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Berman, H. M. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.235 · Cited by 40,196
Self-citationThe protein data bank: A computer-based archival file for macromolecular structures
Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F., Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T., & Tasumi, M. (1977) · Journal of Molecular Biology · doi:10.1016/s0022-2836(77)80200-3 · Cited by 8,574
[30] Macromolecular crystallographic information file
Bourne, P. E., Berman, H. M., McMahon, B., Watenpaugh, K. D., Westbrook, J., & Fitzgerald, P. M. D. (1997) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/s0076-6879(97)77032-0 · Cited by 170
Self-citation
Research works printed but not linked: 1
- Callaway, J. et al. Protein Data Bank Contents Guide: Atomic coordinate entry format description. (Brookhaven National Laboratory, 1996).
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Mistry, J., Chuguransky, S., Williams, L., Qureshi, M., Salazar, G. A., Sonnhammer, E. L. L., Tosatto, S. C. E., Paladin, L., Raj, S., Richardson, L. J., et al. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkaa913 · Cited by 7,452
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Best, R. B., Zhu, X., Shim, J., Lopes, P. E. M., Mittal, J., Feig, M., & MacKerell, A. D. (2012) · Journal of Chemical Theory and Computation · doi:10.1021/ct300400x · Cited by 4,541
MoleculeNet: a benchmark for molecular machine learning
Wu, Z., Ramsundar, B., Feinberg, E. N., Gomes, J., Geniesse, C., Pappu, A. S., Leswing, K., & Pande, V. (2018) · Chemical Science · doi:10.1039/c7sc02664a · Cited by 3,107
Burley, S. K., Bhikadiya, C., Bi, C., Bittrich, S., Chen, L., Crichlow, G. V., Christie, C. H., Dalenberg, K., Di Costanzo, L., Duarte, J. M., et al. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkaa1038 · Cited by 1,581
Ulrich, E. L., Akutsu, H., Doreleijers, J. F., Harano, Y., Ioannidis, Y., Lin, J. C., Livny, M., Mading, S., Maziuk, D., Miller, Z., et al. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm957 · Cited by 1,472
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Burley, S. K., Berman, H. M., Bhikadiya, C., Bi, C., Chen, L., Costanzo, L. D., Christie, C. H., Dalenberg, K., Duarte, J. M., Dutta, S., et al. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky1004 · Cited by 1,268
Self-citationProtein Data Bank (PDB): The Single Global Macromolecular Structure Archive
Burley, S. K., Berman, H. M., Kleywegt, G. J., Markley, J. L., Nakamura, H., & Velankar, S. (2017) · Methods in Molecular Biology · doi:10.1007/978-1-4939-7000-1_26 · Cited by 1,141
Self-citationVenselaar, H., Beek, T. A. H. T., Kuipers, R. K. P., Hekkelman, M. L., & Vriend, G. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-548 · Cited by 1,201
The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data
Berman, H. M., Henrick, K., Nakamura, H., & Markley, J. L. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl971 · Cited by 1,124
Self-citationA series of PDB-related databanks for everyday needs
Touw, W. G., Baakman, C. A. B., Black, J., Beek, T. A. H. T., Krieger, E., Joosten, R. P., & Vriend, G. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku1028 · Cited by 941
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Rose, P. W., Prlić, A., Altunkaya, A., Bi, C., Bradley, A. R., Christie, C. H., Costanzo, L. D., Duarte, J. M., Dutta, S., Feng, Z., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw1000 · Cited by 800
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Design of protein-binding proteins from the target structure alone
Cao, L., Coventry, B., Goreshnik, I., Huang, B., Sheffler, W., Park, J. S., Jude, K. M., Marković, I., Kadam, R. U., Verschueren, K. H. G., et al. (2022) · Nature · doi:10.1038/s41586-022-04654-9 · Cited by 577
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Land, H., & Humble, M. S. (2017) · Methods in molecular biology · doi:10.1007/978-1-4939-7366-8_4 · Cited by 614
Laskowski, R. A. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn860 · Cited by 594
Bugnon, M., Röhrig, U. F., Goullieux, M., Perez, M. A. S., Daina, A., Michielin, O. A., & Zoete, V. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae300 · Cited by 639
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Mulder, N. (2004) · Nucleic Acids Research · doi:10.1093/nar/gki106 · Cited by 546
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Cohen, D., Melamed, S., Millman, A., Shulman, G., Oppenheimer-Shaanan, Y., Kacen, A., Doron, S., Amitai, G., & Sorek, R. (2019) · Nature · doi:10.1038/s41586-019-1605-5 · Cited by 535
The RCSB Protein Data Bank: new resources for research and education
Rose, P. W., Bi, C., Bluhm, W. F., Christie, C. H., Dimitropoulos, D., Dutta, S., Green, R. K., Goodsell, D. S., Prlić, A., Quesada, M., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1200 · Cited by 535
Self-citationFoXS: a web server for rapid computation and fitting of SAXS profiles
Schneidman‐Duhovny, D., Hammel, M., & Šali, A. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq461 · Cited by 524
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Kouranov, A. (2005) · Nucleic Acids Research · doi:10.1093/nar/gkj120 · Cited by 523
The RCSB Protein Data Bank: views of structural biology for basic and applied research and education
Rose, P. W., Prlić, A., Bi, C., Bluhm, W. F., Christie, C. H., Dutta, S., Green, R. K., Goodsell, D. S., Westbrook, J., Woo, J., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku1214 · Cited by 519
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Forging the basis for developing protein-ligand interaction scoring functions.
Liu, Z., Su, M., Han, L., Liu, J., Yang, Q., Li, Y., & Wang, R. (2017) · Accounts of Chemical Research · doi:10.1021/acs.accounts.6b00491 · Cited by 493
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Bohrer, B. C., Merenbloom, S. I., Koeniger, S. L., Hilderbrand, A. E., & Clemmer, D. E. (2008) · Annual Review of Analytical Chemistry · doi:10.1146/annurev.anchem.1.031207.113001 · Cited by 503
Case, J. B., Rothlauf, P. W., Chen, R. E., Liu, Z., Zhao, H., Kim, A. S., Bloyet, L.-M., Zeng, Q., Tahan, S., Droit, L., et al. (2020) · Cell Host & Microbe · doi:10.1016/j.chom.2020.06.021 · Cited by 410
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Kühner, S., van Noort, V., Betts, M. J., Leo-Macias, A., Batisse, C., Rode, M., Yamada, T., Maier, T., Bader, S., Beltran-Alvarez, P., et al. (2009) · Science · doi:10.1126/science.1176343 · Cited by 471
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Pace, C. N., Fu, H., Fryar, K. L., Landua, J. D., Trevino, S. R., Shirley, B. A., McNutt, M., Iimura, S., Gajiwala, K. S., Scholtz, J. M., et al. (2011) · Journal of Molecular Biology · doi:10.1016/j.jmb.2011.02.053 · Cited by 460
Baroni, M., Cruciani, G., Sciabola, S., Perruccio, F., & Mason, J. S. (2007) · Journal of Chemical Information and Modeling · doi:10.1021/ci600253e · Cited by 451
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Self-citationStructure Determination of Membrane Proteins by NMR Spectroscopy
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Nugent, T., & Jones, D. T. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-159 · Cited by 420
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Kleywegt, G. J., Harris, M. R., Zou, J.-Y., Taylor, T. C., Wählby, A., & Jones, T. A. (2004) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444904013253 · Cited by 360
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Valley, C. C., Cembran, A., Perlmutter, J. D., Lewis, A. K., Labello, N. P., Gao, J., & Sachs, J. N. (2012) · Journal of Biological Chemistry · doi:10.1074/jbc.m112.374504 · Cited by 350
Burley, S. K., Bhatt, R., Bhikadiya, C., Bi, C., Biester, A., Biswas, P., Bittrich, S., Blaumann, S., Brown, R., Chao, H., et al. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae1091 · Cited by 390
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Velankar, S. S., Best, C., Beuth, B., Boutselakis, C. H., Cobley, N., Silva, A. W. S. D., Dimitropoulos, D., Golovin, A., Hirshberg, M., John, M., et al. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp916 · Cited by 337
Self-citationGreenidge, P. A., Krämer, C., Mozziconacci, J., & Wolf, R. M. (2012) · Journal of Chemical Information and Modeling · doi:10.1021/ci300425v · Cited by 336
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Stierand, K., & Rarey, M. (2010) · ACS Medicinal Chemistry Letters · doi:10.1021/ml100164p · Cited by 313
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Classification of Current Scoring Functions
Liu, J., & Wang, R. (2015) · Journal of Chemical Information and Modeling · doi:10.1021/ci500731a · Cited by 311
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de Beer, T., Berka, K., Thornton, J. M., & Laskowski, R. A. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt940 · Cited by 300
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Studer, G., Tauriello, G., Bienert, S., Biasini, M., Johner, N. B., & Schwede, T. F. (2021) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1008667 · Cited by 305
Squires, R. B., Noronha, J. M., Hunt, V., García‐Sastre, A., Macken, C. A., Baumgarth, N., Suarez, D. L., Pickett, B. E., Zhang, Y., Larsen, C. N., et al. (2012) · Influenza and Other Respiratory Viruses · doi:10.1111/j.1750-2659.2011.00331.x · Cited by 297
Burley, S. K., Berman, H. M., Christie, C. H., Duarte, J. M., Feng, Z., Westbrook, J., Young, J. Y., & Zardecki, C. (2017) · Protein Science · doi:10.1002/pro.3331 · Cited by 296
Self-citationLerner, E., Barth, A., Hendrix, J., Ambrose, B., Birkedal, V., Blanchard, S. C., Börner, R., Chung, H. S., Cordes, T., Craggs, T. D., et al. (2021) · eLife · doi:10.7554/elife.60416 · Cited by 302
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Butt, S. S., Badshah, Y., Shabbir, M., & Rafiq, M. (2020) · JMIR Bioinformatics and Biotechnology · doi:10.2196/14232 · Cited by 287
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Akhmanova, A. S., & Steinmetz, M. O. (2010) · Journal of Cell Science · doi:10.1242/jcs.062414 · Cited by 299
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Fährrolfes, R., Bietz, S., Flachsenberg, F., Meyder, A., Nittinger, E., Otto, T., Volkamer, A., & Rarey, M. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx333 · Cited by 265
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Lawson, C. L., Baker, M. L., Best, C., Bi, C., Dougherty, M., Feng, P., van Ginkel, G., Devkota, B., Lagerstedt, I. C., Ludtke, S. J., et al. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq880 · Cited by 262
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Wang, S., Witek, J., Landrum, G. A., & Riniker, S. (2020) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.0c00025 · Cited by 286
Caffrey, M. (2014) · Acta Crystallographica Section F Structural Biology Communications · doi:10.1107/s2053230x14026843 · Cited by 261
Dana, J. M., Gutmanas, A., Tyagi, N., Qi, G., O’Donovan, C., Martin, M. J., & Velankar, S. S. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky1114 · Cited by 268
Functional classification of long non-coding RNAs by k-mer content
Kirk, J. M., Kim, S. O., Inoue, K., Smola, M. J., Lee, D. M., Schertzer, M. D., Wooten, J. S., Baker, A. R., Sprague, D., Collins, D. W., et al. (2018) · Nature Genetics · doi:10.1038/s41588-018-0207-8 · Cited by 261
Headd, J. J., Echols, N., Afonine, P. V., Grosse‐Kunstleve, R. W., Chen, V. B., Moriarty, N. W., Richardson, D. C., Richardson, J. S., & Adams, P. D. (2012) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444911047834 · Cited by 253
Automated and accurate deposition of structures solved by X-ray diffraction to the Protein Data Bank
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Self-citationPhaser.MRage : automated molecular replacement
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Rose, Y., Duarte, J. M., Lowe, R., Segura, J., Bi, C., Bhikadiya, C., Chen, L., Rose, A., Bittrich, S., Burley, S. K., et al. (2020) · Journal of Molecular Biology · doi:10.1016/j.jmb.2020.11.003 · Cited by 241
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The Nucleic Acid Database: new features and capabilities
Narayanan, B. C., Westbrook, J., Ghosh, S., Petrov, A. I., Sweeney, B., Zirbel, C. L., Leontis, N. B., & Berman, H. M. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt980 · Cited by 233
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Protein Bioinformatics Databases and Resources
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Best Practices for Alchemical Free Energy Calculations [Article v1.0].
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Metadata
- Authors
- Berman, H., Henrick, K., & Nakamura, H.
- Affiliations
- Institute for Protein Research, The University of Osaka (JP)
- Corresponding author
- Berman, Helen
- Venue
- Nature Structural & Molecular Biology
- Published
- 2003-12-01
- Volume
- 10
- Issue
- 12
- Pages
- 980-980
- ISSN
- 1545-9985 (ISSN-L)
- 1545-9993
- OpenAlex
- W1995808589
- Cited by
- 3,093
- References
- 4
- Citations by year
- 2026: 155 · 2025: 212 · 2024: 266 · 2023: 274 · 2022: 238 · 2021: 240 · 2020: 208 · 2019: 217 · 2018: 141 · 2017: 138 · 2016: 125 · 2015: 89 · 2014: 93 · 2013: 105 · 2012: 103
- FWCI
- 11.50
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Nature Structural & Molecular Biology (publishedVersion)
- PubMed (publishedVersion)
- Rutgers University Community Repository (Rutgers University) (submittedVersion)
- Funders
- National Science Foundation
- U.S. Department of Energy
- Wellcome Trust
- European Molecular Biology Laboratory
- European Commission
- Japan Science and Technology Corporation
- Ministry of Education, Culture, Sports, Science and Technology
- National Institutes of Health
- Directorate for Biological Sciences
- Medical Research Council
- Biotechnology and Biological Sciences Research Council
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
- Physical Sciences › Computer Science › Information Systems › Research Data Management Practices
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Keywords
- wwPDB, structural biology, data repositories, data curation
- MeSH terms
- Archives, International Agencies, Computational Biology, Databases, Protein
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
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