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

Impact of the Protein Data Bank on antineoplastic approvals

Westbrook, J., Soskind, R., Hudson, B. P., & Burley, S. K. (2020) · Drug Discovery Today · doi:10.1016/j.drudis.2020.02.002 · Cited by 31

Can CHARMM36 atomic charges described correctly the interaction between amino acid and water molecules by molecular dynamics simulations?

Oliveira, L. B. A., & Colherinhas, G. (2020) · Journal of Molecular Liquids · doi:10.1016/j.molliq.2020.113919 · Cited by 31

Computer simulations of the interaction between SARS-CoV-2 spike glycoprotein and different surfaces

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How the Protein Data Bank changed biology: An introduction to the JBC Reviews thematic series, part 1

Berman, H. M., & Gierasch, L. M. (2021) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2021.100608 · Cited by 31

Kirkwood–Buff-Derived Force Field for Peptides and Proteins: Philosophy and Development of KBFF20

Ploetz, E. A., Karunaweera, S., Bentenitis, N., Chen, F., Dai, S., Gee, M. B., Jiao, Y., Kang, M., Kariyawasam, N. L., Naleem, N., et al. (2021) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.1c00075 · Cited by 32

The Role of MacroH2A Histone Variants in Cancer

Hsu, C.-J., Meers, O., Buschbeck, M., & Heidel, F. H. (2021) · Cancers · doi:10.3390/cancers13123003 · Cited by 34

Generating tertiary protein structures via interpretable graph variational autoencoders

Guo, X., Du, Y., Tadepalli, S., Zhao, L., & Shehu, A. (2021) · Bioinformatics Advances · doi:10.1093/bioadv/vbab036 · Cited by 49

Evaluation of the stereochemical quality of predicted RNA 3D models in the RNA-Puzzles submissions

Carrascoza, F., Antczak, M., Miao, Z., Westhof, É., & Szachniuk, M. (2021) · RNA · doi:10.1261/rna.078685.121 · Cited by 32

RNA-Specific Force Field Optimization with CMAP and Reweighting

Chen, J., Liu, H., Cui, X., Li, Z., & Chen, H. (2022) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.1c01148 · Cited by 33

Discovery of novel selective inhibitors for EGFR-T790M/L858R

Bai, F., Liu, H., Tong, L., Zhou, W., Liu, L., Zhao, Z., Liu, X., Jiang, H., Wang, X., Xie, H., et al. (2011) · Bioorganic & Medicinal Chemistry Letters · doi:10.1016/j.bmcl.2011.12.067 · Cited by 32

Conformation of Glycopeptides and Glycoproteins

Meyer, B., & Möller, H. M. (2006) · Springer eBooks · doi:10.1007/128_2006_078 · Cited by 31

Conformational dynamics of the EGFR kinase domain reveals structural features involved in activation

Papakyriakou, A., Vourloumis, D., Tzortzatou-Stathopoulou, F. F., & Karpusas, M. (2008) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.22353 · Cited by 31

Carbohydrate 3D structure validation

Joosten, R. P., & Lütteke, T. (2016) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2016.10.010 · Cited by 31

In vitro and in silico study of the biological activity of manganese(III) inverse-[9-MC-3]-metallacrowns and manganese(II) complexes with the anti-inflammatory drugs diclofenac or indomethacin

Geromichalos, G. D., Tarushi, A., Lafazanis, K., Pantazaki, Α. A., Kessissoglou, D. P., & Psomas, G. (2018) · Journal of Inorganic Biochemistry · doi:10.1016/j.jinorgbio.2018.07.007 · Cited by 31

B‐factor Guided Proline Substitutions in Chromobacterium violaceum Amine Transaminase: Evaluation of the Proline Rule as a Method for Enzyme Stabilization

Land, H., Campillo‐Brocal, J. C., Humble, M. S., & Berglund, P. (2019) · ChemBioChem · doi:10.1002/cbic.201800749 · Cited by 30

The Caltech Tomography Database and Automatic Processing Pipeline

Ding, H. J., Oikonomou, C. M., & Jensen, G. J. (2015) · Journal of Structural Biology · doi:10.1016/j.jsb.2015.06.016 · Cited by 31

Elucidating the ensemble of functionally-relevant transitions in protein systems with a robotics-inspired method

Molloy, K., & Shehu, A. (2013) · BMC Structural Biology · doi:10.1186/1472-6807-13-s1-s8 · Cited by 31

Anti-SARS and anti-HCV drugs repurposing against the Papain-like protease of the newly emerged coronavirus (2019-nCoV)Preprint

Elfiky, A. A., & Ibrahim, N. S. (2020) · doi:10.21203/rs.2.23280/v1 · Cited by 31

Synthesis, crystal structure, Hirshfeld surface, energy framework, NCI-RDG, theoretical calculations and molecular docking of (Z)4,4′-bis[-3-N-ethyl-2-N'-(phenylimino) thiazolidin-4-one] methane

Benyahlou, Z. D., Baara, F. T., Yahiaoui, S., Megrouss, Y., Boukabcha, N., Djafri, A., Chouaıh, A., & Hatzidimitriou, A. G. (2022) · Journal of Molecular Structure · doi:10.1016/j.molstruc.2022.134781 · Cited by 30

DiAMoNDBack: Diffusion-Denoising Autoregressive Model for Non-Deterministic Backmapping of Cα Protein Traces

Jones, M. S., Shmilovich, K., & Ferguson, A. L. (2023) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.3c00840 · Cited by 30

Coumarin Antifungal Lead Compounds from Millettia thonningii and Their Predicted Mechanism of Action

Ayine‐Tora, D. M., Kingsford-Adaboh, R., Asomaning, W. A., Harrison, J. D., Mills-Robertson, F. C., Bukari, Y., Sakyi, P. O., Kaminta, S., & Reynisson, J. (2016) · Molecules · doi:10.3390/molecules21101369 · Cited by 30

Structure of the Recombinant Neisseria gonorrhoeae Adhesin Complex Protein (rNg-ACP) and Generation of Murine Antibodies with Bactericidal Activity against Gonococci

Almonacid-Mendoza, H. L., Humbert, M. V., Dijokaite-Guraliuc, A., Cleary, D. W., Soo, Y., Hung, M.-C., Orr, C. M., Machelett, M. M., Tews, I., & Christodoulides, M. (2018) · mSphere · doi:10.1128/msphere.00331-18 · Cited by 30

Configurational Entropy Components and Their Contribution to Biomolecular Complex Formation

Fleck, M., & Žagrović, B. (2019) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.8b01254 · Cited by 30

A Hydrophilic Channel Is Involved in Oxidative Inactivation of a [NiFeSe] Hydrogenase

Zacarias, S., Temporão, A., del Barrio, M., Fourmond, V., Léger, C., Matias, P. M., & Pereira, I. A. C. (2019) · ACS Catalysis · doi:10.1021/acscatal.9b02347 · Cited by 30

Action Potentials and Na + voltage-gated ion channels in Placozoa

Romanova, D. Y., Смирнов, И. В., Nikitin, M. A., Kohn, A. B., Borman, A. I., Malyshev, A. Y., Balaban, P. M., & Moroz, L. L. (2020) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2020.08.020 · Cited by 30

Structure of the 70S Ribosome from the Human Pathogen Acinetobacter baumannii in Complex with Clinically Relevant Antibiotics

Nicholson, D., Edwards, T. A., O’Neill, A. J., & Ranson, N. A. (2020) · Structure · doi:10.1016/j.str.2020.08.004 · Cited by 28

BinaryCIF and CIFTools—Lightweight, efficient and extensible macromolecular data management

Sehnal, D., Bittrich, S., Velankar, S. S., Koča, J., Vařeková, R. S., Burley, S. K., & Rose, A. (2020) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1008247 · Cited by 30

Protein Structure Prediction with Mass Spectrometry Data

Biehn, S. E., & Lindert, S. (2021) · Annual Review of Physical Chemistry · doi:10.1146/annurev-physchem-082720-123928 · Cited by 31

Evaluating cepharanthine analogues as natural drugs against SARS‐CoV‐2

Hijikata, A., Shionyu‐Mitsuyama, C., Nakae, S., Shionyu, M., Ota, M., Kanaya, S., Hirokawa, T., Nakajima, S., Watashi, K., & Shirai, T. (2021) · FEBS Open Bio · doi:10.1002/2211-5463.13337 · Cited by 30

Exploring the synergistic and complementary effects of berberine and paeoniflorin in the treatment of type 2 diabetes mellitus by network pharmacology

Zhang, L., Lin, H., Ma, J., Wu, T., Wei, Y., Zhao, L., & Tong, X. (2022) · European Journal of Pharmacology · doi:10.1016/j.ejphar.2022.174769 · Cited by 30

Analysis of electric moments of RNA-binding proteins: implications for mechanism and prediction

Ahmad, S., & Sarai, A. (2011) · BMC Structural Biology · doi:10.1186/1472-6807-11-8 · Cited by 31

Modeling of the Alcohol Dehydrogenase Active Site: Two Different Modes of Alcohol Binding in Crystals of Zinc and Cadmium Tri‐tert‐butoxysilanethiolates Evidenced by X‐ray Diffraction and Solid‐State Vibrational Spectroscopy

Dołęga, A., Baranowska, K., Gudat, D., Herman, A., Stangret, J., Könitz, A., Śmiechowski, M., & Godlewska, S. (2009) · European Journal of Inorganic Chemistry · doi:10.1002/ejic.200900106 · Cited by 30

SpatialPPI: Three-dimensional space protein-protein interaction prediction with AlphaFold Multimer

(2024) · doi:10.1016/j.csbj.2024.03.009 · Cited by 29

Advances in the field of RNA 3D structure prediction and modeling, with purely theoretical approaches, and with the use of experimental data

Mukherjee, S., Moafinejad, S. N., Badepally, N. G., Merdas, K., & Bujnicki, J. M. (2024) · Structure · doi:10.1016/j.str.2024.08.015 · Cited by 32

Structural investigation on the electrostatic loop of native and mutated SOD1 and their interaction with therapeutic compounds

Keerthana, S., & Kolandaivel, P. G. (2015) · RSC Advances · doi:10.1039/c5ra00286a · Cited by 29

An efficient strategy for high throughput screening of recombinant integral membrane protein expression and stability

Fan, J., Heng, J., Dai, S., Shaw, N., Zhou, B., Huang, B., He, Z., Wang, Y., Jiang, T., Li, X., et al. (2011) · Protein Expression and Purification · doi:10.1016/j.pep.2011.02.010 · Cited by 29

The second round of Critical Assessment of Automated Structure Determination of Proteins by NMR: CASD-NMR-2013

Rosato, A., Vranken, W., Fogh, R. H., Ragan, T. J., Tejero, R., Pederson, K., Lee, H., Prestegard, J. H., Yee, A. A., Wu, B., et al. (2015) · Journal of Biomolecular NMR · doi:10.1007/s10858-015-9953-4 · Cited by 28

Binding of hydroxycitrate to human ATP-citrate lyase

Hu, J., Komakula, A., & Fraser, M. E. (2017) · Acta Crystallographica Section D Structural Biology · doi:10.1107/s2059798317009871 · Cited by 29

Pyrimidine biosynthesis in pathogens – Structures and analysis of dihydroorotases from Yersinia pestis and Vibrio cholerae

Sławek, J., Miks, C. D., Kwon, K., Shuvalova, L., Zheng, H., Lewiński, K., Cooper, D. R., Shabalin, I. G., & Minor, W. (2019) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2019.05.149 · Cited by 30

Structures of capsid and capsid-associated tegument complex inside the Epstein–Barr virus

Liu, W., Cui, Y., Wang, C., Li, Z., Gong, D., Dai, X., Bi, G., Sun, R., & Zhou, Z. H. (2020) · Nature Microbiology · doi:10.1038/s41564-020-0758-1 · Cited by 29

The First Berberine-Based Inhibitors of Tyrosyl-DNA Phosphodiesterase 1 (Tdp1), an Important DNA Repair Enzyme

Gladkova, E. D., Nechepurenko, I. V., Bredikhin, R. A., Chepanova, A. A., Zakharenko, A. L., Luzina, O. A., Ilina, E. S., Dyrkheeva, N. S., Mamontova, E. M., Anarbaev, R. O., et al. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21197162 · Cited by 29

New Hybrid Compounds Combining Fragments of Usnic Acid and Monoterpenoids for Effective Tyrosyl-DNA Phosphodiesterase 1 Inhibition

Dyrkheeva, N. S., Filimonov, A. S., Luzina, O. A., Zakharenko, A. L., Ilina, E. S., Malakhova, A. A., Medvedev, S. P., Reynisson, J., Volcho, K. P., Zakian, S. M., et al. (2021) · Biomolecules · doi:10.3390/biom11070973 · Cited by 29

COVID-19: Invasion, pathogenesis and possible cure – A review

Nitin, P., Nandhakumar, R., Vidhya, B., Rajesh, S., & Ayyasamy, S. (2021) · Journal of Virological Methods · doi:10.1016/j.jviromet.2021.114434 · Cited by 30

Highly Antiproliferative Latonduine and Indolo[2,3-c]quinoline Derivatives: Complex Formation with Copper(II) Markedly Changes the Kinase Inhibitory Profile

Wittmann, C., Bacher, F., Enyedy, É. A., Dömötör, O., Spengler, G., Madejski, C., Reynisson, J., & Arion, V. B. (2022) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.1c01740 · Cited by 29

Structure-Guided Synthesis of FK506 and FK520 Analogs with Increased Selectivity Exhibit In Vivo Therapeutic Efficacy against Cryptococcus

Hoy, M. J., Park, E., Lee, H., Lim, W. Y., Cole, D., DeBouver, N. D., Bobay, B. G., Pierce, P. G., Fox, D., Ciofani, M., et al. (2022) · mBio · doi:10.1128/mbio.01049-22 · Cited by 29

Robust Antiviral Activity of Santonica Flower Extract ( Artemisia cina ) against Avian and Human Influenza A Viruses: In Vitro and Chemoinformatic Studies

Hegazy, A., Mostafa, I., Elshaier, Y. A. M. M., Mahmoud, S. H., Shama, N. M. A., Shehata, M., Yahya, G., Nasr, N. F., Halawany, A. M. E., Ali, M. A., et al. (2022) · ACS Omega · doi:10.1021/acsomega.2c04867 · Cited by 29

PolySac3DB: an annotated data base of 3 dimensional structures of polysaccharides.

Sarkar, A., & Pérez, S. (2012) · Europe PMC (PubMed Central) · doi:10.1186/1471-2105-13-302 · Cited by 29

Acceleration of an Aromatic Claisen Rearrangement via a Designed Spiroligozyme Catalyst that Mimics the Ketosteroid Isomerase Catalytic Dyad

Parker, M. F. L., Osuna, S., Bollot, G., Vaddypally, S., Zdilla, M. J., Houk, K. N., & Schafmeister, C. E. (2014) · Journal of the American Chemical Society · doi:10.1021/ja409214c · Cited by 29

Substrate Binding Process and Mechanistic Functioning of Type 1 11β-Hydroxysteroid Dehydrogenase from Enhanced Sampling Methods

Favia, A. D., Masetti, M., Recanatini, M., & Cavalli, A. (2011) · PLoS ONE · doi:10.1371/journal.pone.0025375 · Cited by 29

Improved ligand geometries in crystallographic refinement usingAFITTinPHENIX

Janowski, P. A., Moriarty, N. W., Kelley, B. P., Case, D. A., York, D. M., Adams, P. D., & Warren, G. L. (2016) · Acta Crystallographica Section D Structural Biology · doi:10.1107/s2059798316012225 · Cited by 29

Structure, folding and stability of a minimal homologue from Anemonia sulcata of the sea anemone potassium channel blocker ShK

Krishnarjuna, B., MacRaild, C. A., Sunanda, P., Morales, R. A. V., Peigneur, S., Macrander, J., Yu, H. H., Daly, M., Raghothama, S., Dhawan, V., et al. (2017) · Peptides · doi:10.1016/j.peptides.2017.10.001 · Cited by 29

Synthesis, folding, structure and activity of a predicted peptide from the sea anemone Oulactis sp. with an ShKT fold

Krishnarjuna, B., Villegas‐Moreno, J., Mitchell, M. L., Csóti, A., Peigneur, S., Amero, C., Pennington, M. W., Tytgat, J., Panyi, G., & Norton, R. S. (2018) · Toxicon · doi:10.1016/j.toxicon.2018.05.006 · Cited by 29

The three-dimensional structure of an H-superfamily conotoxin reveals a granulin fold arising from a common ICK cysteine framework

Nielsen, L. D., Foged, M. M., Albert, A., Bertelsen, A. B., Søltoft, C. L., Robinson, S. D., Petersen, S. V., Purcell, A. W., Olivera, B. M., Norton, R. S., et al. (2019) · Journal of Biological Chemistry · doi:10.1074/jbc.ra119.007491 · Cited by 29

l -Hydroxyproline and d -Proline Catabolism in Sinorhizobium meliloti

Chen, S., White, C. E., diCenzo, G. C., Zhang, Y., Stogios, P. J., Savchenko, A. V., & Finan, T. M. (2016) · Journal of Bacteriology · doi:10.1128/jb.00961-15 · Cited by 29

The MEPS server for identifying protein conformational epitopes

Castrignanò, T., Meo, P. D. D., Carrabino, D., Orsini, M., Floris, M., & Tramontano, A. L. (2007) · BMC Bioinformatics · doi:10.1186/1471-2105-8-s1-s6 · Cited by 29

Benchmarking bacterial taxonomic classification using nanopore metagenomics data of several mock communities

Uffelen, A. V., Posadas, A., Roosens, N. H. C., Marchal, K., Keersmaecker, S. C. J. D., & Vanneste, K. (2024) · Scientific Data · doi:10.1038/s41597-024-03672-8 · Cited by 31

Graphene biosensor as affinity biosensors for biorecognition between Guanine riboswitch and ligand

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Tryptophan-Centric Bioinformatics Identifies New Lasso Peptide Modifications

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MolModa: accessible and secure molecular docking in a web browser

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Rational design of uncleaved prefusion-closed trimer vaccines for human respiratory syncytial virus and metapneumovirus

Lee, Y.-Z., Han, J., Zhang, Y.-N., Ward, G., Gomes, K. B., Auclair, S., Stanfield, R. L., He, L., Wilson, I. A., & Zhu, J. (2024) · Nature Communications · doi:10.1038/s41467-024-54287-x · Cited by 33

Systematic conformational investigations of peptoids and peptoid–peptide chimeras

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From carbohydrates to drug-like fragments: Rational development of novel α-amylase inhibitors

Al‐Asri, J., Fazekas, E., Lehoczki, G., Perdih, A., Görick, C., Melzig, M. F., Gyémánt, G., Wolber, G., & Mortier, J. (2015) · Bioorganic & Medicinal Chemistry · doi:10.1016/j.bmc.2015.09.007 · Cited by 29

An algebraic language for RNA pseudoknots comparison

Quadrini, M., Tesei, L., & Merelli, E. (2019) · BMC Bioinformatics · doi:10.1186/s12859-019-2689-5 · Cited by 28

Delving deep into the structural aspects of a furin cleavage site inserted into the spike protein of SARS-CoV-2: A structural biophysical perspective

Li, W. (2020) · Biophysical Chemistry · doi:10.1016/j.bpc.2020.106420 · Cited by 28

Deoxycholic acid as a molecular scaffold for tyrosyl-DNA phosphodiesterase 1 inhibition: A synthesis, structure–activity relationship and molecular modeling study

Salomatina, O. V., Popadyuk, I. I., Zakharenko, A. L., Zakharova, O. D., Chepanova, A. A., Dyrkheeva, N. S., Комарова, Н. И., Reynisson, J., Anarbaev, R. O., Salakhutdinov, N. F., et al. (2020) · Steroids · doi:10.1016/j.steroids.2020.108771 · Cited by 27

In vitro and in silico evaluation of the inhibitory effect of a curcumin-based oxovanadium (IV) complex on alkaline phosphatase activity and bacterial biofilm formation

Katsipis, G., Tsalouxidou, V., Halevas, E. G., Geromichalou, E. G., Geromichalos, G. D., & Pantazaki, Α. A. (2020) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-020-11004-0 · Cited by 28

Structure-based virtual screening suggests inhibitors of 3-Chymotrypsin-Like Protease of SARS-CoV-2 from Vernonia amygdalina and Occinum gratissimum

Gyebi, G. A., Elfiky, A. A., Ogunyemi, O. M., Ibrahim, I. M., Adegunloye, A. P., Adebayo, J. O., Olaiya, C. O., Ocheje, J. O., & Fabusiwa, M. M. (2021) · Computers in Biology and Medicine · doi:10.1016/j.compbiomed.2021.104671 · Cited by 28

A Brief Review of Machine Learning-Based Bioactive Compound Research

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Rank-ordering of known enzymes as starting points for re-engineering novel substrate activity using a convolutional neural network

Upadhyay, V., Boorla, V. S., & Maranas, C. D. (2023) · Metabolic Engineering · doi:10.1016/j.ymben.2023.06.001 · Cited by 26

Curcumin is a tight-binding inhibitor of the most efficient human daunorubicin reductase – Carbonyl reductase 1

Hintzpeter, J., Hornung, J., Ebert, B., Martin, H.-J., & Maser, E. (2014) · Chemico-Biological Interactions · doi:10.1016/j.cbi.2014.12.019 · Cited by 28

A Combined Ligand‐ and Structure‐Based Virtual Screening Protocol Identifies Submicromolar PPARγ Partial Agonists

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Revisiting the Myths of Protein Interior: Studying Proteins with Mass-Fractal Hydrophobicity-Fractal and Polarizability-Fractal Dimensions

Banerji, A., & Ghosh, I. (2009) · PLoS ONE · doi:10.1371/journal.pone.0007361 · Cited by 28

The Classification of Protein Domains

Dawson, N. L., Sillitoe, I., Marsden, R. L., & Orengo, C. A. (2016) · Methods in molecular biology · doi:10.1007/978-1-4939-6622-6_7 · Cited by 28

Glycoblocks: a schematic three-dimensional representation for glycans and their interactions

McNicholas, S. J., & Agirre, J. (2016) · Acta Crystallographica Section D Structural Biology · doi:10.1107/s2059798316013553 · Cited by 28

Characterization of Cytochrome P450 Enzymes and Their Applications in Synthetic Biology

Jeffreys, L. N., Girvan, H. M., McLean, K. J., & Munro, A. W. (2018) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/bs.mie.2018.06.013 · Cited by 30

Cognate Ligand Domain Mapping for Enzymes

Bashton, M., Nobeli, I., & Thornton, J. M. (2006) · Journal of Molecular Biology · doi:10.1016/j.jmb.2006.09.041 · Cited by 28

The Protein Data Bank and lessons in data management

Bourne, P. E. (2004) · Briefings in Bioinformatics · doi:10.1093/bib/5.1.23 · Cited by 28

Caspase-1 activates gasdermin A in non-mammals

(2024) · doi:10.7554/elife.92362.4 · Cited by 27

AlphaFold 2, but not AlphaFold 3, predicts confident but unrealistic β-solenoid structures for repeat proteins

Pratt, O. S., Elliott, L. G., Haon, M., Mesdaghi, S., Price, R. M., Simpkin, A. J., & Rigden, D. J. (2025) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2025.01.016 · Cited by 27

Data-Driven Prediction of Molecular Biotransformations in Food Fermentation

Zhang, D., Jia, C., Sun, D., Gao, C., Fu, D., Cai, P., & Hu, Q. (2023) · Journal of Agricultural and Food Chemistry · doi:10.1021/acs.jafc.3c01172 · Cited by 27

Single virus fingerprinting by widefield interferometric defocus-enhanced mid-infrared photothermal microscopy

Xia, Q., Guo, Z., Zong, H., Seitz, S., Yurdakul, C., Ünlü, M. S., Wang, L., Connor, J. H., & Cheng, J. (2023) · Nature Communications · doi:10.1038/s41467-023-42439-4 · Cited by 27

A database overview of metal-coordination distances in metalloproteins

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Peripheral (E)‐2‐[(4‐hydroxybenzylidene)‐3,4‐dihydronaphthalen‐1(2H)‐one)]‐coordinated phthalocyanines with improved enzyme inhibition properties and photophysicochemical behaviors

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