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

Unraveling the functional dark matter through global metagenomics

Pavlopoulos, G. A., Baltoumas, F. A., Liu, S., Selvitopi, O., Camargo, A. P., Nayfach, S., Azad, A., Roux, S., Call, L., Ivanova, N., et al. (2023) · Nature · doi:10.1038/s41586-023-06583-7 · Cited by 239

Deep Dive into Machine Learning Models for Protein Engineering

Xu, Y., Verma, D., Sheridan, R. P., Liaw, A. I., Ma, J., Marshall, N., McIntosh, J. A., Sherer, E. C., Svetnik, V., & Johnston, J. M. (2020) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.0c00073 · Cited by 210

AI revolutions in biology: The joys and perils of AlphaFold

Perrakis, A., & Sixma, T. K. (2021) · The EMBO Reports · doi:10.15252/embr.202154046 · Cited by 190

Mutations in FRMD7, a newly identified member of the FERM family, cause X-linked idiopathic congenital nystagmus

Tarpey, P. S., Thomas, S., Sarvananthan, N., Mallya, U., Lisgo, S., Talbot, C. J., Roberts, E. O., Awan, M., Surendran, M., McLean, R. J., et al. (2006) · Nature Genetics · doi:10.1038/ng1893 · Cited by 203

RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D

Burley, S. K., Bhikadiya, C., Bi, C., Bittrich, S., Chen, L., Crichlow, G. V., Duarte, J. M., Dutta, S., Fayazi, M., Feng, Z., et al. (2021) · Protein Science · doi:10.1002/pro.4213 · Cited by 210

EMPIAR: the Electron Microscopy Public Image Archive

Iudin, A., Korir, P. K., Somasundharam, S., Weyand, S. N., Cattavitello, C., Fonseca, N., Salih, O., Kleywegt, G. J., & Patwardhan, A. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac1062 · Cited by 202

Bridging structural and cell biology with cryo-electron microscopy

Nogales, E., & Mahamid, J. (2024) · Nature · doi:10.1038/s41586-024-07198-2 · Cited by 220

Chemical Modifications in Therapeutic Protein Aggregates Generated under Different Stress Conditions

Luo, Q., Joubert, M. K., Stevenson, R., Ketchem, R. R., Narhi, L. O., & Wypych, J. (2011) · Journal of Biological Chemistry · doi:10.1074/jbc.m110.160440 · Cited by 204

The chemical component dictionary: complete descriptions of constituent molecules in experimentally determined 3D macromolecules in the Protein Data Bank

Westbrook, J., Shao, C., Feng, Z., Zhuravleva, M. A., Velankar, S. S., & Young, J. Y. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu789 · Cited by 208

OpenStructure: an integrated software framework for computational structural biology

Biasini, M., Schmidt, T., Bienert, S., Mariani, V., Studer, G., Haas, J., Johner, N. B., Schenk, A. D., Philippsen, A., & Schwede, T. F. (2013) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444913007051 · Cited by 215

Adaptations to a Subterranean Environment and Longevity Revealed by the Analysis of Mole Rat Genomes

Fang, X., Seim, I., Huang, Z., Gerashchenko, M. V., Xiong, Z., Turanov, A. A., Zhu, Y., Lobanov, A. V., Fan, D., Yim, S. H., et al. (2014) · Cell Reports · doi:10.1016/j.celrep.2014.07.030 · Cited by 205

Structure–Activity Studies on Suramin Analogues as Inhibitors of NAD+‐Dependent Histone Deacetylases (Sirtuins)

Trapp, J., Meier, R., Hongwiset, D., Kassack, M. U., Sippl, W., & Jung, M. (2007) · ChemMedChem · doi:10.1002/cmdc.200700003 · Cited by 198

Quantitative FRET studies and integrative modeling unravel the structure and dynamics of biomolecular systems

Dimura, M., Peulen, T.-O., Hanke, C. A., Prakash, A., Gohlke, H., & Seidel, C. A. M. (2016) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2016.11.012 · Cited by 195

Shining Light into Black Boxes

Morin, A., Urban, J. M., Adams, P. D., Foster, I. T., Šali, A., Baker, D. A., & Piotr Sliz, A. (2012) · Science · doi:10.1126/science.1218263 · Cited by 190

Membrane-attached mammalian cytochromes P450: An overview of the membrane's effects on structure, drug binding, and interactions with redox partners

Šrejber, M., Navrátilová, V., Paloncýová, M., Bazgier, V., Berka, K., Anzenbacher, P., & Otyepka, M. (2018) · Journal of Inorganic Biochemistry · doi:10.1016/j.jinorgbio.2018.03.002 · Cited by 202

Biotechnology for the acceleration of carbon dioxide capture and sequestration

Savile, C. K., & Lalonde, J. J. (2011) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2011.06.006 · Cited by 188

Design, Molecular Modeling, Synthesis, and Anti-HIV-1 Activity of New Indolyl Aryl Sulfones. Novel Derivatives of the Indole-2-carboxamide

Ragno, R., Coluccia, A., Regina, G. L., Martino, G. D., Piscitelli, F., Lavecchia, A., Novellino, E., Bergamini, A., Ciaprini, C., Sinistro, A., et al. (2006) · Journal of Medicinal Chemistry · doi:10.1021/jm0512490 · Cited by 183

A review on drug repurposing applicable to COVID-19

Dotolo, S., Marabotti, A., Facchiano, A. M., & Tagliaferri, R. (2020) · Briefings in Bioinformatics · doi:10.1093/bib/bbaa288 · Cited by 186

Machine learning in scanning transmission electron microscopy

Kalinin, S. V., Ophus, C., Voyles, P. M., Erni, R., Kepaptsoglou, D. M., Grillo, V., Lupini, A. R., Oxley, M. P., Schwenker, E., Chan, M. K. Y., et al. (2022) · Nature Reviews Methods Primers · doi:10.1038/s43586-022-00095-w · Cited by 192

A multiscale coarse-grained model of the SARS-CoV-2 virion

Yu, A., Pak, A. J., He, P., Monje‐Galvan, V., Casalino, L., Gaieb, Z., Dommer, A. C., Amaro, R. E., & Voth, G. A. (2020) · Biophysical Journal · doi:10.1016/j.bpj.2020.10.048 · Cited by 169

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

Šali, A., Berman, H. M., Schwede, T. F., Trewhella, J., Kleywegt, G. J., Burley, S. K., Markley, J. L., Nakamura, H., Adams, P. D., Bonvin, A. M. J. J., et al. (2015) · Structure · doi:10.1016/j.str.2015.05.013 · Cited by 170

Understanding the Functional Roles of Amino Acid Residues in Enzyme Catalysis

Holliday, G. L., Mitchell, J. B. O., & Thornton, J. M. (2009) · Journal of Molecular Biology · doi:10.1016/j.jmb.2009.05.015 · Cited by 175

Polyoxidovanadates' interactions with proteins: An overview

Aureliano, M., Gumerova, N. I., Sciortino, G., Garribba, E., McLauchlan, C. C., Rompel, A., & Crans, D. C. (2021) · Coordination Chemistry Reviews · doi:10.1016/j.ccr.2021.214344 · Cited by 174

Crystallographic refinement of ligand complexes

Kleywegt, G. J. (2006) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444906022657 · Cited by 178

Visualization of macromolecular structures

O’Donoghue, S. I., Goodsell, D. S., Frangakis, A. S., Jossinet, F., Laskowski, R. A., Nilges, M., Saibil, H. R., Schafferhans, A., Wade, R. C., Westhof, É., et al. (2010) · Nature Methods · doi:10.1038/nmeth.1427 · Cited by 167

Recommendations of the wwPDB NMR Validation Task Force

Montelione, G. T., Nilges, M., Bax, A., Güntert, P., Herrmann, T., Richardson, J. S., Schwieters, C. D., Vranken, W., Vuister, G. W., Wishart, D. S., et al. (2013) · Structure · doi:10.1016/j.str.2013.07.021 · Cited by 162

Intrinsic protein disorder and conditional folding in AlphaFoldDB

Piovesan, D., Monzon, A. M., & Tosatto, S. C. E. (2022) · Protein Science · doi:10.1002/pro.4466 · Cited by 160

Order and Disorder: Differential Structural Impacts of Myricetin and Ethyl Caffeate on Human Amylase, an Antidiabetic Target

Williams, L. K., Li, C., Withers, S. G., & Brayer, G. D. (2012) · Journal of Medicinal Chemistry · doi:10.1021/jm301273u · Cited by 166

Cardiac cell modelling: Observations from the heart of the cardiac physiome project

Fink, M., Niederer, S., Cherry, E. M., Fenton, F. H., Koivumäki, J. T., Seemann, G., Thul, R., Zhang, H., Sachse, F. B., Beard, D. A., et al. (2010) · Progress in Biophysics and Molecular Biology · doi:10.1016/j.pbiomolbio.2010.03.002 · Cited by 164

Limitations and lessons in the use of X-ray structural information in drug design

Davis, A. M., St-Gallay, S. A., & Kleywegt, G. J. (2008) · Drug Discovery Today · doi:10.1016/j.drudis.2008.06.006 · Cited by 168

RCSB Protein Data Bank: A Resource for Chemical, Biochemical, and Structural Explorations of Large and Small Biomolecules

Zardecki, C., Dutta, S., Goodsell, D. S., Voigt, M., & Burley, S. K. (2016) · Journal of Chemical Education · doi:10.1021/acs.jchemed.5b00404 · Cited by 164

New tools in MolProbity validation: CaBLAM for CryoEM backbone, UnDowser to rethink “waters,” and NGL Viewer to recapture online 3D graphics

Prisant, M. G., Williams, C. J., Chen, V. B., Richardson, J. S., & Richardson, D. C. (2019) · Protein Science · doi:10.1002/pro.3786 · Cited by 146

EzMol: A Web Server Wizard for the Rapid Visualization and Image Production of Protein and Nucleic Acid Structures

Reynolds, C. R., Islam, S. A., & Sternberg, M. J. E. (2018) · Journal of Molecular Biology · doi:10.1016/j.jmb.2018.01.013 · Cited by 161

Femtosecond-to-millisecond structural changes in a light-driven sodium pump

Skopintsev, P., Ehrenberg, D., Weinert, T., James, D., Kar, R. K., Johnson, P. J. M., Ozerov, D., Furrer, A., Martiel, I., Dworkowski, F., et al. (2020) · Nature · doi:10.1038/s41586-020-2307-8 · Cited by 169

The BioImage Archive – Building a Home for Life-Sciences Microscopy Data

Hartley, M., Kleywegt, G. J., Patwardhan, A., Sarkans, U., Swedlow, J. R., & Brazma, A. (2022) · Journal of Molecular Biology · doi:10.1016/j.jmb.2022.167505 · Cited by 159

High-resolution structure of human carbonic anhydrase II complexed with acetazolamide reveals insights into inhibitor drug design

Sippel, K. H., Robbins, A. H., Domsic, J. F., Genis, C., Agbandje‐McKenna, M., & McKENNA, R. V. (2009) · Acta Crystallographica Section F Structural Biology and Crystallization Communications · doi:10.1107/s1744309109036665 · Cited by 159

E-MSD: an integrated data resource for bioinformatics

Golovin, A. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh078 · Cited by 159

OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive

Young, J. Y., Westbrook, J., Feng, Z., Sala, R., Peisach, E., Oldfield, T. J., Sen, S., Gutmanas, A., Armstrong, D. R., Berrisford, J. M., et al. (2017) · Structure · doi:10.1016/j.str.2017.01.004 · Cited by 159

Akt-targeted therapy as a promising strategy to overcome drug resistance in breast cancer – A comprehensive review from chemotherapy to immunotherapy

Kaboli, P. J., Salimian, F., Aghapour, S., Xiang, S., Zhao, Q., Li, M., Wu, X., Du, F., Zhao, Y., Shen, J., et al. (2020) · Pharmacological Research · doi:10.1016/j.phrs.2020.104806 · Cited by 159

The Transcription Factor Encyclopedia

Yusuf, D., Butland, S. L., Swanson, M. I., Bolotin, E., Ticoll, A., Cheung, W., Zhang, X. Y. C., Dickman, C. T., Fulton, D. L., Lim, J. S., et al. (2012) · Genome biology · doi:10.1186/gb-2012-13-3-r24 · Cited by 155

Integr8 and Genome Reviews: integrated views of complete genomes and proteomes

Kersey, P. J. (2004) · Nucleic Acids Research · doi:10.1093/nar/gki039 · Cited by 154

The Protein Data Bank archive as an open data resource

Berman, H. M., Kleywegt, G. J., Nakamura, H., & Markley, J. L. (2014) · Journal of Computer-Aided Molecular Design · doi:10.1007/s10822-014-9770-y · Cited by 156

Bioinformatics approaches to discovering food-derived bioactive peptides: Reviews and perspectives

Du, Z., Comer, J. R., & Li, Y. (2023) · TrAC Trends in Analytical Chemistry · doi:10.1016/j.trac.2023.117051 · Cited by 164

Outcome of a Workshop on Applications of Protein Models in Biomedical Research

Schwede, T. F., Šali, A., Honig, B. H., Levitt, M., Berman, H. M., Jones, D. T., Brenner, S. E., Burley, S. K., Das, R., Dokholyan, N. V., et al. (2009) · Structure · doi:10.1016/j.str.2008.12.014 · Cited by 148

Mathematical modeling in cancer nanomedicine: a review

Dogra, P., Butner, J. D., Chuang, Y.-L., Caserta, S., Goel, S., Brinker, C. J., Vittorio Cristini, C., & Wang, Z. (2019) · Biomedical Microdevices · doi:10.1007/s10544-019-0380-2 · Cited by 154

Structural Characterization of Zinc-deficient Human Superoxide Dismutase and Implications for ALS

Roberts, B. R., Tainer, J. A., Getzoff, E. D., Malencik, D. A., Anderson, S. R., Bomben, V. C., Meyers, K. R., Karplus, P. A., & Beckman, J. S. (2007) · Journal of Molecular Biology · doi:10.1016/j.jmb.2007.07.043 · Cited by 151

Community-acquired methicillin-resistant Staphylococcus aureus: community transmission, pathogenesis, and drug resistance

Yamamoto, T., Nishiyama, A., Takano, T., Yabe, S., Higuchi, W., Razvina, O., & Shi, D. (2010) · Journal of Infection and Chemotherapy · doi:10.1007/s10156-010-0045-9 · Cited by 153

Novel Cinnamic Acid Derivatives as Antioxidant and Anticancer Agents: Design, Synthesis and Modeling Studies

Pontiki, E. A., Hadjipavlou‐Litina, D., Litinas, Κ. E., & Geromichalos, G. D. (2014) · Molecules · doi:10.3390/molecules19079655 · Cited by 150

PDBML: the representation of archival macromolecular structure data in XML

Westbrook, J., Ito, N., Nakamura, H., Henrick, K., & Berman, H. M. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bti082 · Cited by 150

Fast end-to-end learning on protein surfaces

Sverrisson, F., Feydy, J., Correia, B. E., & Bronstein, M. M. (2021) · IEEE Computer Society Conference on Computer Vision and Pattern Recognition/Proceedings - IEEE Computer Society Conference on Computer Vision and Pattern Recognition/Proceedings · doi:10.1109/cvpr46437.2021.01502 · Cited by 146

PRODIGY: A Contact-based Predictor of Binding Affinity in Protein-protein Complexes

Vangone, A., & Bonvin, A. M. J. J. (2017) · BIO-PROTOCOL · doi:10.21769/bioprotoc.2124 · Cited by 154

LiteMol suite: interactive web-based visualization of large-scale macromolecular structure data

Sehnal, D., Deshpande, M., Vařeková, R. S., Mir, S., Berka, K., Midlik, A., Pravda, L., Velankar, S. S., & Koča, J. (2017) · Nature Methods · doi:10.1038/nmeth.4499 · Cited by 148

The forkhead-box family of transcription factors: key molecular players in colorectal cancer pathogenesis

Laissue, P. (2019) · Molecular Cancer · doi:10.1186/s12943-019-0938-x · Cited by 147

PDBe: improved accessibility of macromolecular structure data from PDB and EMDB

Velankar, S. S., van Ginkel, G., Alhroub, Y., Battle, G. M., Berrisford, J. M., Conroy, M. J., Dana, J. M., Gore, S. P., Gutmanas, A., Haslam, P., et al. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv1047 · Cited by 148

Gcn4-Mediator Specificity Is Mediated by a Large and Dynamic Fuzzy Protein-Protein Complex

Tuttle, L. M., Pacheco, D., Warfield, L., Luo, J., Ranish, J. A., Hahn, S., & Klevit, R. E. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.02.097 · Cited by 142

Visualizing biological data—now and in the future

O’Donoghue, S. I., Gavin, A., Gehlenborg, N., Goodsell, D. S., Hèriché, J.-K., Nielsen, C. B., North, C. L., Olson, A. J., Procter, J. B., Shattuck, D. W., et al. (2010) · Nature Methods · doi:10.1038/nmeth.f.301 · Cited by 144

PDBe: Protein Data Bank in Europe

Gutmanas, A., Alhroub, Y., Battle, G. M., Berrisford, J. M., Bochet, E., Conroy, M. J., Dana, J. M., Montecelo, M. A. F., van Ginkel, G., Gore, S. P., et al. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt1180 · Cited by 142

BioLiP2: an updated structure database for biologically relevant ligand–protein interactions

Zhang, C., Zhang, X., Freddolino, L., & Zhang, Y. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad630 · Cited by 152

Determination of Protein-ligand Interactions Using Differential Scanning Fluorimetry

Vivoli, M., Novak, H. R., Littlechild, J. A., & Harmer, N. J. (2014) · Journal of Visualized Experiments · doi:10.3791/51809 · Cited by 139

Remediation of the protein data bank archive

Henrick, K., Feng, Z., Bluhm, W. F., Dimitropoulos, D., Doreleijers, J. F., Dutta, S., Flippen-Anderson, J. L., Ionides, J., Kamada, C., Krissinel, E., et al. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm937 · Cited by 139

Polysaccharides for tissue engineering: Current landscape and future prospects

Tchobanian, A., Oosterwyck, H. V., & Fardim, P. (2018) · Carbohydrate Polymers · doi:10.1016/j.carbpol.2018.10.039 · Cited by 145

Protein Data Bank: A Comprehensive Review of 3D Structure Holdings and Worldwide Utilization by Researchers, Educators, and Students

Burley, S. K., Berman, H. M., Duarte, J. M., Feng, Z., Flatt, J. W., Hudson, B. P., Lowe, R., Peisach, E., Piehl, D. W., Rose, Y., et al. (2022) · Biomolecules · doi:10.3390/biom12101425 · Cited by 152

Systems medicine and metabolic modelling

Mardinoğlu, A., & Nielsen, J. (2011) · Journal of Internal Medicine · doi:10.1111/j.1365-2796.2011.02493.x · Cited by 139

Quinoline derivatives as possible lead compounds for anti-malarial drugs: Spectroscopic, DFT and MD study

Sureshkumar, B., Mary, Y. S., Panicker, C. Y., Suma, S., Armaković, S., Armaković, S. J., Alsenoy, C. V., & Narayana, B. (2017) · Arabian Journal of Chemistry · doi:10.1016/j.arabjc.2017.07.006 · Cited by 141

Small molecules that inhibit TNF signalling by stabilising an asymmetric form of the trimer

O’Connell, J. P., Porter, J. R., Kroeplien, B., Norman, T., Rapecki, S., Davis, R., McMillan, D., Arakaki, T. L., Burgin, A. B., Fox, D., III, et al. (2019) · Nature Communications · doi:10.1038/s41467-019-13616-1 · Cited by 137

A Survey on Applications of Artificial Intelligence in Fighting Against COVID-19

Chen, J., Li, K., Zhang, Z., Li, K., & Yu, P. S. (2021) · ACM Computing Surveys · doi:10.1145/3465398 · Cited by 154

Machine learning predictions of MHC-II specificities reveal alternative binding mode of class II epitopes

Racle, J., Guillaume, P., Schmidt, J., Michaux, J., Larabi, A., Lau, K., Perez, M. A. S., Croce, G., Genolet, R., Coukos, G., et al. (2023) · Immunity · doi:10.1016/j.immuni.2023.03.009 · Cited by 136

BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositions

Markley, J. L., Ulrich, E. L., Berman, H. M., Henrick, K., Nakamura, H., & Akutsu, H. (2008) · Journal of Biomolecular NMR · doi:10.1007/s10858-008-9221-y · Cited by 134

The Protein Model Portal

Arnold, K., Kiefer, F., Kopp, J., Battey, J. N. D., Podvinec, M., Westbrook, J., Berman, H. M., Bordoli, L., & Schwede, T. F. (2008) · Journal of Structural and Functional Genomics · doi:10.1007/s10969-008-9048-5 · Cited by 134

The Protein Data Bank at 40: Reflecting on the Past to Prepare for the Future

Berman, H. M., Kleywegt, G. J., Nakamura, H., & Markley, J. L. (2012) · Structure · doi:10.1016/j.str.2012.01.010 · Cited by 130

pHLA3D: An online database of predicted three-dimensional structures of HLA molecules

Oliveira, D. M. T. E., Brandão, R. M. S. D. S., Sousa, L. C. D. D. M., Lima, F. D. C. A., do Monte, S. J. H., Marroquim, M. S. C., Lima, A. V. D. S., Coelho, A. G. B., Costa, J. M. S., Ramos, R. M., et al. (2019) · Human Immunology · doi:10.1016/j.humimm.2019.06.009 · Cited by 129

Topological Classification of RNA Structures

Bon, M., Graziano Vernizzi, C., Orland, H., & Zee, A. (2008) · Journal of Molecular Biology · doi:10.1016/j.jmb.2008.04.033 · Cited by 128

idock: A multithreaded virtual screening tool for flexible ligand docking

Li, H., Leung, K., & Wong, M. (2012) · IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB) · doi:10.1109/cibcb.2012.6217214 · Cited by 128

Structural classification of CDR‐H3 revisited: A lesson in antibody modeling

Kuroda, D., Shirai, H., Kobori, M., & Nakamura, H. (2008) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.22087 · Cited by 127

istar: A Web Platform for Large-Scale Protein-Ligand Docking

Li, H., Leung, K., Ballester, P. J., & Wong, M. (2014) · PLoS ONE · doi:10.1371/journal.pone.0085678 · Cited by 123

Interplay of Structure and Dynamics in Functional Macromolecular and Supramolecular Systems As Revealed by Magnetic Resonance Spectroscopy

Hansen, M. R., Graf, R., & Spiess, H. W. (2015) · Chemical Reviews · doi:10.1021/acs.chemrev.5b00258 · Cited by 127

Assessing protein–ligand interaction scoring functions with the CASF-2013 benchmark

Li, Y., Su, M., Liu, Z., Li, J., Liu, J., Han, L., & Wang, R. (2018) · Nature Protocols · doi:10.1038/nprot.2017.114 · Cited by 130

PDB ‐101: Educational resources supporting molecular explorations through biology and medicine

Zardecki, C., Dutta, S., Goodsell, D. S., Lowe, R., Voigt, M., & Burley, S. K. (2021) · Protein Science · doi:10.1002/pro.4200 · Cited by 127

Atlas of the Radical SAM Superfamily: Divergent Evolution of Function Using a “Plug and Play” Domain

Holliday, G. L., Akiva, E., Meng, E. C., Brown, S. D., Calhoun, S., Pieper, U., Šali, A., Booker, S. J., & Babbitt, P. C. (2018) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/bs.mie.2018.06.004 · Cited by 124

p53 tetramerization: at the center of the dominant-negative effect of mutant p53Preprint

Gencel‐Augusto, J., & Lozano, G. (2020) · Genes & Development · doi:10.1101/gad.340976.120 · Cited by 136

Fibrin Clot Structure and Mechanics Associated with Specific Oxidation of Methionine Residues in Fibrinogen

Weigandt, K. M., White, N. J., Chung, D. W., Ellingson, E., Wang, Y., Fu, X., & Pozzo, D. C. (2012) · Biophysical Journal · doi:10.1016/j.bpj.2012.10.036 · Cited by 123

Data publication with the structural biology data grid supports live analysis

Meyer, P. A., Socias, S., Key, J., Ransey, E., Tjon, E. C., Buschiazzo, A., Lei, M., Botka, C., Withrow, J., Neau, D. B., et al. (2016) · Nature Communications · doi:10.1038/ncomms10882 · Cited by 121

Characterization of Wise Protein and Its Molecular Mechanism to Interact with both Wnt and BMP Signals

Lintern, K., Guidato, S., Rowe, A., Saldanha, J. W., & Itasaki, N. (2009) · Journal of Biological Chemistry · doi:10.1074/jbc.m109.025478 · Cited by 122

The Protein Data Bank Archive

Velankar, S. S., Burley, S. K., Kurisu, G., Hoch, J. C., & Markley, J. L. (2021) · Methods in molecular biology · doi:10.1007/978-1-0716-1406-8_1 · Cited by 122

Data-Based Chemical Class Regions for Van Krevelen Diagrams

Laszakovits, J. R., & MacKay, A. A. (2021) · Journal of the American Society for Mass Spectrometry · doi:10.1021/jasms.1c00230 · Cited by 119

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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) · Protein Science · doi:10.1002/pro.4482 · Cited by 123

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Zhang, L., Han, L., Wang, X., Wei, Y., Zheng, J., Zhao, L., & Tong, X. (2021) · Bioscience Reports · doi:10.1042/bsr20203520 · Cited by 125

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Shanmugasundram, A., Starns, D., Böhme, U., Amos, B., Wilkinson, P. A., Harb, O. S., Warrenfeltz, S. W., Kissinger, J. C., McDowell, M. A., Roos, D. S., et al. (2023) · PLoS neglected tropical diseases · doi:10.1371/journal.pntd.0011058 · Cited by 117

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Sun, S., Yang, F., Tan, G., Costanzo, M., Oughtred, R., Hirschman, J., Theesfeld, C. L., Bansal, P., Sahni, N., Yi, S. S., et al. (2016) · Genome Research · doi:10.1101/gr.192526.115 · Cited by 119

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Emsley, P., & Crispin, M. (2018) · Acta Crystallographica Section D Structural Biology · doi:10.1107/s2059798318005119 · Cited by 117

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Zhang, B., Li, H., Yu, K., & Jin, Z. (2022) · CCF Transactions on High Performance Computing · doi:10.1007/s42514-021-00086-5 · Cited by 132

Invertebrate lysozymes: Diversity and distribution, molecular mechanism and in vivo function

Herreweghe, J. M. V., & Michiels, C. W. (2012) · Journal of Biosciences · doi:10.1007/s12038-012-9201-y · Cited by 117

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Juvvadi, P. R., Fox, D., Bobay, B. G., Hoy, M. J., Gobeil, S. M. C., Venters, R. A., Chang, Z., Lin, J. J., Averette, A. F., Cole, D. C., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-12199-1 · Cited by 116

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Taherzadeh, G., Yang, Y., Zhang, T., Liew, A. W., & Zhou, Y. (2016) · Journal of Computational Chemistry · doi:10.1002/jcc.24314 · Cited by 111

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Dutta, S., Burkhardt, K., Young, J. Y., Swaminathan, G. J., Matsuura, T., Henrick, K., Nakamura, H., & Berman, H. M. (2008) · Molecular Biotechnology · doi:10.1007/s12033-008-9127-7 · Cited by 114

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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

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

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Berman, H. M., Henrick, K., Nakamura, H., & Markley, J. L. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl971 · Cited by 1,124

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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

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