The PCDDB (Protein Circular Dichroism Data Bank): A Bioinformatics Resource for Protein Characterisations and Methods Development |
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| Affiliation: | 1. Institute of Structural and Molecular Biology, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK;2. School of Biological and Behavioural Sciences, Queen Mary University of London, London E1 4NS, UK;1. Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, Barcelona 08028, Spain;2. Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway;3. Department of Chemistry, University of Bergen, Allégaten 41, 5007 Bergen, Norway;4. Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, Barcelona 08010, Spain;1. Department of Clinical Biochemistry and Pharmacology, Ben-Gurion University of the Negev, Be’er Sheva, Israel;2. The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be’er Sheva, Israel;1. Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA;2. Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA;3. Department of Chemistry, Boston University, Boston, MA 02215, USA;1. Department of Computer Science, Lakehead University, Thunder Bay, ON, Canada;2. Ontario Institute for Cancer Research, Toronto, ON, Canada;3. Indian Institute of Technology, Kharagpur, India;4. Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute (DFCI), Boston, MA, USA;5. Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA;6. Department of Cancer Biology, Dana-Farber Cancer Institute (DFCI), Boston, MA, USA;7. Institute of Molecular Biology (IMB), Mainz, Germany;8. The Donnelly Centre, University of Toronto, Toronto, ON, Canada;9. Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada;10. Department of Computer Science, University of Toronto, Toronto, ON, Canada;11. Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada;12. The Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada;1. Computational Systems Biology Group, Systems Biology Department, National Center for Biotechnology (CNB-CSIC), c/ Darwin, 3, Madrid 28049, Spain;2. Department of Molecular Biology and Biochemistry, University of Malaga, Malaga 29071, Spain;3. CIBER de Enfermedades Raras, Instituto de Salud Carlos III, Madrid, Spain;4. Institute of Biomedical Research in Malaga (IBIMA), Malaga, Spain |
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| Abstract: | The Protein Circular Dichroism Data Bank (PCDDB) [https://pcddb.cryst.bbk.ac.uk] is an established resource for the biological, biophysical, chemical, bioinformatics, and molecular biology communities. It is a freely-accessible repository of validated protein circular dichroism (CD) spectra and associated sample and metadata, with entries having links to other bioinformatics resources including, amongst others, structure (PDB), AlphaFold, and sequence (UniProt) databases, as well as to published papers which produced the data and cite the database entries. It includes primary (unprocessed) and final (processed) spectral data, which are available in both text and pictorial formats, as well as detailed sample and validation information produced for each of the entries. Recently the metadata content associated with each of the entries, as well as the number and structural breadth of the protein components included, have been expanded. The PCDDB includes data on both wild-type and mutant proteins, and because CD studies primarily examine proteins in solution, it also contains examples of the effects of different environments on their structures, plus thermal unfolding/folding series. Methods for both sequence and spectral comparisons are included.The data included in the PCDDB complement results from crystal, cryo-electron microscopy, NMR spectroscopy, bioinformatics characterisations and classifications, and other structural information available for the proteins via links to other databases. The entries in the PCDDB have been used for the development of new analytical methodologies, for interpreting spectral and other biophysical data, and for providing insight into structures and functions of individual soluble and membrane proteins and protein complexes. |
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| Keywords: | circular dichroism spectroscopy protein structural and spectroscopic database data deposition and accession protein stability and environmental effects resource for bioinformatics developments CD" },{" #name" :" keyword" ," $" :{" id" :" k0035" }," $$" :[{" #name" :" text" ," _" :" circular dichroism IDP" },{" #name" :" keyword" ," $" :{" id" :" k0055" }," $$" :[{" #name" :" text" ," _" :" intrinsically disordered protein MRE" },{" #name" :" keyword" ," $" :{" id" :" k0065" }," $$" :[{" #name" :" text" ," _" :" mean residue ellipticity NMR" },{" #name" :" keyword" ," $" :{" id" :" k0075" }," $$" :[{" #name" :" text" ," _" :" nuclear magnetic resonance NRMSD" },{" #name" :" keyword" ," $" :{" id" :" k0085" }," $$" :[{" #name" :" text" ," _" :" normalised root mean square deviation PCDDB" },{" #name" :" keyword" ," $" :{" id" :" k0095" }," $$" :[{" #name" :" text" ," _" :" Protein Circular Dichroism Data Bank PCDDBid" },{" #name" :" keyword" ," $" :{" id" :" k0105" }," $$" :[{" #name" :" text" ," _" :" unique acquisition code for a PCDDB entry PDB" },{" #name" :" keyword" ," $" :{" id" :" k0115" }," $$" :[{" #name" :" text" ," _" :" Protein Data Bank SRCD" },{" #name" :" keyword" ," $" :{" id" :" k0125" }," $$" :[{" #name" :" text" ," _" :" synchrotron radiation circular dichroism HT" },{" #name" :" keyword" ," $" :{" id" :" pc_FX2O0ycLR5" }," $$" :[{" #name" :" text" ," _" :" high tension IntEnz" },{" #name" :" keyword" ," $" :{" id" :" pc_W2yxiXWTm5" }," $$" :[{" #name" :" text" ," _" :" enzyme classification |
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