Announcing the worldwide Protein Data Bank

The Protein Data Bank

Berman, H. M. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.235 · Cited by 40,196

The 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

In Vivo Neuropharmacological Effects of Neophytadiene

González-Rivera, M. L., Barragán‐Gálvez, J. C., Gasca‐Martínez, D., Hidalgo‐Figueroa, S., Isiordia‐Espinoza, M. A., & Alonso‐Castro, Á. J. (2023) · Molecules · doi:10.3390/molecules28083457 · Cited by 111

Evolutionary rates vary among rRNA structural elements

Smit, S., Widmann, J. J., & Knight, R. D. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm101 · Cited by 118

TMbed: transmembrane proteins predicted through language model embeddings

Bernhofer, M., & Rost, B. (2022) · BMC Bioinformatics · doi:10.1186/s12859-022-04873-x · Cited by 109

I-TASSER gateway: A protein structure and function prediction server powered by XSEDE

Zheng, W. H., Zhang, C., Bell, E. W., & Zhang, Y. (2019) · Future Generation Computer Systems · doi:10.1016/j.future.2019.04.011 · Cited by 108

Functional and Evolutionary Analysis of the CASPARIAN STRIP MEMBRANE DOMAIN PROTEIN Family

Roppolo, D., Boeckmann, B., Pfister, A., Boutet, E., Rubio, M. C., Tendon, V. D., Vermeer, J. E. M., Gheyselinck, J., Xénarios, I., & Geldner, N. (2014) · PLANT PHYSIOLOGY · doi:10.1104/pp.114.239137 · Cited by 108

Structural basis for the design of selective phosphodiesterase 4B inhibitors

Fox, D. N. A., Burgin, A. B., & Gurney, M. E. (2013) · Cellular Signalling · doi:10.1016/j.cellsig.2013.12.003 · Cited by 109

CING: an integrated residue-based structure validation program suite

Doreleijers, J. F., da Silva, A. S., Krieger, E., Nabuurs, S. B., Spronk, C. A. E. M., Stevens, T. J., Vranken, W., Vriend, G., & Vuister, G. W. (2012) · Journal of Biomolecular NMR · doi:10.1007/s10858-012-9669-7 · Cited by 107

Evaluation and ranking of enzyme designs

Kiss, G., Röthlisberger, D., Baker, D. A., & Houk, K. N. (2010) · Protein Science · doi:10.1002/pro.462 · Cited by 107

The protein structure initiative structural genomics knowledgebase

Berman, H. M., Westbrook, J., Gabanyi, M. J., Tao, W., Shah, R., Kouranov, A., Schwede, T. F., Arnold, K., Kiefer, F., Bordoli, L., et al. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn790 · Cited by 107

xiView: A common platform for the downstream analysis of Crosslinking Mass Spectrometry dataPreprint

Graham, M., Combe, C., Kolbowski, L., & Rappsilber, J. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/561829 · Cited by 97

Structural Insight into the Heme-based Redox Sensing by DosS from Mycobacterium tuberculosis

Cho, H. Y., Cho, H. J., Kim, Y., Oh, J. I., & Kang, B. S. (2009) · Journal of Biological Chemistry · doi:10.1074/jbc.m808905200 · Cited by 106

AquaSAXS: a web server for computation and fitting of SAXS profiles with non-uniformally hydrated atomic models

Poitevin, F., Orland, H., Doniach, S., Koehl, P., & Delarue, M. H. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr430 · Cited by 105

Residue-Specific Force Field Based on the Protein Coil Library. RSFF1: Modification of OPLS-AA/L

Jiang, F., Zhou, C., & Wu, Y. (2014) · The Journal of Physical Chemistry B · doi:10.1021/jp5017449 · Cited by 106

Thiol–Disulfide Exchange Reactions in the Mammalian Extracellular Environment

Yi, M. C., & Khosla, C. (2016) · Annual Review of Chemical and Biomolecular Engineering · doi:10.1146/annurev-chembioeng-080615-033553 · Cited by 104

The Protein Data Bank (PDB), Its Related Services and Software Tools as Key Components for In Silico Guided Drug Discovery

Kirchmair, J., Markt, P., Distinto, S., Schuster, D., Spitzer, G. M., Liedl, K. R., Langer, T., & Wolber, G. (2008) · Journal of Medicinal Chemistry · doi:10.1021/jm8005977 · Cited by 105

Tomatidine and Patchouli Alcohol as Inhibitors of SARS-CoV-2 Enzymes (3CLpro, PLpro and NSP15) by Molecular Docking and Molecular Dynamics Simulations

Zrieq, R. M., Ahmad, I., Snoussi, M., Noumi, E., Iriti, M., Algahtani, F. D., Patel, H., Saeed, M., Tasleem, M., Sulaiman, S., et al. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms221910693 · Cited by 103

The RCSB PDB “Molecule of the Month”: Inspiring a Molecular View of Biology

Goodsell, D. S., Dutta, S., Zardecki, C., Voigt, M., Berman, H. M., & Burley, S. K. (2015) · PLoS Biology · doi:10.1371/journal.pbio.1002140 · Cited by 109

Models of protein–ligand crystal structures: trust, but verify

Deller, M. C., & Rupp, B. (2015) · Journal of Computer-Aided Molecular Design · doi:10.1007/s10822-015-9833-8 · Cited by 103

The European Bioinformatics Institute's data resources: towards systems biology

Brooksbank, C. (2004) · Nucleic Acids Research · doi:10.1093/nar/gki026 · Cited by 103

Multiepitope-Based Subunit Vaccine Design and Evaluation against Respiratory Syncytial Virus Using Reverse Vaccinology Approach

Qamar, M. T. U., Shokat, Z., Muneer, I., Ashfaq, U. A., Javed, H., Anwar, F., Bari, A., Zahid, B., & Saari, N. (2020) · Vaccines · doi:10.3390/vaccines8020288 · Cited by 100

Combining structure and dynamics: non-denaturing high-pressure effect on lysozyme in solution

Ortore, M. G., Spinozzi, F., Mariani, P., Paciaroni, A., Barbosa, L. R. S., Amenitsch, H. W., Steinhart, M., Ollivier, J., & Russo, D. (2009) · Journal of The Royal Society Interface · doi:10.1098/rsif.2009.0163.focus · Cited by 102

The Origin of CDR H3 Structural Diversity

Weitzner, B. D., Dunbrack, R. L., & Gray, J. J. (2015) · Structure · doi:10.1016/j.str.2014.11.010 · Cited by 109

Using Intrinsic X-ray Absorption Spectral Differences To Identify and Map Peptides and Proteins

Stewart-Ornstein, J., Hitchcock, A. P., Hernández‐Cruz, D., Henklein, P., Overhage, J., Hilpert, K., Hale, J. D. F., & Hancock, R. E. W. (2007) · The Journal of Physical Chemistry B · doi:10.1021/jp0720993 · Cited by 101

Hydration Water and Bulk Water in Proteins Have Distinct Properties in Radial Distributions Calculated from 105 Atomic Resolution Crystal Structures

Chen, X., Weber, I. T., & Harrison, R. W. (2008) · The Journal of Physical Chemistry B · doi:10.1021/jp802795a · Cited by 101

Nonlinear finite-element analysis of nanoindentation of viral capsids

Gibbons, M. M., & Klug, W. S. (2007) · Physical Review E · doi:10.1103/physreve.75.031901 · Cited by 100

Defining the subcellular distribution and metabolic channeling of phosphatidylinositol

Pemberton, J. G., Kim, Y. J., Humpolíčková, J., Eisenreichová, A., Sengupta, N., Tóth, D. J., Bouřa, E., & Balla, T. (2019) · The Journal of Cell Biology · doi:10.1083/jcb.201906130 · Cited by 97

Sterol binding by OSBP-related protein 1L regulates late endosome motility and function

Vihervaara, T., Uronen, R., Wohlfahrt, G., Björkhem, I., Ikonen, E., & Olkkonen, V. M. (2010) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-010-0470-z · Cited by 99

The Strawberry Pathogenesis-related 10 (PR-10) Fra a Proteins Control Flavonoid Biosynthesis by Binding to Metabolic Intermediates

Casañal, A., Zander, U., Muñoz, C., Dupeux, F., Luque, I., Botella, M. A., Schwab, W. G., Valpuesta, V., & Márquez, J. A. (2013) · Journal of Biological Chemistry · doi:10.1074/jbc.m113.501528 · Cited by 103

The challenge of modeling protein assemblies: the CASP12‐CAPRI experiment

Lensink, M. F., Velankar, S. S., Baek, M., Heo, L., Seok, C., & Wodak, S. J. (2017) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.25419 · Cited by 97

Advances, Interactions, and Future Developments in the CNS, Phenix, and Rosetta Structural Biology Software Systems

Adams, P. D., Baker, D. A., Brünger, A. T., Das, R., DiMaio, F., Read, R. J., Richardson, D. C., Richardson, J. S., & Terwilliger, T. C. (2013) · Annual Review of Biophysics · doi:10.1146/annurev-biophys-083012-130253 · Cited by 101

Mapping Protein Interactions between Dengue Virus and Its Human and Insect Hosts

Doolittle‐Hall, J., & Gomez, S. M. (2011) · PLoS neglected tropical diseases · doi:10.1371/journal.pntd.0000954 · Cited by 100

PharmGKB: Understanding the Effects of Individual Genetic Variants

Sangkuhl, K., Berlin, D. S., Altman, R. B., & Klein, T. E. (2008) · Drug Metabolism Reviews · doi:10.1080/03602530802413338 · Cited by 97

Predicting Polypharmacology by Binding Site Similarity: From Kinases to the Protein Universe

Milletti, F., & Vulpetti, A. (2010) · Journal of Chemical Information and Modeling · doi:10.1021/ci1001263 · Cited by 102

Data sharing in the sciences

Kowalczyk, S., & Shankar, K. (2011) · Annual Review of Information Science and Technology · doi:10.1002/aris.2011.1440450113 · Cited by 97

Blind prediction performance of RosettaAntibody 3.0: Grafting, relaxation, kinematic loop modeling, and full CDR optimization

Weitzner, B. D., Kuroda, D., Marze, N. A., Xu, J., & Gray, J. J. (2014) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24534 · Cited by 94

Structure‐based prediction of DNA‐binding sites on proteins Using the empirical preference of electrostatic potential and the shape of molecular surfaces

Tsuchiya, Y., Kinoshita, K., & Nakamura, H. (2004) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.20111 · Cited by 97

Current Assessment of Docking into GPCR Crystal Structures and Homology Models: Successes, Challenges, and Guidelines

Beuming, T., & Sherman, W. (2012) · Journal of Chemical Information and Modeling · doi:10.1021/ci300411b · Cited by 98

Reverse vaccinology assisted designing of multiepitope-based subunit vaccine against SARS-CoV-2

Qamar, M. T. U., Shahid, F., Aslam, S., Ashfaq, U. A., Aslam, S., Fatima, I., Fareed, M. M., Zohaib, A., & Chen, L. (2020) · Infectious Diseases of Poverty · doi:10.1186/s40249-020-00752-w · Cited by 98

Multicoil2: Predicting Coiled Coils and Their Oligomerization States from Sequence in the Twilight Zone

Trigg, J., Gutwin, K., Keating, A. E., & Berger, B. (2011) · PLoS One · doi:10.1371/journal.pone.0023519 · Cited by 91

Working Together Apart: Collaboration over the Internet

Olson, J. S., & Olson, G. M. (2014) · Synthesis Lectures on Human-Centered Informatics · doi:10.2200/s00542ed1v01y201310hci020 · Cited by 95

Anticancer Ruthenium(η6-p-cymene) Complexes of Nonsteroidal Anti-inflammatory Drug Derivatives

Aman, F., Hanif, M., Siddiqui, W. A., Ashraf, A., Filak, L. K., Reynisson, J., Söhnel, T., Jamieson, S. M. F., & Hartinger, C. G. (2014) · Organometallics · doi:10.1021/om500825h · Cited by 94

Lowering intercellular melatonin levels by transgenic analysis of indoleamine 2,3-dioxygenase from rice in tomato plants

Okazaki, M., Higuchi, K., Aouini, A., & Ezura, H. (2010) · Journal of Pineal Research · doi:10.1111/j.1600-079x.2010.00788.x · Cited by 94

Accurate Structural Correlations from Maximum Likelihood Superpositions

Theobald, D. L., & Wuttke, D. S. (2008) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0040043 · Cited by 94

OUP accepted manuscript

Flissi, A., Ricart, E., Campart, C., Chevalier, M., Dufresne, Y., Michálik, J., Jacques, P., Flahaut, C., Lisacek, F., Leclère, V., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz1000 · Cited by 93

Dirigent Protein Mode of Action Revealed by the Crystal Structure of AtDIR6

Gasper, R., Effenberger, I., Kolesiński, P., Terlecka, B., Hofmann, E., & Schaller, A. (2016) · PLANT PHYSIOLOGY · doi:10.1104/pp.16.01281 · Cited by 93

Design, Synthesis, and Anti-Inflammatory Activity of Some Coumarin Schiff Base Derivatives: In silico and in vitro Study

Hamid, S. J., & Salih, T. M. (2022) · Drug Design Development and Therapy · doi:10.2147/dddt.s364746 · Cited by 92

Establishing a conceptual framework for holistic cell states and state transitions

Rafelski, S. M., & Theriot, J. A. (2024) · Cell · doi:10.1016/j.cell.2024.04.035 · Cited by 96

Identification of the ligand binding sites on the molecular surface of proteins

Kinoshita, K., & Nakamura, H. (2005) · Protein Science · doi:10.1110/ps.041080105 · Cited by 92

Resolution ofab initioshapes determined from small-angle scattering

Tuukkanen, A. T., Kleywegt, G. J., & Svergun, D. I. (2016) · IUCrJ · doi:10.1107/s2052252516016018 · Cited by 91

Structural insights into the disruption of TNF-TNFR1 signalling by small molecules stabilising a distorted TNF

McMillan, D., Martinez-Fleites, C., Porter, J. R., Fox, D., Davis, R., Mori, P., Ceska, T., Carrington, B., Lawson, A. D. G., Bourne, T., et al. (2021) · Nature Communications · doi:10.1038/s41467-020-20828-3 · Cited by 91

Fusion protein strategies for cryo-EM study of G protein-coupled receptors

Zhang, K., Wu, H., Hoppe, N., Manglik, A., & Cheng, Y. (2022) · Nature Communications · doi:10.1038/s41467-022-32125-2 · Cited by 91

Structural basis for substrate recognition by Erwinia chrysanthemi GH30 glucuronoxylanase

Urbanikova, L., Vršanská, M., Krogh, K. B. R. M., Hoff, T., & Biely, P. (2011) · FEBS Journal · doi:10.1111/j.1742-4658.2011.08127.x · Cited by 91

Design, Synthesis, and Biological Evaluation of Imidazolyl Derivatives of 4,7-Disubstituted Coumarins as Aromatase Inhibitors Selective over 17-α-Hydroxylase/C17−20 Lyase

Stefanachi, A., Favia, A. D., Nicolotti, O., Leonetti, F., Pisani, L., Catto, M., Zimmer, C., Hartmann, R. W., & Carotti, A. (2011) · Journal of Medicinal Chemistry · doi:10.1021/jm101120u · Cited by 91

Issues in bioinformatics benchmarking: the case study of multiple sequence alignment

Aniba, M. R., Poch, O., & Thompson, J. D. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq625 · Cited by 72

Glyco3D: A Portal for Structural Glycosciences

Pérez, S., Sarkar, A., Rivet, A., Breton, C., & Imberty, A. (2015) · Methods in molecular biology · doi:10.1007/978-1-4939-2343-4_18 · Cited by 91

Synthesis and biological evaluation of novel tyrosyl-DNA phosphodiesterase 1 inhibitors with a benzopentathiepine moiety

Zakharenko, A. L., Khomenko, T. M., Zhukova, S., Koval, O. A., Zakharova, O. D., Anarbaev, R. O., Lebedeva, N., Викторовна, К. Д., Комарова, Н. И., Vasiliev, V. G., et al. (2015) · Bioorganic & Medicinal Chemistry · doi:10.1016/j.bmc.2015.03.020 · Cited by 90

Basin Hopping as a General and Versatile Optimization Framework for the Characterization of Biological Macromolecules

Olson, B., Hashmi, I., Molloy, K., & Shehu, A. (2012) · Advances in Artificial Intelligence · doi:10.1155/2012/674832 · Cited by 96

Deciphering Cryptic Binding Sites on Proteins by Mixed-Solvent Molecular Dynamics

Kimura, S. R., Hu, H. P., Ruvinsky, A. M., Sherman, W., & Favia, A. D. (2017) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.6b00623 · Cited by 90

The American lobster genome reveals insights on longevity, neural, and immune adaptations

Polinski, J. M., Zimin, A. V., Clark, K. F., Kohn, A. B., Sadowski, N., Timp, W., Ptitsyn, A. A., Khanna, P., Romanova, D. Y., Williams, P., et al. (2021) · Science Advances · doi:10.1126/sciadv.abe8290 · Cited by 93

Substituting random forest for multiple linear regression improves binding affinity prediction of scoring functions: Cyscore as a case study

Li, H., Leung, K., Wong, M., & Ballester, P. J. (2014) · BMC Bioinformatics · doi:10.1186/1471-2105-15-291 · Cited by 92

Structural Determinants of Isoform Selectivity in PI3K Inhibitors

Miller, M. S., Thompson, P. E., & Gabelli, S. B. (2019) · Biomolecules · doi:10.3390/biom9030082 · Cited by 89

The dimer-monomer equilibrium of SARS-CoV-2 main protease is affected by small molecule inhibitors

Silvestrini, L., Belhaj, N., Comez, L., Gerelli, Y., Lauria, A., Libera, V., Mariani, P., Marzullo, P., Ortore, M. G., Piccionello, A. P., et al. (2021) · Scientific Reports · doi:10.1038/s41598-021-88630-9 · Cited by 87

Public Domain Databases for Medicinal Chemistry

Nicola, G., Liu, T., & Gilson, M. K. (2012) · Journal of Medicinal Chemistry · doi:10.1021/jm300501t · Cited by 89

CASP9 Target Classification

Kinch, L. N., Shi, S.-Y., Cheng, H., Cong, Q., Pei, J.-M., Mariani, V., Schwede, T., & Grishin, N. V. (2011) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.23190 · Cited by 66

How Structural Biologists and the Protein Data Bank Contributed to Recent FDA New Drug Approvals

Westbrook, J., & Burley, S. K. (2018) · Structure · doi:10.1016/j.str.2018.11.007 · Cited by 90

Optimization of Acetazolamide-Based Scaffold as Potent Inhibitors of Vancomycin-Resistant Enterococcus

Kaur, J. P., Cao, X., Abutaleb, N. S., Elkashif, A., Graboski, A. L., Krabill, A. D., AbdelKhalek, A., An, W., Bhardwaj, A., Seleem, M. N., et al. (2020) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.0c00734 · Cited by 86

Structure-based design of prefusion-stabilized human metapneumovirus fusion proteins

Hsieh, C., Rush, S. A., Palomo, C., Chou, C., Pickens, W., Más, V., & McLellan, J. S. (2022) · Nature Communications · doi:10.1038/s41467-022-28931-3 · Cited by 85

Seeding the aggregation of TDP-43 requires post-fibrillization proteolytic cleavage

Kumar, S. T., Nazarov, S., Porta, S., Maharjan, N., Cendrowska, U., Kabani, M., Finamore, F., Xu, Y., Lee, V. M. ‐., & Lashuel, H. A. (2023) · Nature Neuroscience · doi:10.1038/s41593-023-01341-4 · Cited by 93

CREDO: A Protein–Ligand Interaction Database for Drug Discovery

Schreyer, A. M., & Blundell, T. L. (2009) · Chemical Biology & Drug Design · doi:10.1111/j.1747-0285.2008.00762.x · Cited by 88

Glutamine-linked and Non-consensus Asparagine-linked Oligosaccharides Present in Human Recombinant Antibodies Define Novel Protein Glycosylation Motifs

Valliere-Douglass, J. F., Eakin, C., Wallace, A., Ketchem, R. R., Wang, W., Treuheit, M., & Balland, A. (2010) · Journal of Biological Chemistry · doi:10.1074/jbc.m109.096412 · Cited by 87

Improving Docking Results via Reranking of Ensembles of Ligand Poses in Multiple X-ray Protein Conformations with MM-GBSA

Greenidge, P. A., Krämer, C., Mozziconacci, J., & Sherman, W. (2014) · Journal of Chemical Information and Modeling · doi:10.1021/ci5003735 · Cited by 90

Visualization of Biomedical Data

O’Donoghue, S. I., Baldi, B. F., Clark, S. J., Darling, A. E., Hogan, J. M., Kaur, S., Maier‐Hein, L., McCarthy, D. J., Moore, W. J., Stenau, E., et al. (2018) · Annual Review of Biomedical Data Science · doi:10.1146/annurev-biodatasci-080917-013424 · Cited by 92

PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology

Westbrook, J., Young, J. Y., Shao, C., Feng, Z., Guranović, V., Lawson, C. L., Vallat, B. K., Adams, P. D., Berrisford, J. M., Bricogne, G., et al. (2022) · Journal of Molecular Biology · doi:10.1016/j.jmb.2022.167599 · Cited by 91

Bioinformatics analysis of alternative splicing

Lee, C. J. (2005) · Briefings in Bioinformatics · doi:10.1093/bib/6.1.23 · Cited by 86

Current trends in protein crystallization

Gavira, J. A. (2015) · Archives of Biochemistry and Biophysics · doi:10.1016/j.abb.2015.12.010 · Cited by 87

Characterization of activating mutations of NOTCH3 in T-cell acute lymphoblastic leukemia and anti-leukemic activity of NOTCH3 inhibitory antibodies

Bernasconi-Elias, P., Hu, T., Jenkins, D., Firestone, B., Gans, S., Kurth, E., Capodieci, P., Deplazes-Lauber, J., Petropoulos, K., Thiel, P., et al. (2016) · Oncogene · doi:10.1038/onc.2016.133 · Cited by 87

Ligand−Protein Cross-Docking with Water Molecules

Thilagavathi, R., & Mancera, R. L. (2010) · Journal of Chemical Information and Modeling · doi:10.1021/ci900345h · Cited by 87

On the abundance of chiral crystals

Dryzun, C., & Avnir, D. (2012) · Chemical Communications · doi:10.1039/c2cc17727g · Cited by 86

Curcumin analogues as possible anti-proliferative & anti-inflammatory agents

Katsori, A., Chatzopoulou, M., Dimas, K., Kontogiorgis, C. A., Patsilinakos, A., Trangas, T. T., & Hadjipavlou‐Litina, D. (2011) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2011.03.060 · Cited by 86

Multiscale Simulations Reveal Conserved Patterns of Lipid Interactions with Aquaporins

Stansfeld, P. J., Jefferys, E. E., & Sansom, M. S. P. (2013) · Structure · doi:10.1016/j.str.2013.03.005 · Cited by 85

Germline-encoded amino acid–binding motifs drive immunodominant public antibody responses

Shrock, E. L., Timms, R. T., Kula, T., Mena, E. L., West, A. P., Guo, R., Lee, I., Cohen, A. A., McKay, L. G. A., Bi, C., et al. (2023) · Science · doi:10.1126/science.adc9498 · Cited by 88

Classifying the metal dependence of uncharacterized nitrogenases

McGlynn, S. E., Boyd, E. S., Peters, J. W., & Orphan, V. J. (2013) · Frontiers in Microbiology · doi:10.3389/fmicb.2012.00419 · Cited by 87

Structural similarity-based predictions of protein interactions between HIV-1 and Homo sapiens

Doolittle‐Hall, J., & Gomez, S. M. (2010) · Virology Journal · doi:10.1186/1743-422x-7-82 · Cited by 85

Tools for ligand validation inCoot

Emsley, P. (2017) · Acta Crystallographica Section D Structural Biology · doi:10.1107/s2059798317003382 · Cited by 85

Configurational Entropy in Protein–Peptide Binding:

Killian, B. J., Kravitz, J. Y., Somani, S., Dasgupta, P., Pang, Y., & Gilson, M. K. (2009) · Journal of Molecular Biology · doi:10.1016/j.jmb.2009.04.003 · Cited by 85

Materials and 3D Designs of Helix Nanostructures for Chirality at Optical Frequencies

Passaseo, A., Esposito, M., Cuscunà, M., & Tasco, V. (2017) · Advanced Optical Materials · doi:10.1002/adom.201601079 · Cited by 83

From integrative structural biology to cell biology

Šali, A. (2021) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2021.100743 · Cited by 84

Molecular dynamics simulation study of the binding of purine bases to the aptamer domain of the guanine sensing riboswitch

Villa, A., Wöhnert, J., & Stock, G. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp486 · Cited by 84

Prediction of function for the polyprenyl transferase subgroup in the isoprenoid synthase superfamily

Wallrapp, F. H., Pan, J.-J., Ramamoorthy, G., Almonacid, D. E., Hillerich, B., Seidel, R. D., III, Patskovsky, Y., Babbitt, P. C., Almo, S. C., Jacobson, M. P., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1300632110 · Cited by 84

Biosynthesis of the tunicamycin antibiotics proceeds via unique exo-glycal intermediates

Wyszyński, F. J., Lee, S. S., Yabe, T., Wang, H., Gomez‐Escribano, J. P., Bibb, M. J., Lee, S. J., Davies, G. J., & Davis, B. G. (2012) · Nature Chemistry · doi:10.1038/nchem.1351 · Cited by 84

PDBe: towards reusable data delivery infrastructure at protein data bank in Europe

Mir, S., Alhroub, Y., Anyango, S., Armstrong, D. R., Berrisford, J. M., Clark, A. R., Conroy, M. J., Dana, J. M., Deshpande, M., Gupta, D. S., et al. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx1070 · Cited by 84

Structure and evolution of the Fam20 kinases

Zhang, H., Zhu, Q., Cui, J., Wang, Y., Chen, J., Guo, X., Tagliabracci, V. S., Dixon, J. E., & Xiao, J. (2018) · Nature Communications · doi:10.1038/s41467-018-03615-z · Cited by 84

Public Chemical Compound Databases

Williams, A. J. (2013) · PubMed · doi:10.6084/m9.figshare.654769 · Cited by 83

Generating stereochemically acceptable protein pathways

Farrell, D., Speranskiy, K., & Thorpe, M. F. (2010) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.22810 · Cited by 82

BindingDB and ChEMBL: online compound databases for drug discovery

Wassermann, A. M., & Bajorath, J. (2011) · Expert Opinion on Drug Discovery · doi:10.1517/17460441.2011.579100 · Cited by 84

Trendspotting in the Protein Data Bank

Berman, H. M., Narayanan, B. C., Costanzo, L. D., Dutta, S., Ghosh, S., Hudson, B. P., Lawson, C. L., Peisach, E., Prlić, A., Rose, P. W., et al. (2013) · FEBS Letters · doi:10.1016/j.febslet.2012.12.029 · Cited by 83

CCP 4 Cloud for structure determination and project management in macromolecular crystallography

Krissinel, E., Lebedev, A. A., Uski, V., Ballard, C. B., Keegan, R. M., Kovalevskiy, O. V., Nicholls, R. A., Pannu, N. S., Skubák, P., Berrisford, J. M., et al. (2022) · Acta Crystallographica Section D Structural Biology · doi:10.1107/s2059798322007987 · Cited by 82

Report of the wwPDB Small-Angle Scattering Task Force: Data Requirements for Biomolecular Modeling and the PDB

Trewhella, J., Hendrickson, W. A., Kleywegt, G. J., Šali, A., Sato, M., Schwede, T. F., Svergun, D. I., Tainer, J. A., Westbrook, J., & Berman, H. M. (2013) · Structure · doi:10.1016/j.str.2013.04.020 · Cited by 82

Cryo-EM structure of the native rhodopsin dimer in nanodiscs

Zhao, D. Y., Pöge, M., Morizumi, T., Gulati, S., Eps, N. V., Zhang, J., Miszta, P., Filipek, S., Mahamid, J., Plitzko, J. M., et al. (2019) · Journal of Biological Chemistry · doi:10.1074/jbc.ra119.010089 · Cited by 86

Gene3D: comprehensive structural and functional annotation of genomes

Yeats, C., Lees, J. G., Reid, A. J., Kellam, P., Martin, N., Liu, X., & Orengo, C. A. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm1019 · Cited by 81

The Worldwide Protein Data Bank

Berman, H. M., Henrick, K., Kleywegt, G. J., Nakamura, H., & Markley, J. L. (2012) · International Tables for Crystallography · doi:10.1107/97809553602060000896 · Cited by 29

The future of the protein data bank

Berman, H. M., Kleywegt, G. J., Nakamura, H., & Markley, J. L. (2012) · Biopolymers · doi:10.1002/bip.22132 · Cited by 80

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

Protein 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

Abstract 2370 RCSB Protein Data Bank: Updated resources and new developments driving research and education in the biosciences

Zardecki, C., Duarte, J. M., Raymond, D., Rose, Y., Young, J. Y., & Burley, S. K. (2026) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2026.112700 · Cited by 1