Announcing the worldwide Protein Data Bank

The Protein Data Bank

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The protein data bank: A computer-based archival file for macromolecular structures

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[30] Macromolecular crystallographic information file

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A Second Actin-Like MamK Protein in Magnetospirillum magneticum AMB-1 Encoded Outside the Genomic Magnetosome Island

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Novel tyrosyl-DNA phosphodiesterase 1 inhibitors enhance the therapeutic impact of topoteсan on in vivo tumor models

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Digital open science—Teaching digital tools for reproducible and transparent research

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The future of the protein data bank

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A novel HPV prophylactic peptide vaccine, designed by immunoinformatics and structural vaccinology approaches

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Identifying natural compounds as multi-target-directed ligands against Alzheimer’s disease: an in silico approach

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Efficiently Detecting Protein Complexes from Protein Interaction Networks via Alternating Direction Method of Multipliers

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Ecology and molecular targets of hypermutation in the global microbiome

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Rapid SERS Quantification of Trace Fentanyl Laced in Recreational Drugs with a Portable Raman Module

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The case for post-predictional modifications in the AlphaFold Protein Structure Database

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Dependence of Amino Acid Side Chain 13C Shifts on Dihedral Angle: Application to Conformational Analysis

London, R. E., Wingad, B. D., & Mueller, G. A. (2008) · Journal of the American Chemical Society · doi:10.1021/ja802729t · Cited by 80

Tautomer Preference in PDB Complexes and its Impact on Structure-Based Drug Discovery

Milletti, F., & Vulpetti, A. (2010) · Journal of Chemical Information and Modeling · doi:10.1021/ci900501c · Cited by 81

Knowledge-Based Conformer Generation Using the Cambridge Structural Database

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In Silico Identification and In Vitro and In Vivo Validation of Anti-Psychotic Drug Fluspirilene as a Potential CDK2 Inhibitor and a Candidate Anti-Cancer Drug

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Potential aggregation-prone regions in complementarity-determining regions of antibodies and their contribution towards antigen recognition: a computational analysis

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Targeting G protein-coupled receptor signaling at the G protein level with a selective nanobody inhibitor

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Chemical composition and acetylcholinesterase inhibitory potential, in silico, of Myrciaria floribunda (H. West ex Willd.) O. Berg fruit peel essential oil

Barbosa, D. C. D. S., Holanda, V. N., Assis, C. R. D., de Aguiar, J. C. R. D. O. F., doNascimento, P. H., da Silva, W. V., Navarro, D. M. D. A. F., da Silva, M. V., Lima, V. L. D. M., & Correia, M. T. D. S. (2020) · Industrial Crops and Products · doi:10.1016/j.indcrop.2020.112372 · Cited by 82

PDBe: Protein Data Bank in Europe

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Impact of AlphaFold on structure prediction of protein complexes: The CASP15‐CAPRI experiment

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ProtDCal: A program to compute general-purpose-numerical descriptors for sequences and 3D-structures of proteins

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Mutation of HERC2 causes developmental delay with Angelman-like features

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Probing Enzyme Promiscuity of SGNH Hydrolases

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MACiE: exploring the diversity of biochemical reactions

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Capture and X-ray diffraction studies of protein microcrystals in a microfluidic trap array

Lyubimov, A. Y., Murray, T. D., Koehl, A., Araci, I. E., Uervirojnangkoorn, M., Zeldin, O. B., Cohen, A. E., Soltis, S. M., Baxter, E. L., Brewster, A. S., et al. (2015) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s1399004715002308 · Cited by 78

Molecular Docking with Ligand Attached Water Molecules

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A new hydrogen-bonding potential for the design of protein-RNA interactions predicts specific contacts and discriminates decoys

Chen, Y. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh785 · Cited by 78

Design and Synthesis of Selective Phosphodiesterase 4D (PDE4D) Allosteric Inhibitors for the Treatment of Fragile X Syndrome and Other Brain Disorders

Gurney, M. E., Nugent, R. A., Mo, X., Sindac, J. A., Hagen, T. J., Fox, D. N. A., O’Donnell, J. M., Zhang, C., Xu, Y., Zhang, H., et al. (2019) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.9b00193 · Cited by 78

DNAproDB: an expanded database and web-based tool for structural analysis of DNA–protein complexes

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E-MSD: an integrated data resource for bioinformatics

Velankar, S. S. (2004) · Nucleic Acids Research · doi:10.1093/nar/gki058 · Cited by 77

Structural and functional basis of mammalian microRNA biogenesis by Dicer

Zapletal, D., Táborská, E., Pasulka, J., Malı́k, R., Kubíček, K., Zanova, M., Much, C., Šebesta, M., Buccheri, V., Horvat, F., et al. (2022) · Molecular Cell · doi:10.1016/j.molcel.2022.10.010 · Cited by 80

Targeting TLR4 Signaling by TLR4 Toll/IL-1 Receptor Domain-Derived Decoy Peptides: Identification of the TLR4 Toll/IL-1 Receptor Domain Dimerization Interface

Toshchakov, V. Y., Szmacinski, H., Couture, L. A., Lakowicz, J. R., & Vogel, S. N. (2011) · The Journal of Immunology · doi:10.4049/jimmunol.1002424 · Cited by 77

To what extent do structural changes in catalytic metal sites affect enzyme function?

Valasatava, Y., Rosato, A., Furnham, N., Thornton, J. M., & Andreini, C. (2018) · Journal of Inorganic Biochemistry · doi:10.1016/j.jinorgbio.2017.11.002 · Cited by 77

Expanding the space of protein geometries by computational design of de novo fold families

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The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods

Gabanyi, M. J., Adams, P. D., Arnold, K., Bordoli, L., Carter, L. G., Flippen-Andersen, J., Gifford, L. K., Haas, J., Kouranov, A., McLaughlin, W. A., et al. (2011) · Journal of Structural and Functional Genomics · doi:10.1007/s10969-011-9106-2 · Cited by 76

A Bicyclic 1-Deoxygalactonojirimycin Derivative as a Novel Pharmacological Chaperone for GM1 Gangliosidosis

Takai, T., Higaki, K., Aguilar‐Moncayo, M., Mena‐Barragán, T., Hirano, Y., Yura, K., Yu, L., Ninomiya, H., García‐Moreno, M. I., Sakakibara, Y., et al. (2013) · Molecular Therapy · doi:10.1038/mt.2012.263 · Cited by 76

Sequence-Specific Resonance Assignment of Soluble Nonglobular Proteins by 7D APSY-NMR Spectroscopy

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Evolution of gene knockout strains of E. coli reveal regulatory architectures governed by metabolism

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MISATO: machine learning dataset of protein–ligand complexes for structure-based drug discovery

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Large-scale integration of small molecule-induced genome-wide transcriptional responses, Kinome-wide binding affinities and cell-growth inhibition profiles reveal global trends characterizing systems-level drug action

Vidović, D., Koleti, A., & Schürer, S. C. (2014) · Frontiers in Genetics · doi:10.3389/fgene.2014.00342 · Cited by 74

Small protein folds at the root of an ancient metabolic network

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Artificial intelligence for science in quantum, atomistic, and continuum systems

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Structural genomics of infectious disease drug targets: the SSGCID

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Protein structure databases with new web services for structural biology and biomedical research

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Synchrotron Big Data Science

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In situ structures of rotavirus polymerase in action and mechanism of mRNA transcription and release

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Serendipitous Fatty Acid Binding Reveals the Structural Determinants for Ligand Recognition in Apolipoprotein M

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On the reproducibility of protein crystal structures: five atomic resolution structures of trypsin

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Comparing sixteen scoring functions for predicting biological activities of ligands for protein targets

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Protein Domain-Level Landscape of Cancer-Type-Specific Somatic Mutations

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Large-scale analysis of water stability in bromodomain binding pockets with grand canonical Monte Carlo

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Avoidable errors in deposited macromolecular structures: an impediment to efficient data mining

Dauter, Z., Wlodawer, A., Minor, W., Jaskólski, M., & Rupp, B. (2014) · IUCrJ · doi:10.1107/s2052252514005442 · Cited by 74

A General Computational Approach for Repeat Protein Design

Parmeggiani, F., Huang, P., Vorobiev, S. M., Xiao, R., Park, K., Caprari, S., Su, M., Seetharaman, J., Mao, L., Janjua, H., et al. (2014) · Journal of Molecular Biology · doi:10.1016/j.jmb.2014.11.005 · Cited by 74

The disruptive effect of lysozyme on the bacterial cell wall explored by an in‐silico structural outlook

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Antiviral activities of plant-derived indole and β-carboline alkaloids against human and avian influenza viruses

Hegazy, A., Mahmoud, S. H., Elshaier, Y. A. M. M., Shama, N. M. A., Nasr, N. F., Ali, M. A., El-Shazly, A. M., Mostafa, I., & Mostafa, A. (2023) · Scientific Reports · doi:10.1038/s41598-023-27954-0 · Cited by 72

Stability Effect of Quinary Interactions Reversed by Single Point Mutations

Gnutt, D., Timr, Š., Ahlers, J., König, B., Manderfeld, E., Heyden, M., Sterpone, F., & Ebbinghaus, S. (2019) · Journal of the American Chemical Society · doi:10.1021/jacs.8b13025 · Cited by 71

Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB)

Adams, P. D., Afonine, P. V., Baskaran, K., Berman, H. M., Berrisford, J. M., Bricogne, G., Brown, D. G., Burley, S. K., Chen, M., Feng, Z., et al. (2019) · Acta Crystallographica Section D Structural Biology · doi:10.1107/s2059798319004522 · Cited by 72

A molecular‐level perspective on the frequency, distribution, and consequences of messenger RNA modifications

Jones, J. D., Monroe, J. G., & Koutmou, K. S. (2020) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1586 · Cited by 72

Life in Phases: Intra- and Inter- Molecular Phase Transitions in Protein Solutions

Uversky, V. N., & Finkelstein, A. V. (2019) · Biomolecules · doi:10.3390/biom9120842 · Cited by 72

Structure‐Based Drug Discovery with Deep Learning**

Özçelik, R., van Tilborg, D., Jiménez-Luna, J., & Grisoni, F. (2023) · ChemBioChem · doi:10.1002/cbic.202200776 · Cited by 71

Influence of Nonuniform Geometry on Nanoindentation of Viral Capsids

Gibbons, M. M., & Klug, W. S. (2008) · Biophysical Journal · doi:10.1529/biophysj.108.136176 · Cited by 71

Pharmacophore-based discovery of FXR-agonists. Part II: Identification of bioactive triterpenes from Ganoderma lucidum

Grienke, U., Mihaly‐Bison, J., Schuster, D., Afonyushkin, T., Binder, M., Guan, S., Cheng, C., Wolber, G., Stuppner, H., Guo, D., et al. (2011) · Bioorganic & Medicinal Chemistry · doi:10.1016/j.bmc.2011.09.039 · Cited by 71

Crystal Structure and Enantiomer Selection by d -Alanyl Carrier Protein Ligase DltA from Bacillus cereus

Du, L., He, Y., & Luo, Y. (2008) · Biochemistry · doi:10.1021/bi801363b · Cited by 71

Synthesis and cytotoxicity of thieno[2,3-b]pyridine and furo[2,3-b]pyridine derivatives

Hung, J. M., Arabshahi, H. J., Leung, E. Y., Reynisson, J., & Barker, D. L. A. (2014) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2014.09.001 · Cited by 72

A novel protocol for three-dimensional structure prediction of RNA-protein complexes

Huang, Y., Liu, S., Guo, D., Li, L., & Xiao, Y. (2013) · Scientific Reports · doi:10.1038/srep01887 · Cited by 70

Protein microcrystallography using synchrotron radiation

Yamamoto, M., Hirata, K., Yamashita, K., Hasegawa, K., Ueno, G., Ago, H., & Kumasaka, T. (2017) · IUCrJ · doi:10.1107/s2052252517008193 · Cited by 70

The In Silico Drug Discovery Toolbox: Applications in Lead Discovery and Optimization

Bruno, A., Costantino, G., Sartori, L., & Radi, M. (2019) · Current Medicinal Chemistry · doi:10.2174/0929867324666171107101035 · Cited by 73

Benchmarking the Ability of Common Docking Programs to Correctly Reproduce and Score Binding Modes in SARS-CoV-2 Protease Mpro

Zev, S., Raz, K., Schwartz, R., Tarabeh, R., Gupta, P. K., & Major, D. T. (2021) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.1c00263 · Cited by 70

Medicinal Chemistry Strategies for the Modification of Bioactive Natural Products

Ding, Y., & Xue, X. (2024) · Molecules · doi:10.3390/molecules29030689 · Cited by 79

Docking and 3-D QSAR Studies on Indolyl Aryl Sulfones. Binding Mode Exploration at the HIV-1 Reverse Transcriptase Non-Nucleoside Binding Site and Design of Highly Active N-(2-Hydroxyethyl)carboxamide and N-(2-Hydroxyethyl)carbohydrazide Derivatives

Ragno, R., Artico, M., Martino, G. D., Regina, G. L., Coluccia, A., Pasquali, A. D., & Silvestri, R. (2004) · Journal of Medicinal Chemistry · doi:10.1021/jm040854k · Cited by 70

MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms

Holliday, G. L., Almonacid, D. E., Bartlett, G. J., O’Boyle, N. M., Torrance, J., Murray‐Rust, P., Mitchell, J. B. O., & Thornton, J. M. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl774 · Cited by 70

Design, synthesis and pharmacobiological evaluation of novel acrylic acid derivatives acting as lipoxygenase and cyclooxygenase-1 inhibitors with antioxidant and anti-inflammatory activities

Pontiki, E. A., Hadjipavlou‐Litina, D., Litinas, Κ. E., Nicolotti, O., & Carotti, A. (2010) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2010.10.035 · Cited by 70

HIV-Reverse Transcriptase Inhibition: Inclusion of Ligand-Induced Fit by Cross-Docking Studies

Ragno, R., Frasca, S., Manetti, F., Brizzi, A., & Massa, S. (2004) · Journal of Medicinal Chemistry · doi:10.1021/jm0493921 · Cited by 70

In silico drug design for Staphylococcus aureus and development of host-pathogen interaction network

Wadapurkar, R. M., Shilpa, M., Katti, A. K. S., & Sulochana, M. B. (2017) · Informatics in Medicine Unlocked · doi:10.1016/j.imu.2017.11.002 · Cited by 69

Genetic Spectrum and Distinct Evolution Patterns of SARS-CoV-2

Liu, S., Shen, J., Fang, S., Li, K., Liu, J., Yang, L., Hu, C., & Wan, J. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.593548 · Cited by 63

3D-QSAR as a Tool for Understanding and Improving Single-Site Polymerization Catalysts. A Review

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Genetic heterogeneity in autism: From single gene to a pathway perspective

An, J., & Claudianos, C. (2016) · Neuroscience & Biobehavioral Reviews · doi:10.1016/j.neubiorev.2016.06.013 · Cited by 68

Outcome of a Workshop on Archiving Structural Models of Biological Macromolecules

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Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop

Adams, P. D., Aertgeerts, K., Bauer, C. B., Bell, J. A., Berman, H. M., Bhat, T. N., Blaney, J., Bolton, E., Bricogne, G., Brown, D. G., et al. (2016) · Structure · doi:10.1016/j.str.2016.02.017 · Cited by 67

BioMagResBank (BMRB) as a Resource for Structural Biology

Romero, P. R., Kobayashi, N., Wedell, J. R., Baskaran, K., Iwata, T., Yokochi, M., Maziuk, D., Yao, H., Fujiwara, T., Kurisu, G., et al. (2020) · Methods in molecular biology · doi:10.1007/978-1-0716-0270-6_14 · Cited by 67

Repurposing the estrogen receptor modulator raloxifene to treat SARS-CoV-2 infection

Allegretti, M., Cesta, M. C., Zippoli, M., Beccari, A. R., Talarico, C., Mantelli, F., Bucci, E. M., Scorzolini, L., & Nicastri, E. (2021) · Cell Death and Differentiation · doi:10.1038/s41418-021-00844-6 · Cited by 67

Current biotechnologies on depolymerization of polyethylene terephthalate (PET) and repolymerization of reclaimed monomers from PET for bio-upcycling: A critical review

Kim, N. K., Lee, S., & Park, H. (2022) · Bioresource Technology · doi:10.1016/j.biortech.2022.127931 · Cited by 68

A log-likelihood-gain intensity target for crystallographic phasing that accounts for experimental error

Read, R. J., & McCoy, A. J. (2016) · Acta Crystallographica Section D Structural Biology · doi:10.1107/s2059798315013236 · Cited by 65

Protein crystallography beamline (PX-BL21) at Indus-2 synchrotron

Kumar, A., Ghosh, B., Poswal, H. K., Pandey, K. K., Jagannath, J., Hosur, M. V., Dwivedi, A., Makde, R. D., & Sharma, S. M. (2016) · Journal of Synchrotron Radiation · doi:10.1107/s160057751600076x · Cited by 67

Proper modelling of ligand binding requires an ensemble of bound and unbound states

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The structural impact of cancer-associated missense mutations in oncogenes and tumor suppressors

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