Announcing the worldwide Protein Data Bank
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For certain types of important digital objects, there are well-curated, deeply-integrated, special-purpose repositories such as Genbank, wwPDB, UniProt, SPDF, and SIMBAD.
“For certain types of important digital objects, there are well-curated, deeply-integrated, special-purpose repositories such as Genbank3, Worldwide Protein Data Bank (wwPDB4), and UniProt5 in the life sciences; Space Physics Data Facility (SPDF; http://spdf.gsfc.nasa.gov/) and Set of Identifications, Measurements and Bibliography for Astronomical Data (SIMBAD6) in the space sciences.”
From The FAIR Guiding Principles for scientific data management and stewardship (2016) · cites this paper as [4]
The VirB8-like protein-minibinder complex structure quality was assessed using MolProbity before deposition in the PDB.
“Structure quality was assessed using Molprobity56 before deposition in the PDB82,83”
From Design of protein-binding proteins from the target structure alone (2022) · cites this paper as [83]
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Berman, H. M. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.235 · Cited by 40,196 · see citing works
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 8,582 · see citing works
[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 · see citing works
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VESTA 3 for three-dimensional visualization of crystal, volumetric and morphology data
Momma, K., & Izumi, F. (2011) · Journal of Applied Crystallography · doi:10.1107/s0021889811038970 · Cited by 26,123 · see citing works
The FAIR Guiding Principles for scientific data management and stewardship
Wilkinson, M. D., Dumontier, M., Aalbersberg, I. J., Appleton, G., Axton, M., Baak, A., Blomberg, N., Boiten, J.-W., da Silva Santos, L. B., Bourne, P. E., et al. (2016) · Scientific Data · doi:10.1038/sdata.2016.18 · Cited by 18,423 · see citing works
UCSF ChimeraX : Structure visualization for researchers, educators, and developers
Pettersen, E. F., Goddard, T. D., Huang, C. C., Meng, E. C., Couch, G. S., Croll, T. I., Morris, J. H., & Ferrin, T. E. (2020) · Protein Science · doi:10.1002/pro.3943 · Cited by 9,327 · see citing works
Pfam: The protein families database in 2021
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 · see citing works
UCSF ChimeraX: Meeting modern challenges in visualization and analysis
Goddard, T. D., Huang, C. C., Meng, E. C., Pettersen, E. F., Couch, G. S., Morris, J. H., & Ferrin, T. E. (2018) · Protein Science · doi:10.1002/pro.3235 · Cited by 5,267 · see citing works
The Pfam protein families database in 2019
El-Gebali, S., Mistry, J., Bateman, A., Eddy, S. R., Luciani, A., Potter, S. C., Qureshi, M., Richardson, L. J., Salazar, G. A., Smart, A., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gky995 · Cited by 4,602 · see citing works
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 4,472 · see citing works
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 · see citing works
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 · see citing works
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 · see citing works
Improved Docking of Polypeptides with Glide
Tubert-Brohman, I., Sherman, W., Repasky, M., & Beuming, T. (2013) · Journal of Chemical Information and Modeling · doi:10.1021/ci400128m · Cited by 1,308 · see citing works
A series of PDB related databases for everyday needs
Joosten, R., Beek, T. T. T., Krieger, E., Hekkelman, M., Hooft, R., Schneider, R., Sander, C., & Vriend, G. (2010) · Nucleic Acids Res. · doi:10.1093/nar/gkq1105 · Cited by 1,050 · see citing works
Protein Data Bank: the single global archive for 3D macromolecular structure data
wwPDB consortium, Burley, S. K., Berman, H. M., Bhikadiya, C., Bi, C., Chen, L., Costanzo, L. D., Christie, C., Duarte, J. M., Dutta, S., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gky949 · Cited by 1,163 · see citing works
Self-citationUltrasensitive detection and characterization of biomolecules using superchiral fields
Hendry, E., Carpy, T., Johnston, J., Popland, M., Mikhaylovskiy, R. V., Lapthorn, A. J., Kelly, S. M., Barron, L. D., Gadegaard, N., & Kadodwala, M. (2010) · Nature Nanotechnology · doi:10.1038/nnano.2010.209 · Cited by 1,260 · see citing works
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 1,249 · see citing works
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. S. (2017) · Methods in molecular biology · doi:10.1007/978-1-4939-7000-1_26 · Cited by 1,192 · see citing works
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 1,162 · see citing works
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 · see citing works
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 936 · see citing works
Elfiky, A. A. (2020) · Life Sciences · doi:10.1016/j.lfs.2020.117592 · Cited by 929 · see citing works
Burley, S. K., Bhikadiya, C., Bi, C., Bittrich, S., Chao, H., Chen, L., Craig, P., Crichlow, G. V., Dalenberg, K., Duarte, J. M., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac1077 · Cited by 903 · see citing works
Perspective: Coarse-grained models for biomolecular systems
Noid, W. G. (2013) · The Journal of Chemical Physics · doi:10.1063/1.4818908 · Cited by 884 · see citing works
CDD: conserved domains and protein three-dimensional structure
Marchler‐Bauer, A., Zheng, C., Chitsaz, F., Derbyshire, M. K., Geer, L. Y., Geer, R. C., Gonzales, N. R., Gwadz, M., Hurwitz, D. I., Lanczycki, C. J., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1243 · Cited by 872 · see citing works
Data‐Driven Materials Science: Status, Challenges, and Perspectives
Himanen, L., Geurts, A., Foster, A. S., & Rinke, P. (2019) · Advanced Science · doi:10.1002/advs.201900808 · Cited by 808 · see citing works
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 · see citing works
Self-citationStructural Biology in the Clouds: The WeNMR-EOSC Ecosystem
Honorato, R. V., Koukos, P. I., Jiménez‐García, B., Tsaregorodtsev, A., Verlato, M., Giachetti, A., Rosato, A., & Bonvin, A. M. J. J. (2021) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2021.729513 · Cited by 36 · see citing works
Uniclust databases of clustered and deeply annotated protein sequences and alignments
Mirdita, M., von den Driesch, L., Galiez, C., Martin, M. J., Söding, J., & Steinegger, M. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw1081 · Cited by 710 · see citing works
Anti-HCV, nucleotide inhibitors, repurposing against COVID-19
Elfiky, A. A. (2020) · Life Sciences · doi:10.1016/j.lfs.2020.117477 · Cited by 719 · see citing works
ViPR: an open bioinformatics database and analysis resource for virology research
Pickett, B. E., Sadat, E. L., Zhang, Y., Noronha, J. M., Squires, R. B., Hunt, V., Liu, M., Kumar, S., Zaremba, S., Gu, Z., et al. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr859 · Cited by 677 · see citing works
Coumarin: A Natural, Privileged and Versatile Scaffold for Bioactive Compounds
Stefanachi, A., Leonetti, F., Pisani, L., Catto, M., & Carotti, A. (2018) · Molecules · doi:10.3390/molecules23020250 · Cited by 679 · see citing works
The RCSB Protein Data Bank: redesigned web site and web services
Rose, P. W., Beran, B., Bi, C., Bluhm, W. F., Dimitropoulos, D., Goodsell, D. S., Prlić, A., Quesada, M., Quinn, G. B., Westbrook, J., et al. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq1021 · Cited by 659 · see citing works
Self-citationZhang, C., Freddolino, L., & Zhang, Y. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx366 · Cited by 606 · see citing works
PDB-wide collection of binding data: current status of the PDBbind database
Liu, Z., Li, Y., Han, L., Li, J., Liu, J., Zhao, Z., Nie, W., Liu, Y., & Wang, R. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu626 · Cited by 650 · see citing works
Computational philosophy of science
Thagard, P. R. (1989) · Choice Reviews Online · doi:10.5860/choice.26-2691 · Cited by 640 · see citing works
CREBBP mutations in relapsed acute lymphoblastic leukaemia
Mullighan, C. G., Zhang, J., Kasper, L. H., Lerach, S., Payne-Turner, D., Phillips, L. A., Heatley, S. L., Holmfeldt, L., Collins-Underwood, J. R., Ma, J., et al. (2011) · Nature · doi:10.1038/nature09727 · Cited by 628 · see citing works
Intrinsically disordered proteins: a 10-year recap
Tompa, P. (2012) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2012.08.004 · Cited by 624 · see citing works
Visualization of omics data for systems biology
Gehlenborg, N., O’Donoghue, S. I., Baliga, N. S., Goesmann, A., Hibbs, M., Kitano, H., Kohlbacher, O., Neuweger, H., Schneider, R., Tenenbaum, D., et al. (2010) · Nature Methods · doi:10.1038/nmeth.1436 · Cited by 622 · see citing works
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 · see citing works
YASARA: A Tool to Obtain Structural Guidance in Biocatalytic Investigations
Land, H., & Humble, M. S. (2017) · Methods in molecular biology · doi:10.1007/978-1-4939-7366-8_4 · Cited by 614 · see citing works
Laskowski, R. A. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn860 · Cited by 594 · see citing works
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 584 · see citing works
InterPro, progress and status in 2005
Mulder, N. (2004) · Nucleic Acids Research · doi:10.1093/nar/gki106 · Cited by 546 · see citing works
Cyclic GMP–AMP signalling protects bacteria against viral infection
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 537 · see citing works
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 523 · see citing works
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 · see citing works
The RCSB PDB information portal for structural genomics
Kouranov, A. (2005) · Nucleic Acids Research · doi:10.1093/nar/gkj120 · Cited by 523 · see citing works
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 · see citing works
Self-citationCOVID-19 spike-host cell receptor GRP78 binding site prediction
Ibrahim, I. M., Abdelmalek, D. H., El-Shahat, M., & Elfiky, A. A. (2020) · Journal of Infection · doi:10.1016/j.jinf.2020.02.026 · Cited by 509 · see citing works
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 · see citing works
Biomolecule Analysis by Ion Mobility Spectrometry
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 493 · see citing works
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 · see citing works
Proteome organization in a genome-reduced bacterium
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 · see citing works
A New Generation of Crystallographic Validation Tools for the Protein Data Bank
Read, R. J., Adams, P. D., Arendall, W. B., Brünger, A. T., Emsley, P., Joosten, R. P., Kleywegt, G. J., Krissinel, E., Lütteke, T., Otwinowski, Z., et al. (2011) · Structure · doi:10.1016/j.str.2011.08.006 · Cited by 468 · see citing works
Contribution of Hydrophobic Interactions to Protein Stability
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 · see citing works
Baroni, M., Cruciani, G., Sciabola, S., Perruccio, F., & Mason, J. S. (2007) · Journal of Chemical Information and Modeling · doi:10.1021/ci600253e · Cited by 442 · see citing works
The Protein Data Bank: a historical perspective
Berman, H. M. (2007) · Acta Crystallographica Section A Foundations of Crystallography · doi:10.1107/s0108767307035623 · Cited by 430 · see citing works
Self-citationStructure Determination of Membrane Proteins by NMR Spectroscopy
Opella, S. J., & Marassi, F. M. (2004) · Chemical Reviews · doi:10.1021/cr0304121 · Cited by 425 · see citing works
Transmembrane protein topology prediction using support vector machines
Nugent, T., & Jones, D. T. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-159 · Cited by 420 · see citing works
Validation of the Crystallography Open Database using the Crystallographic Information Framework
Vaitkus, A., Merkys, A., & Gražulis, S. (2021) · Journal of Applied Crystallography · doi:10.1107/s1600576720016532 · Cited by 373 · see citing works
Homology modeling in drug discovery: Overview, current applications, and future perspectives
Muhammed, M. T., & Aki, E. (2018) · Chemical Biology & Drug Design · doi:10.1111/cbdd.13388 · Cited by 367 · see citing works
The Uppsala Electron-Density Server
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 359 · see citing works
The Methionine-aromatic Motif Plays a Unique Role in Stabilizing Protein Structure
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 · see citing works
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 342 · see citing works
PDBe: Protein Data Bank in Europe
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 · see citing works
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 · see citing works
Lytic xylan oxidases from wood-decay fungi unlock biomass degradation.
Couturier, M., Ladevèze, S., Sulzenbacher, G., Ciano, L., Fanuel, M., Moreau, C., Villares, A., Cathala, B., Chaspoul, F., Frandsen, K. E. H., et al. (2018) · Nature Chemical Biology · doi:10.1038/nchembio.2558 · Cited by 294 · see citing works
Drawing the PDB: Protein−Ligand Complexes in Two Dimensions
Stierand, K., & Rarey, M. (2010) · ACS Medicinal Chemistry Letters · doi:10.1021/ml100164p · Cited by 313 · see citing works
Gerasimavicius, L., Livesey, B., & Marsh, J. A. (2022) · Nature Communications · doi:10.1038/s41467-022-31686-6 · Cited by 310 · see citing works
Classification of Current Scoring Functions
Liu, J., & Wang, R. (2015) · Journal of Chemical Information and Modeling · doi:10.1021/ci500731a · Cited by 302 · see citing works
Bringing Molecular Dynamics Simulation Data into View
Hildebrand, P. W., Rose, A., & Tiemann, J. K. S. (2019) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2019.06.004 · Cited by 303 · see citing works
de Beer, T., Berka, K., Thornton, J. M., & Laskowski, R. A. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt940 · Cited by 300 · see citing works
ProMod3—A versatile homology modelling toolbox
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 300 · see citing works
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 · see citing works
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 · see citing works
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 297 · see citing works
Molecular Docking Using Chimera and Autodock Vina Software for Nonbioinformaticians
Butt, S. S., Badshah, Y., Shabbir, M., & Rafiq, M. (2020) · JMIR Bioinformatics and Biotechnology · doi:10.2196/14232 · Cited by 287 · see citing works
A Million Crystal Structures: The Whole Is Greater than the Sum of Its Parts
Taylor, R., & Wood, P. A. (2019) · Chemical Reviews · doi:10.1021/acs.chemrev.9b00155 · Cited by 280 · see citing works
Validation of Structures in the Protein Data Bank
Gore, S., Sanz-García, E., Hendrickx, P., Gutmanas, A., Westbrook, J., Yang, H.-W., Feng, Z.-K., Baskaran, K., Berrisford, J., Hudson, B., et al. (2017) · Structure · doi:10.1016/j.str.2017.10.009 · Cited by 245 · see citing works
Self-citationSIFTS: Structure Integration with Function, Taxonomy and Sequences resource
Velankar, S. S., Dana, J. M., Jacobsen, J. O. B., van Ginkel, G., Gane, P. J., Luo, J., Oldfield, T. J., O’Donovan, C., Martin, M. J., & Kleywegt, G. J. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1258 · Cited by 277 · see citing works
Akhmanova, A. S., & Steinmetz, M. O. (2010) · Journal of Cell Science · doi:10.1242/jcs.062414 · Cited by 272 · see citing works
Protein X-ray Crystallography and Drug Discovery
Maveyraud, L., & Mourey, L. (2020) · Molecules · doi:10.3390/molecules25051030 · Cited by 271 · see citing works
ProteinsPlus: a web portal for structure analysis of macromolecules
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 · see citing works
EMDataBank.org: unified data resource for CryoEM
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 263 · see citing works
Self-citationUpdate of human and mouse forkhead box (FOX) gene families
Jackson, B. C., Carpenter, C. F., Nebert, D. W., & Vasiliou, V. (2010) · Human Genomics · doi:10.1186/1479-7364-4-5-345 · Cited by 261 · see citing works
Wang, S., Witek, J., Landrum, G. A., & Riniker, S. (2020) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.0c00025 · Cited by 261 · see citing works
Caffrey, M. (2014) · Acta Crystallographica Section F Structural Biology Communications · doi:10.1107/s2053230x14026843 · Cited by 260 · see citing works
Dana, J., Gutmanas, A., Tyagi, N., Qi, G., O'Donovan, C., Martin, M., & Velankar, S. (2018) · Nucleic Acids Res. · doi:10.1093/nar/gky1114 · Cited by 258 · see citing works
Functional classification of long non-coding RNAs by kmer content
Kirk, J. M., Kim, S. O., Inoue, K., Smola, M. J., Lee, D. M., Schertzer, M. D., Wooten, J., Baker, A., Sprague, D., Collins, D. W., et al. (2018) · Nature Genetics · doi:10.1038/s41588-018-0207-8 · Cited by 204 · see citing works
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 255 · see citing works
Automated and accurate deposition of structures solved by X-ray diffraction to the Protein Data Bank
Yang, H., Guranović, V., Dutta, S., Feng, Z., Berman, H. M., & Westbrook, J. (2004) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444904019419 · Cited by 252 · see citing works
Self-citationPhaser.MRage : automated molecular replacement
Bunkòczi, G., Echols, N., McCoy, A. J., Oeffner, R. D., Adams, P. D., & Read, R. J. (2013) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444913022750 · Cited by 247 · see citing works
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 · see citing works
PDB_REDO: automated re-refinement of X-ray structure models in the PDB
Joosten, R. P., Salzemann, J., Bloch, V., Heinz Stockinger, C., Berglund, A.-C., Blanchet, C., Bongcam‐Rudloff, E., Combet, C., da Costa, A. L., Deléage, G., et al. (2009) · Journal of Applied Crystallography · doi:10.1107/s0021889809008784 · Cited by 237 · see citing works
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 · see citing works
Self-citationStructural snapshots of TRPV1 reveal mechanism of polymodal functionality
Zhang, K., Julius, D. J., & Cheng, Y. (2021) · Cell · doi:10.1016/j.cell.2021.08.012 · Cited by 230 · see citing works
Protein Bioinformatics Databases and Resources
Chen, C., Huang, H., & Wu, C. H. (2017) · Methods in molecular biology · doi:10.1007/978-1-4939-6783-4_1 · Cited by 224 · see citing works
Best Practices for Alchemical Free Energy Calculations [Article v1.0].
Mey, A. S. J. S., Allen, B. K., Macdonald, H. E. B., Chodera, J. D., Hahn, D. F., Kuhn, M., Michel, J., Mobley, D. L., Naden, L. N., Prasad, S., et al. (2020) · eScholarship (California Digital Library) · Cited by 217 · see citing works
Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics
Maximova, T., Moffatt, R., Ma, B., Nussinov, R., & Shehu, A. (2016) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1004619 · Cited by 211 · see citing works
Metabolomics: small molecules that matter more
Muthubharathi, B. C., Gowripriya, T., & Balamurugan, K. (2021) · Molecular Omics · doi:10.1039/d0mo00176g · Cited by 214 · see citing works
PDB_REDO: constructive validation, more than just looking for errors
Joosten, R. P., Joosten, K., Murshudov, G. N., & Anastassis Perrakis, A. (2012) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444911054515 · Cited by 213 · see citing works
- 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
- Physical Sciences › Materials Science › Materials Chemistry › 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.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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