UCSF ChimeraX: Meeting modern challenges in visualization and analysis

VMD: visual molecular dynamics

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UCSF Chimera—A visualization system for exploratory research and analysis

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

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Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

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Comparative Protein Modelling by Satisfaction of Spatial Restraints

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Database resources of the National Center for Biotechnology Information: update

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The NumPy Array: A Structure for Efficient Numerical Computation

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UniProt: the Universal Protein knowledgebase

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Electrostatics of nanosystems: Application to microtubules and the ribosome

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The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible

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SCOP: A structural classification of proteins database for the investigation of sequences and structures

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The Pfam protein families database: towards a more sustainable future

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The interpretation of protein structures: Estimation of static accessibility

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UniProt: the universal protein knowledgebase

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CDD: NCBI's conserved domain database

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The Anatomy and Taxonomy of Protein Structure

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Announcing the worldwide Protein Data Bank

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Integration of biological networks and gene expression data using Cytoscape

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UniProt: the universal protein knowledgebase

The UniProt Consortium (2018) · Nucleic Acids Research · doi:10.1093/nar/gky092 · Cited by 2,043 · see citing works

Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution

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Database resources of the National Center for Biotechnology Information

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ModBase, a database of annotated comparative protein structure models, and associated resources

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Visualizing density maps with UCSF Chimera

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Tools for integrated sequence-structure analysis with UCSF Chimera

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The RCSB Protein Data Bank: redesigned web site and web services

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Reduced surface: an efficient way to compute molecular surfaces.

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Determining the architectures of macromolecular assemblies

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Ambient Occlusion and Edge Cueing for Enhancing Real Time Molecular Visualization

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CATH: an expanded resource to predict protein function through structure and sequence

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Software Extensions to UCSF Chimera for Interactive Visualization of Large Molecular Assemblies

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Web Services at the European Bioinformatics Institute

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OpenMM: A Hardware Independent Framework for Molecular Simulations

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BioCatalogue: a universal catalogue of web services for the life sciences

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Cytoscape App Store

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HELANAL: A Program to Characterize Helix Geometry in Proteins

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Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop

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Visualization of macromolecular structures

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Structural Characterization by Cross-linking Reveals the Detailed Architecture of a Coatomer-related Heptameric Module from the Nuclear Pore Complex

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Algorithm for ribbon models of proteins

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New electron microscopy database and deposition system

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Actin-based protrusions of migrating neutrophils are intrinsically lamellar and facilitate direction changes

Fritz‐Laylin, L. K., Riel-Mehan, M. M., Chen, B., Lord, S. J., Goddard, T. D., Ferrin, T. E., Nicholson-Dykstra, S., Higgs, H. N., Johnson, G. T., Betzig, E., et al. (2017) · eLife · doi:10.7554/elife.26990 · Cited by 138 · see citing works

Imaging polysaccharides by atomic force microscopy

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Cryo-EM of macromolecular assemblies at near-atomic resolution

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STAR/mmCIF: An ontology for macromolecular structure

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Validated near-atomic resolution structure of bacteriophage epsilon15 derived from cryo-EM and modeling

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Web services at the European Bioinformatics Institute-2009

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On the interpretation of electron microscopic maps of biological macromolecules

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The PDB format, mmCIF, and other data formats.

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Re-evaluation of low-resolution crystal structuresviainteractive molecular-dynamics flexible fitting (iMDFF): a case study in complement C4

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Nano-mechanical measurements of protein-DNA interactions with a silicon nitride pulley

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Multi-scale Visualization of Molecular Architecture Using Real-Time Ambient Occlusion in Sculptor

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ProfileGrids: a sequence alignment visualization paradigm that avoids the limitations of Sequence Logos

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Author response: Actin-based protrusions of migrating neutrophils are intrinsically lamellar and facilitate direction changes

Fritz‐Laylin, L. K., Riel-Mehan, M. M., Chen, B., Lord, S. J., Goddard, T. D., Ferrin, T. E., Nicholson-Dykstra, S., Higgs, H. N., Johnson, G. T., Betzig, E., et al. (2017) · eLife · doi:10.7554/elife.26990.040 · Cited by 4 · see citing works

Three-dimensional actin-based protrusions of migrating neutrophils are intrinsically lamellar and facilitate direction changesPreprint

Fritz‐Laylin, L. K., Riel-Mehan, M. M., Chen, B., et al. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/120444 · Cited by 2 · see citing works

Structure, function and antigenicity of the SARS-CoV-2 spike glycoprotein

Walls, A. C., Park, Y.-J., Tortorici, M. A., Wall, A., McGuire, A. T., & Veesler, D. (2020) · doi:10.1101/2020.02.19.956581 · Cited by 8,586 · see citing works

MolProbity: More and better reference data for improved all‐atom structure validation

Williams, C. J., Headd, J. J., Moriarty, N. W., Prisant, M. G., Videau, L. L., Deis, L. N., Verma, V., Keedy, D. A., Hintze, B. J., Chen, V. B., et al. (2018) · Protein Science · doi:10.1002/pro.3330 · Cited by 4,599 · see citing works

Cross-neutralization of SARS-CoV-2 by a human monoclonal SARS-CoV antibody

Pinto, D., Park, Y.-J., Beltramello, M., Walls, A. C., Tortorici, M. A., Bianchi, S., Jaconi, S., Culap, K., Zatta, F., De Marco, A., et al. (2020) · Nature · doi:10.1038/s41586-020-2349-y · Cited by 1,885 · see citing works

The inner junction complex of the cilia is an interaction hub that involves tubulin post-translational modifications

Khalifa, A. A. Z., Ichikawa, M., Dai, D., Kubo, S., Black, C. S., Peri, K., McAlear, T. S., Veyron, S., Yang, S. K., Vargas, J., et al. (2020) · eLife · doi:10.7554/elife.52760 · Cited by 1,676 · see citing works

Potent neutralizing antibodies against multiple epitopes on SARS-CoV-2 spike

Liu, L., Wang, P., Nair, M. S., Yu, J., Rapp, M., Wang, Q., Luo, Y., Chan, J. F.-W., Sahi, V., Figueroa, A., et al. (2020) · Nature · doi:10.1038/s41586-020-2571-7 · Cited by 1,349 · see citing works

SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies

Barnes, C. O., Jette, C. A., Abernathy, M. E., Dam, K.-M. A., Esswein, S. R., Gristick, H. B., Malyutin, A. G., Sharaf, N. G., Huey-Tubman, K. E., Lee, Y. E., et al. (2020) · Nature · doi:10.1038/s41586-020-2852-1 · Cited by 1,599 · see citing works

mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants

Wang, Z., Schmidt, F., Weisblum, Y., Muecksch, F., Barnes, C. O., Finkin, S., Schaefer-Babajew, D., Cipolla, M., Gaebler, C., Lieberman, J. A., et al. (2021) · Nature · doi:10.1038/s41586-021-03324-6 · Cited by 1,343 · see citing works

Molecular Architecture of the SARS-CoV-2 Virus

Yao, H., Song, Y., Chen, Y., Wu, N., Xu, J., Sun, C., Zhang, J., Weng, T., Zhang, Z., Wu, Z., et al. (2020) · Cell · doi:10.1016/j.cell.2020.09.018 · Cited by 1,060 · see citing works

N-terminal domain antigenic mapping reveals a site of vulnerability for SARS-CoV-2

McCallum, M., De Marco, A., Lempp, F. A., Tortorici, M. A., Pinto, D., Walls, A. C., Beltramello, M., Chen, A., Liu, Z., Zatta, F., et al. (2021) · Cell · doi:10.1016/j.cell.2021.03.028 · Cited by 901 · see citing works

Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies

Chen, R. E., Zhang, X., Case, J. B., Winkler, E. S., Liu, Y., VanBlargan, L. A., Liu, J., Errico, J. M., Xie, X., Suryadevara, N., et al. (2021) · Nature Medicine · doi:10.1038/s41591-021-01294-w · Cited by 881 · see citing works

Macromolecular modeling and design in Rosetta: recent methods and frameworks

Leman, J. K., Weitzner, B. D., Lewis, S. M., Adolf-Bryfogle, J., Alam, N., Alford, R. F., Aprahamian, M., Baker, D., Barlow, K. A., Barth, P., et al. (2020) · Nature Methods · doi:10.1038/s41592-020-0848-2 · Cited by 888 · see citing works

De novo design of picomolar SARS-CoV-2 miniprotein inhibitors

Cao, L., Goreshnik, I., Coventry, B., Case, J. B., Miller, L., Kozodoy, L., Chen, R. E., Carter, L., Walls, A. C., Park, Y.-J., et al. (2020) · Science · doi:10.1126/science.abd9909 · Cited by 742 · see citing works

SARS-CoV-2 Omicron variant: Antibody evasion and cryo-EM structure of spike protein–ACE2 complex

Mannar, D., Saville, J. W., Zhu, X., Srivastava, S. S., Berezuk, A. M., Tuttle, K. S., Marquez, A. C., Sekirov, I., & Subramaniam, S. (2022) · Science · doi:10.1126/science.abn7760 · Cited by 630 · see citing works

Ultrapotent human antibodies protect against SARS-CoV-2 challenge via multiple mechanisms

Tortorici, M. A., Beltramello, M., Lempp, F. A., Pinto, D., Dang, H. V., Rosen, L. E., McCallum, M., Bowen, J., Minola, A., Jaconi, S., et al. (2020) · Science · doi:10.1126/science.abe3354 · Cited by 510 · see citing works

Elicitation of Potent Neutralizing Antibody Responses by Designed Protein Nanoparticle Vaccines for SARS-CoV-2

Walls, A. C., Fiala, B., Schäfer, A., Wrenn, S., Pham, M. N., Murphy, M., Tse, L. V., Shehata, L., O’Connor, M. A., Chen, C., et al. (2020) · Cell · doi:10.1016/j.cell.2020.10.043 · Cited by 532 · see citing works

Unexpected Receptor Functional Mimicry Elucidates Activation of Coronavirus Fusion

Walls, A. C., Xiong, X., Park, Y.-J., Tortorici, M. A., Snijder, J., Quispe, J., Cameroni, E., Gopal, R., Dai, M., Lanzavecchia, A., et al. (2019) · Cell · doi:10.1016/j.cell.2018.12.028 · Cited by 582 · see citing works

Structural basis of SARS-CoV-2 Omicron immune evasion and receptor engagement

McCallum, M., Czudnochowski, N., Rosen, L. E., Zepeda, S. K., Bowen, J. E., Walls, A. C., Hauser, K., Joshi, A., Stewart, C., Dillen, J. R., et al. (2022) · Science · doi:10.1126/science.abn8652 · Cited by 535 · see citing works

SARS-CoV-2 immune evasion by the B.1.427/B.1.429 variant of concern

McCallum, M., Bassi, J., De Marco, A., Chen, A., Walls, A. C., Di Iulio, J., Tortorici, M. A., Navarro, M.-J., Silacci-Fregni, C., Saliba, C., et al. (2021) · Science · doi:10.1126/science.abi7994 · Cited by 412 · see citing works

Akkermansia muciniphila phospholipid induces homeostatic immune responses

Bae, M., Cassilly, C. D., Liu, X., Park, S.-M., Tusi, B. K., Chen, X., Kwon, J., Filipčík, P., Bolze, A. S., Liu, Z., et al. (2022) · Nature · doi:10.1038/s41586-022-04985-7 · Cited by 413 · see citing works

Structure of the neurotensin receptor 1 in complex with β-arrestin 1

Huang, W., Masureel, M., Qu, Q., Janetzko, J., Inoue, A., Kato, H. E., Robertson, M. J., Nguyen, K. C., Glenn, J. S., Skiniotis, G., et al. (2020) · Nature · doi:10.1038/s41586-020-1953-1 · Cited by 373 · see citing works

AI-based structure prediction empowers integrative structural analysis of human nuclear pores

Mosalaganti, S., Obarska-Kosinska, A., Siggel, M., Taniguchi, R., Turoňová, B., Zimmerli, C. E., Buczak, K., Schmidt, F. H., Margiotta, E., Mackmull, M.-T., et al. (2022) · Science · doi:10.1126/science.abm9506 · Cited by 355 · see citing works

Collided ribosomes form a unique structural interface to induce Hel2-driven quality control pathways

Ikeuchi, K., Tesina, P., Matsuo, Y., Sugiyama, T., Cheng, J., Saeki, Y., Tanaka, K., Becker, T., Beckmann, R., & Inada, T. (2019) · The EMBO Journal · doi:10.15252/embj.2018100276 · Cited by 315 · see citing works

Structure, lipid scrambling activity and role in autophagosome formation of ATG9A

Maeda, S., Yamamoto, H., Kinch, L. N., Garza, C. M., Takahashi, S., Otomo, C., Grishin, N. V., Forli, S., Mizushima, N., & Otomo, T. (2020) · Nature Structural & Molecular Biology · doi:10.1038/s41594-020-00520-2 · Cited by 305 · see citing works

Structures of MERS-CoV spike glycoprotein in complex with sialoside attachment receptors

Park, Y.-J., Walls, A. C., Wang, Z., Sauer, M. M., Li, W., Tortorici, M. A., Bosch, B.-J., DiMaio, F., & Veesler, D. (2019) · Nature Structural & Molecular Biology · doi:10.1038/s41594-019-0334-7 · Cited by 260 · see citing works

In-cell architecture of an actively transcribing-translating expressome

O’Reilly, F. J., Xue, L., Graziadei, A., Sinn, L., Lenz, S., Tegunov, D., Blötz, C., Singh, N., Hagen, W. J. H., Cramer, P., et al. (2020) · Science · doi:10.1126/science.abb3758 · Cited by 284 · see citing works

ScanNet: an interpretable geometric deep learning model for structure-based protein binding site prediction

Tubiana, J., Schneidman-Duhovny, D., & Wolfson, H. J. (2022) · Nature Methods · doi:10.1038/s41592-022-01490-7 · Cited by 274 · see citing works

Structure of the bacterial ribosome at 2 Å resolution

Watson, Z. L., Ward, F. R., Méheust, R., Ad, O., Schepartz, A., Banfield, J. F., & Cate, J. H. (2020) · eLife · doi:10.7554/elife.60482 · Cited by 263 · see citing works

Structural basis for sequestration and autoinhibition of cGAS by chromatin

Michalski, S., de Oliveira Mann, C. C., Stafford, C. A., Witte, G., Bartho, J., Lammens, K., Hornung, V., & Hopfner, K.-P. (2020) · Nature · doi:10.1038/s41586-020-2748-0 · Cited by 256 · see citing works

Structural Basis for Cholesterol Transport-like Activity of the Hedgehog Receptor Patched

Zhang, Y., Bulkley, D. P., Xin, Y., Roberts, K. J., Asarnow, D. E., Sharma, A., Myers, B. R., Cho, W., Cheng, Y., & Beachy, P. A. (2018) · Cell · doi:10.1016/j.cell.2018.10.026 · Cited by 239 · see citing works

Structural basis for regulation of human acetyl-CoA carboxylase

Hunkeler, M., Hagmann, A., Stuttfeld, E., Chami, M., Guri, Y., Stahlberg, H., & Maier, T. (2018) · Nature · doi:10.1038/s41586-018-0201-4 · Cited by 229 · see citing works

Structure of mycobacterial ATP synthase bound to the tuberculosis drug bedaquiline

Guo, H., Courbon, G. M., Bueler, S. A., Mai, J., Liu, J., & Rubinstein, J. L. (2021) · Nature · doi:10.1038/s41586-020-3004-3 · Cited by 200 · see citing works

Molecular glue CELMoD compounds are regulators of cereblon conformation

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ATP Synthase Diseases of Mitochondrial Genetic Origin

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Structural basis for placental malaria mediated by Plasmodium falciparum VAR2CSA.

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Substrate and product complexes reveal mechanisms of Hedgehog acylation by HHAT

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Structure and regulation of the nuclear exosome targeting complex guides RNA substrates to the exosome

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STK19 positions TFIIH for cell-free transcription-coupled DNA repair

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Structure of a P element transposase–DNA complex reveals unusual DNA structures and GTP-DNA contacts

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SMC motor proteins extrude DNA asymmetrically and can switch directions

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Mouse α-synuclein fibrils are structurally and functionally distinct from human fibrils associated with Lewy body diseases

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Structures and comparison of endogenous 2-oxoglutarate and pyruvate dehydrogenase complexes from bovine kidney

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PAM binding ensures orientational integration during Cas4-Cas1-Cas2-mediated CRISPR adaptation

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