · Cited by 163

Early-onset autoimmunity associated with SOCS1 haploinsufficiency

Hadjadj, J., Castro, C. N., Tusseau, M., Stolzenberg, M.-C., Mazerolles, F., Aladjidi, N., Armstrong, M., Ashrafian, H., Cutcutache, I., Ebetsberger-Dachs, G., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-18925-4 · Cited by 156

Structural insights into integrin α 5 β 1 opening by fibronectin ligand

Schumacher, S., Dedden, D., Nunez, R. V., Matoba, K., Takagi, J., Biertümpfel, C., & Mizuno, N. (2021) · Science Advances · doi:10.1126/sciadv.abe9716 · Cited by 150

Mechanism of tetracycline resistance by ribosomal protection protein Tet(O)

Li, W., Atkinson, G. C., Thakor, N. S., Allas, Ü., Lu, C.-C., Chan, K.-Y., Tenson, T., Schulten, K., Wilson, K. S., Hauryliuk, V., et al. (2013) · Nature Communications · doi:10.1038/ncomms2470 · Cited by 147

Protein interaction network of alternatively spliced isoforms from brain links genetic risk factors for autism

Corominas, R., Yang, X., Lin, G. N., Kang, S., Shen, Y., Ghamsari, L., Broly, M., Rodriguez, M., Tam, S., Wanamaker, S. A., et al. (2014) · Nature Communications · doi:10.1038/ncomms4650 · Cited by 140

Characterization of Choline Trimethylamine-Lyase Expands the Chemistry of Glycyl Radical Enzymes

Craciun, S., Marks, J. A., & Balskus, E. P. (2014) · ACS Chemical Biology · doi:10.1021/cb500113p · Cited by 139

Elongation factor Tu is a multifunctional and processed moonlighting protein

Widjaja, M., Harvey, K. L., Hagemann, L., Berry, I. J., Jarocki, V. M., Raymond, B. B. A., Tacchi, J. L., Gründel, A., Steele, J. R., Padula, M. P., et al. (2017) · Scientific Reports · doi:10.1038/s41598-017-10644-z · Cited by 131

Structure-Based Design and Synthesis of Novel Inhibitors Targeting HDAC8 from Schistosoma mansoni for the Treatment of Schistosomiasis

Heimburg, T., Chakrabarti, A., Lancelot, J., Marek, M., Melesina, J., Hauser, A.-T., Shaik, T. B., Duclaud, S., Robaa, D., Erdmann, F., et al. (2016) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.5b01478 · Cited by 124

AI-Based Protein Structure Prediction in Drug Discovery: Impacts and Challenges

Schauperl, M., & Denny, R. A. (2022) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.2c00026 · Cited by 122

Apolipoprotein E4 inhibits autophagy gene products through direct, specific binding to CLEAR motifs

Parcon, P. A., Balasubramaniam, M., Ayyadevara, S., Jones, R. A., Liu, L., Shmookler Reis, R. J., Barger, S. W., Mrak, R. E., & Griffin, W. S. T. (2018) · Alzheimer's & Dementia · doi:10.1016/j.jalz.2017.07.754 · Cited by 122

Towards elucidating the stability, dynamics and architecture of the nucleosome remodeling and deacetylase complex by using quantitative interaction proteomics

Kloet, S. L., Baymaz, H. I., Makowski, M., Groenewold, V., Jansen, P. W. T. C., Berendsen, M., Niazi, H., Kops, G. J., & Vermeulen, M. (2015) · The FEBS Journal · doi:10.1111/febs.12972 · Cited by 107

Modeling the binding of diverse ligands within the Ah receptor ligand binding domain

Giani Tagliabue, S., Faber, S. C., Motta, S., Denison, M. S., & Bonati, L. (2019) · Scientific Reports · doi:10.1038/s41598-019-47138-z · Cited by 106

Receptor Activity-modifying Protein-directed G Protein Signaling Specificity for the Calcitonin Gene-related Peptide Family of Receptors

Weston, C., Winfield, I., Harris, M., Hodgson, R., Shah, A., Dowell, S. J., Mobarec, J. C., Woodlock, D. A., Reynolds, C. A., Poyner, D. R., et al. (2016) · Journal of Biological Chemistry · doi:10.1074/jbc.m116.751362 · Cited by 95

A structural mechanism for directing corepressor-selective inverse agonism of PPARγ

Brust, R., Shang, J., Fuhrmann, J., Mosure, S. A., Bass, J., Cano, A., Heidari, Z., Chrisman, I. M., Nemetchek, M. D., Blayo, A.-L., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-07133-w · Cited by 94

The molecular architecture of the nuclear basket

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Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation

Usmanova, D. R., Bogatyreva, N. S., Ariño Bernad, J., Eremina, A. A., Gorshkova, A. A., Kanevskiy, G. M., Lonishin, L. R., Meister, A. V., Yakupova, A. G., Kondrashov, F. A., et al. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty340 · Cited by 93

RosettaDDGPrediction for high‐throughput mutational scans: From stability to binding

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Visualization of the HIV-1 Env glycan shield across scales

Berndsen, Z. T., Chakraborty, S., Wang, X., Cottrell, C. A., Torres, J. L., Diedrich, J. K., López, C. A., Yates, J. R., van Gils, M. J., Paulson, J. C., et al. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2000260117 · Cited by 86

Accurate modeling of peptide-MHC structures with AlphaFold

Mikhaylov, V., Brambley, C. A., Keller, G. L. J., Arbuiso, A. G., Weiss, L. I., Baker, B. M., & Levine, A. J. (2024) · Structure · doi:10.1016/j.str.2023.11.011 · Cited by 72

Towards simple kinetic models of functional dynamics for a kinase subfamily

Sultan, M. M., Kiss, G., & Pande, V. S. (2018) · Nature Chemistry · doi:10.1038/s41557-018-0077-9 · Cited by 68

Deimmunization of protein therapeutics - Recent advances in experimental and computational epitope prediction and deletion

Zinsli, L. V., Stierlin, N., Loessner, M. J., & Schmelcher, M. (2021) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2020.12.024 · Cited by 63

Optimization of a Small Tropomyosin-Related Kinase B (TrkB) Agonist 7,8-Dihydroxyflavone Active in Mouse Models of Depression

Liu, X., Chan, C.-B., Qi, Q., Xiao, G., Luo, H. R., He, X., & Ye, K. (2012) · Journal of Medicinal Chemistry · doi:10.1021/jm301099x · Cited by 60

Molecular architecture and dynamics of SARS-CoV-2 envelope by integrative modeling

Pezeshkian, W., Grünewald, F., Narykov, O., Lu, S., Arkhipova, V., Solodovnikov, A., Wassenaar, T. A., Marrink, S. J., & Korkin, D. (2023) · Structure · doi:10.1016/j.str.2023.02.006 · Cited by 60

1′-Ribose cyano substitution allows Remdesivir to effectively inhibit nucleotide addition and proofreading during SARS-CoV-2 viral RNA replication

Zhang, L., Zhang, D., Wang, X., Yuan, C., Li, Y., Jia, X., Gao, X., Yen, H.-L., Cheung, P. P.-H., & Huang, X. (2021) · Physical Chemistry Chemical Physics · doi:10.1039/d0cp05948j · Cited by 52

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

Explore Protein Conformational Space With Variational Autoencoder

Tian, H., Jiang, X., Trozzi, F., Xiao, S., Larson, E. C., & Tao, P. (2021) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2021.781635 · Cited by 51

Structural and Functional Characterization of a Multifunctional Alanine-Rich Peptide Analogue from Pleuronectes americanus

Migliolo, L., Silva, O. N., Silva, P. A., Costa, M. P., Costa, C. R., Nolasco, D. O., Barbosa, J. A. R. G., Silva, M. R. R., Bemquerer, M. P., Lima, L. M. P., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0047047 · Cited by 48

DIP/Dpr interactions and the evolutionary design of specificity in protein families

Sergeeva, A. P., Katsamba, P. S., Cosmanescu, F., Brewer, J. J., Ahlsen, G., Mannepalli, S., Shapiro, L., & Honig, B. (2020) · Nature Communications · doi:10.1038/s41467-020-15981-8 · Cited by 38

Improving homology modeling from low-sequence identity templates in Rosetta: A case study in GPCRs

Bender, B. J., Marlow, B., & Meiler, J. (2020) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1007597 · Cited by 44

APOGEE 2: multi-layer machine-learning model for the interpretable prediction of mitochondrial missense variants

Bianco, S. D., Parca, L., Petrizzelli, F., Biagini, T., Giovannetti, A., Liorni, N., Napoli, A., Carella, M., Procaccio, V., Lott, M. T., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-40797-7 · Cited by 44

A Rare Mutation in SMAD9 Associated With High Bone Mass Identifies the SMAD-Dependent BMP Signaling Pathway as a Potential Anabolic Target for Osteoporosis

Gregson, C. L., Bergen, D. J. M., Leo, P., Sessions, R. B., Wheeler, L., Hartley, A., Youlten, S., Croucher, P. I., McInerney-Leo, A. M., Fraser, W., et al. (2020) · Journal of Bone and Mineral Research · doi:10.1002/jbmr.3875 · Cited by 44

The Human Mixed Lineage Leukemia 5 (MLL5), a Sequentially and Structurally Divergent SET Domain-Containing Protein with No Intrinsic Catalytic Activity

Mas-y-Mas, S., Barbon, M., Teyssier, C., Déméné, H., Carvalho, J. E., Bird, L. E., Lebedev, A., Fattori, J., Schubert, M., Dumas, C., et al. (2016) · PLOS ONE · doi:10.1371/journal.pone.0165139 · Cited by 43

Memdock: an α-helical membrane protein docking algorithm

Hurwitz, N., Schneidman-Duhovny, D., & Wolfson, H. J. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw184 · Cited by 40

Assessment of the CASP14 assembly predictions

Ozden, B., Kryshtafovych, A., & Karaca, E. (2021) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.26199 · Cited by 41

Structural hot spots determine functional diversity of the Candida glabrata epithelial adhesin family

Diderrich, R., Kock, M., Maestre-Reyna, M., Keller, P., Steuber, H., Rupp, S., Essen, L.-O., & Mösch, H.-U. (2015) · Journal of Biological Chemistry · doi:10.1074/jbc.m115.655654 · Cited by 40

A distal regulatory region of a class I human histone deacetylase

Werbeck, N. D., Shukla, V. K., Kunze, M. B. A., Yalinca, H., Pritchard, R. B., Siemons, L., Mondal, S., Greenwood, S. O. R., Kirkpatrick, J., Marson, C. M., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-17610-w · Cited by 40

Structural basis of host protein hijacking in human T-cell leukemia virus integration

Bhatt, V., Shi, K., Salamango, D. J., Moeller, N. H., Pandey, K. K., Bera, S., Bohl, H. O., Kurniawan, F., Orellana, K., Zhang, W., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-16963-6 · Cited by 39

Functional characterization and stability improvement of a ‘thermophilic-like’ ene-reductase from Rhodococcus opacus 1CP

Riedel, A., Mehnert, M., Paul, C. E., Westphal, A. H., van Berkel, W. J. H., & Tischler, D. (2015) · Frontiers in Microbiology · doi:10.3389/fmicb.2015.01073 · Cited by 38

Microexon-based regulation of ITSN1 and Src SH3 domains specificity relies on introduction of charged amino acids into the interaction interface

Dergai, M., Tsyba, L., Dergai, O., Zlatskii, I., Skrypkina, I., Kovalenko, V., & Rynditch, A. (2010) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2010.07.080 · Cited by 35

Comparative In Vitro and In Silico Analysis of the Selectivity of Indirubin as a Human Ah Receptor Agonist

Faber, S. C., Soshilov, A. A., Giani Tagliabue, S., Bonati, L., & Denison, M. S. (2018) · International Journal of Molecular Sciences · doi:10.3390/ijms19092692 · Cited by 36

Identifying Extrinsic versus Intrinsic Drivers of Variation in Cell Behavior in Human iPSC Lines from Healthy Donors

Vigilante, A., Laddach, A., Moens, N., Meleckyte, R., Leha, A., Ghahramani, A., Culley, O. J., Kathuria, A., Hurling, C., Vickers, A., et al. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.01.094 · Cited by 34

Structure and mechanism of a tripartite ATP-independent periplasmic TRAP transporter

Davies, J. S., Currie, M. J., North, R. A., Scalise, M., Wright, J. D., Copping, J. M., Remus, D. M., Gulati, A., Morado, D. R., Jamieson, S. A., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-36590-1 · Cited by 34

Advancements in Nanobody Epitope Prediction: A Comparative Study of AlphaFold2Multimer vs AlphaFold3

Eshak, F., & Goupil-Lamy, A. (2025) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.4c01877 · Cited by 34

Accurate protein stability predictions from homology models

Valanciute, A., Nygaard, L., Zschach, H., Maglegaard Jepsen, M., Lindorff-Larsen, K., & Stein, A. (2023) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2022.11.048 · Cited by 33

Structural features of Dnase1L3 responsible for serum antigen clearance

McCord, J. J., Engavale, M., Masoumzadeh, E., Villarreal, J., Mapp, B., Latham, M. P., Keyel, P. A., & Sutton, R. B. (2022) · Communications Biology · doi:10.1038/s42003-022-03755-5 · Cited by 31

Lateral distribution of phosphatidylinositol 4,5-bisphosphate in membranes regulates formin- and ARP2/3-mediated actin nucleation

Bucki, R., Wang, Y.-H., Yang, C., Kandy, S. K., Fatunmbi, O., Bradley, R., Pogoda, K., Svitkina, T., Radhakrishnan, R., & Janmey, P. A. (2019) · Journal of Biological Chemistry · doi:10.1074/jbc.ra118.005552 · Cited by 31

Modeling the Orthosteric Binding Site of the G Protein-Coupled Odorant Receptor OR5K1

Nicoli, A., Haag, F., Marcinek, P., He, R., Kreißl, J., Stein, J., Marchetto, A., Dunkel, A., Hofmann, T., Krautwurst, D., et al. (2023) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.2c00752 · Cited by 28

ZnuD, a Potential Candidate for a Simple and Universal Neisseria meningitidis Vaccine

Hubert, K., Devos, N., Mordhorst, I., Tans, C., Baudoux, G., Feron, C., Goraj, K., Tommassen, J., Vogel, U., Poolman, J. T., et al. (2013) · Infection and Immunity · doi:10.1128/iai.01312-12 · Cited by 28

Glucocorticoid receptor complexes form cooperatively with the Hsp90 co-chaperones Pp5 and FKBPs

Kaziales, A., Barkovits, K., Marcus, K., & Richter, K. (2020) · Scientific Reports · doi:10.1038/s41598-020-67645-8 · Cited by 24

Architecture of the biofilm-associated archaic Chaperone-Usher pilus CupE from Pseudomonas aeruginosa

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Structural basis for receptor selectivity and inverse agonism in S1P5 receptors

Lyapina, E., Marin, E., Gusach, A., Orekhov, P., Gerasimov, A., Luginina, A., Vakhrameev, D., Ergasheva, M., Kovaleva, M., Khusainov, G., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-32447-1 · Cited by 26

A Practical Guide to All-Atom and Coarse-Grained Molecular Dynamics Simulations Using Amber and Gromacs: A Case Study of Disulfide-Bond Impact on the Intrinsically Disordered Amyloid Beta

(2024) · doi:10.3390/ijms25126698 · Cited by 26

A Model of a MAPK•Substrate Complex in an Active Conformation: A Computational and Experimental Approach

Lee, S., Warthaka, M., Yan, C., Kaoud, T. S., Piserchio, A., Ghose, R., Ren, P., & Dalby, K. N. (2011) · PLoS ONE · doi:10.1371/journal.pone.0018594 · Cited by 26

Characterizing and explaining the impact of disease-associated mutations in proteins without known structures or structural homologs

Sen, N., Anishchenko, I., Bordin, N., Sillitoe, I., Velankar, S., Baker, D., & Orengo, C. (2022) · Briefings in Bioinformatics · doi:10.1093/bib/bbac187 · Cited by 25

Redefining the architecture of ferlin proteins: Insights into multi-domain protein structure and function

Dominguez, M. J., McCord, J. J., & Sutton, R. B. (2022) · PLOS ONE · doi:10.1371/journal.pone.0270188 · Cited by 24

EnzyHTP Computational Directed Evolution with Adaptive Resource Allocation

Shao, Q., Jiang, Y., & Yang, Z. J. (2023) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.3c00618 · Cited by 23

The prolactin receptor scaffolds Janus kinase 2 via co-structure formation with phosphoinositide-4,5-bisphosphate

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DIP2 is a unique regulator of diacylglycerol lipid homeostasis in eukaryotes

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