Protein Circular Dichroism Data Bank Research Articles

DichroPipeline: A suite of online and downloadable tools and resources for protein circular dichroism spectroscopic data analyses, interpretations, and their interoperability with other bioinformatics tools and resources.

Circular Dichroism (CD) spectroscopy is a widely-used method for characterizing individual protein structures in solutions, membranes, films and macromolecular complexes, as well as for probing macromolecular interactions, conformational changes associated with binding substrates, and in different functionally-related environments. This paper describes a series of related computational and display tools that have been developed over many years to aid in those characterizations and functional interpretations. The new DichroPipeline described herein links a series of format-compatible data processing, analysis, and display tools to enable users to facilely produce the spectra, which can then be made available in the Protein Circular Dichroism Data Bank (https://pcddb.cryst.bbk.ac.uk/) resource, in which the CD spectral and associated metadata for each entry are linked to other structural and functional data bases including the Protein Data Bank (PDB), and the UniProt sequence data base, amongst others. These tools and resources thus provide the basis for a wide range of traceable structural characterizations of soluble, membrane and intrinsically-disordered proteins.

The PCDDB project: Tools and resources for CD analyses, archiving, display, and sharing.

The Protein Circular Dichroism Data Bank Project was initiated more than 20 years ago as a means of creating an integrated set of software and tools to aid in analyses, interpretations, visual displays, and data sharing of circular dichroism (CD) and synchrotron radiation circular dichroism (SRCD) spectra and metadata. It has been a basis for the creation of a wide range of novel biophysical and computational methods, and has resulted from the coordinated effort of our two labs and many collaborators. At its heart has been the DichroWeb analysis server, which has been used for ∼2 M secondary structure analyses by >9000 users, and which has included the creation of new computational methods and associated reference databases for examining soluble, membrane, and intrinsically-disordered proteins. The PCDDB itself was created as a repository for CD data and metadata with links to a wide range of bioinformatics, computational, and structural databases and tools, encouraging interoperability of CD and other biophysical methods. It includes links to primary sequence (UniProt) and structural (PDB) databases, as well as to secondary databases such as the Enzyme Commission functional database and the CATH fold database. In addition, tools were created for data processing, and display of CD spectra, for validation of spectral quality (ValiDichro), for integration with other methods such as PDB2CD, PDBMD2CD, 2StructCompare. and DichroCompare, plus novel methods of visualisation, including kinetics of protein folding. Software created is available online via GitHub. In addition to providing widely-used research tools, this project has also been the core teaching tool for CD summer schools and courses worldwide, and has benefitted from the contributions of many biophysicis groups worldwide. [Supported by grants from the UK Biotechnology and Biological Resources programme of the BBSRC).

The PCDDB (Protein Circular Dichroism Data Bank): A Bioinformatics Resource for Protein Characterisations and Methods Development

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.

Wavelength Calibration Uncertainty in Protein Circular Dichroism Data Bank Spectra.

Algorithms to objectively compare the circular dichroism spectra of biopharmaceuticals, as a measure of consistent higher order structure, are sensitive to errors in spectropolarimeter wavelength calibration. A public database, the Protein Circular Dichroism Data Bank contains 108 unique calibration spectra of d-camphor-10-sulphonic acid, mainly collected on synchrotron-based instruments. Deconvolution of these spectra and statistical evaluation of the peaks located near 290 and 190 nm shows significant mean peak wavelength differences between instruments, with data ranges of 1.8 and 2.3 nm. Peak positions and peak height ratios for individual instruments changed significantly through time, and the difference between wavelength maxima was instrument dependent.

Tools and Resources for Circular Dichroism Spectroscopy

Circular Dichroism (CD) Spectroscopy is a popular method in biophysics for the characterisation of the structure, dynamics, and stability of proteins. Our consortium has developed a number of widely-used tools for analyses and access to CD-related resources. These include the Protein Circular Dichroism Data Bank [PCDDB] (http://pcddb.cryst.bbk.ac.uk/home.php), a freely-accessible deposition and retrieval site for protein CD spectra and associated meta-data, which includes the “gold-standard” SP175 and SMP180 reference data sets (currently used for both spectral analyses and software development), a data validation site (ValiDichro), software for spectral data processing and component analyses (CDtoolX), and websites for secondary structure analyses (DichroWeb), spectral comparisons (DichroMatch and DichroCompare), and for predicting spectra from 3-dimensional structures (PDB2CD), as well as for undertaking structure comparisons (2StrucCompare). Accompanying these tools are YouTube educational videos (located at the “PCDDB Channel”) on topics such as good practice in instrument and spectral calibration, sample preparations, types of analyses, such as singular value deconvolutions and Data Bank depositions and access. New tools and resources continue to be developed for use in both research and teaching. Supported by grants from U.K. BBSRC (to BAW and RWJ).

DichroMatch at the protein circular dichroism data bank (DM@PCDDB): A web-based tool for identifying protein nearest neighbors using circular dichroism spectroscopy.

Circular dichroism spectroscopy is a well‐used, but simple method in structural biology for providing information on the secondary structure and folds of proteins. DichroMatch (DM@PCDDB) is an online tool that is newly available in the Protein Circular Dichroism Data Bank (PCDDB), which takes advantage of the wealth of spectral and metadata deposited therein, to enable identification of spectral nearest neighbors of a query protein based on four different methods of spectral matching. DM@PCDDB can potentially provide novel information about structural relationships between proteins and can be used in comparison studies of protein homologs and orthologs.

PDB2CD: a web-based application for the generation of circular dichroism spectra from protein atomic coordinates.

MotivationCircular dichroism (CD) spectroscopy is extensively utilized for determining the percentages of secondary structure content present in proteins. However, although a large contributor, secondary structure is not the only factor that influences the shape and magnitude of the CD spectrum produced. Other structural features can make contributions so an entire protein structural conformation can give rise to a CD spectrum. There is a need for an application capable of generating protein CD spectra from atomic coordinates. However, no empirically derived method to do this currently exists.ResultsPDB2CD has been created as an empirical-based approach to the generation of protein CD spectra from atomic coordinates. The method utilizes a combination of structural features within the conformation of a protein; not only its percentage secondary structure content, but also the juxtaposition of these structural components relative to one another, and the overall structure similarity of the query protein to proteins in our dataset, the SP175 dataset, the ‘gold standard’ set obtained from the Protein Circular Dichroism Data Bank (PCDDB). A significant number of the CD spectra associated with the 71 proteins in this dataset have been produced with excellent accuracy using a leave-one-out cross-validation process. The method also creates spectra in good agreement with those of a test set of 14 proteins from the PCDDB. The PDB2CD package provides a web-based, user friendly approach to enable researchers to produce CD spectra from protein atomic coordinates.Availability and implementation http://pdb2cd.cryst.bbk.ac.uk Supplementary information Supplementary data are available at Bioinformatics online.

PCDDB: new developments at the Protein Circular Dichroism Data Bank.

The Protein Circular Dichroism Data Bank (PCDDB) has been in operation for more than 5 years as a public repository for archiving circular dichroism spectroscopic data and associated bioinformatics and experimental metadata. Since its inception, many improvements and new developments have been made in data display, searching algorithms, data formats, data content, auxillary information, and validation techniques, as well as, of course, an increase in the number of holdings. It provides a site (http://pcddb.cryst.bbk.ac.uk) for authors to deposit experimental data as well as detailed information on methods and calculations associated with published work. It also includes links for each entry to bioinformatics databases. The data are freely available to accessors either as single files or as complete data bank downloads. The PCDDB has found broad usage by the structural biology, bioinformatics, analytical and pharmaceutical communities, and has formed the basis for new software and methods developments.

The Protein Circular Dichroism Data Bank: A Resource for Data Sharing

The Protein Circular Dichroism Data Bank (PCDDB) (http://pcddb.cryst.bbk.ac.uk) is a resource for circular dichroism (CD) spectroscopic data and meta-data, with links to sequence and structure databases and citation references. For depositors it provides a means of fulfilling granting body and journal data sharing requirements. For users it enables access to raw and processed data associated with published studies.The PCDDB website also includes software for spectral matching and analyses, as well as a format-conversion website that produces versions of the data in a wide variety of formats, including the new instrument-independent JCAMP-DX-CD format. It also includes validation software (ValiDichro) for verification of the quality of data measurement and processing, including providing to the depositor a validation report that can be included in publication submissions as evidence of data quality and the availability of the data that will be released on publication. In many cases the entries in the PCDDB contain additional information to that included in the publication, which will be of particular value to the biophysics and bioinformatics communities. Making these data available for meta-analyses opens the potential for their use in a wide range of applications, including methodology development, comparisons of modelled and experimental structures, identification of new protein folds, and comparisons of wild type and mutant proteins.From the initial release of the 71 proteins that comprise the SP175 reference dataset that is widely used for CD analyses, the holdings have grown to include a wide range of soluble and membrane proteins, as well as thermal denaturation series; more than 90000 files have been downloaded thus far by users across a wide range of disciplines.(Supported by the U.K. Biotechnology and Biological Sciences Research Council, and the International Union of Pure and Applied Chemistry)

JCAMP-DX for circular dichroism spectra and metadata (IUPAC Recommendations 2012)

Circular dichroism (CD) spectroscopy is a widely used technique for the characterisation of proteins. A number of CD instruments are currently on the market, and there are more than a dozen synchrotron radiation circular dichroism (SRCD) beamlines in operation worldwide. All produce different output formats and contents. In order for users of CD and SRCD data to be able simply to compare and contrast data and the associated recorded or unrecorded metadata, it is essential to have a common data format. For this reason, the JCAMP-DX-CD format for CD spectroscopy has been developed, based on extensive consultations with users and senior representatives of all the instrument manufacturers and beamlines, and under the auspices of IUPAC, based on the Joint Committee on Atomic and Physical Data Exchange protocols. The availability of a common format is also important for deposition to, and access from, the Protein Circular Dichroism Data Bank, the public repository for CD and SRCD data and metadata. The JCAMP-DX-CD format can be read by standard JCAMP programs such as JSpecView. We have also created a series of parsers, available at the DichroJCAMP web site (http://valispec.cryst.bbk.ac.uk/formatConverter/dichroJCAMPDX-CD.html), which will enable the conversion between instrument and beamline formats and the JCAMP-DX-CD format.

Circular Dichroism Spectral Data and Metadata in the Protein Circular Dichroism Data Bank (PCDDB): A Tutorial Guide to Accession and Deposition

The Protein Circular Dichroism Data Bank (PCDDB) is a web-based resource containing circular dichroism (CD) and synchrotron radiation circular dichroism spectral and associated metadata located at http://pcddb.cryst.bbk.ac.uk. This resource provides a freely available, user-friendly means of accessing validated CD spectra and their associated experimental details and metadata, thereby enabling broad usage of this material and new developments across the structural biology, chemistry, and bioinformatics communities. The resource also enables researchers utilizing CD as an experimental technique to have a means of storing their data at a secure site from which it is easily retrievable, thereby making their results publicly accessible, a current requirement of many grant-funding agencies world-wide, as well as meeting the data-sharing requirements for journal publications. This tutorial provides extensive information on searching, accessing, and downloading procedures for those who wish to utilize the data available in the data bank, and detailed information on deposition procedures for creating and validating entries, including comprehensive explanations of their contents and formats, for those who wish to include their data in the data bank.

DichroMatch: a website for similarity searching of circular dichroism spectra

Circular dichroism (CD) spectroscopy is a widely used method for examining the structure, folding and conformational changes of proteins. A new online CD analysis server (DichroMatch) has been developed for identifying proteins with similar spectral characteristics by detecting possible structurally and functionally related proteins and homologues. DichroMatch includes six different methods for determining the spectral nearest neighbours to a query protein spectrum and provides metrics of how similar these spectra are and, if corresponding crystal structures are available for the closest matched proteins, information on their secondary structures and fold classifications. By default, DichroMatch uses all the entries in the Protein Circular Dichroism Data Bank (PCDDB) for its comparison set, providing the broadest range of publicly available protein spectra to match with the unknown protein. Alternatively, users can download or create their own specialized data sets, thereby enabling comparisons between the structures of related proteins such as wild-type versus mutants or homologues or a series of spectra of the same protein under different conditions. The DichroMatch server is freely available at http://dichromatch.cryst.bbk.ac.uk.

A reference dataset for the analyses of membrane protein secondary structures and transmembrane residues using circular dichroism spectroscopy.

Empirical analyses of protein secondary structures based on circular dichroism (CD) and synchrotron radiation circular dichroism (SRCD) spectroscopic data rely on the availability of reference datasets comprised of spectra of relevant proteins, whose crystal structures have been determined. Datasets comprised of only soluble proteins have not proven suitable for analysing the spectra of membrane proteins. A new reference dataset, MP180, has been created containing the spectra of 30 membrane proteins encompassing the secondary structure and fold space covered by all known membrane protein structures. In addition a mixed soluble and membrane protein dataset, SMP180, has been created, which includes 98 soluble protein spectra (SP) plus the MP180 spectra. Calculations of both membrane and soluble protein secondary structures using SMP180 are significantly improved with respect to those produced, using soluble protein-only datasets. The SMP180 dataset also enables determination of the percentage of transmembrane residues, thus enhancing the information previously obtainable from CD spectroscopy. Reference dataset online at the DichroWeb analysis server (http://dichroweb.cryst.bbk.ac.uk); individual protein spectra in the Protein Circular Dichroism Data Bank (http://pcddb.cryst.bbk.ac.uk).

Validichro, a Software Tool for Validation of Circular Dichroism (CD) Spectroscopic Data

Circular Dichroism (CD) spectroscopy is a widely used technique in structural biology for examining protein structures, interactions and folding, and is used in industry for quality control of bioprocesses and pharmaceutical products. There currently exist a number of validation/checking programs for crystallographic and NMR data, such as PROCHECK, MolProbity and WHAT_IF, but no such validation programs exist for CD data. We have recently created VALIDICHRO, a software suite for assaying the quality/validity of circular dichroism data. With the recent launch of the Protein Circular Dichroism Data Bank (PCDDB), a public repository for CD spectral and associated metadata, the need for such validation software became paramount to ensure the integrity of the data bank and its utility for a wide range of bioinformatics and structural biology usages. In addition this software provides a means of establishing standards for “good practice” and quality control throughout the CD data-collecting community. The validation criteria were established through wide and open consultations with members of the CD user community and the PCDDB Technical Advisory Board. VALIDICHRO does more than 20 types of checks for completeness, consistency and quality of CD spectra and their associated metadata and produces a user-friendly report. This can be employed as a guideline for users (either depositors or accessors), attached to a PCDDB entry, or provided to journal reviewers as evidence of data quality. (Supported by grants from the U.K. BBSRC)

PCDDB: the protein circular dichroism data bank, a repository for circular dichroism spectral and metadata

The Protein Circular Dichroism Data Bank (PCDDB) is a public repository that archives and freely distributes circular dichroism (CD) and synchrotron radiation CD (SRCD) spectral data and their associated experimental metadata. All entries undergo validation and curation procedures to ensure completeness, consistency and quality of the data included. A web-based interface enables users to browse and query sample types, sample conditions, experimental parameters and provides spectra in both graphical display format and as downloadable text files. The entries are linked, when appropriate, to primary sequence (UniProt) and structural (PDB) databases, as well as to secondary databases such as the Enzyme Commission functional classification database and the CATH fold classification database, as well as to literature citations. The PCDDB is available at: http://pcddb.cryst.bbk.ac.uk.

The Protein Circular Dichroism Data Bank, A Web-Based Site for Access to Circular Dichroism Spectroscopic Data

The Protein Circular Dichroism Data Bank (PCDDB) is a newly released resource for structural biology. It is a web-accessible (http://pcddb.cryst.bbk.ac.uk) data bank for circular dichroism (CD) and synchrotron radiation circular dichroism (SRCD) spectra and their associated experimental and secondary metadata, with links to protein sequence and structure data banks. It is designed to provide a public repository for CD spectroscopic data on macromolecules, to parallel the Protein Data Bank (PDB) for crystallographic, electron microscopic, and nuclear magnetic resonance spectroscopic data. Similarly to the PDB, it includes validation checking procedures to ensure good practice and the integrity of the deposited data. This paper reports on the first public release of the PCDDB, which provides access to spectral data that comprise standard reference datasets.

Synchrotron radiation circular dichroism (SRCD) spectroscopy: an enhanced method for examining protein conformations and protein interactions

CD (circular dichroism) spectroscopy is a well-established technique in structural biology. SRCD (synchrotron radiation circular dichroism) spectroscopy extends the utility and applications of conventional CD spectroscopy (using laboratory-based instruments) because the high flux of a synchrotron enables collection of data at lower wavelengths (resulting in higher information content), detection of spectra with higher signal-to-noise levels and measurements in the presence of absorbing components (buffers, salts, lipids and detergents). SRCD spectroscopy can provide important static and dynamic structural information on proteins in solution, including secondary structures of intact proteins and their domains, protein stability, the differences between wild-type and mutant proteins, the identification of natively disordered regions in proteins, and the dynamic processes of protein folding and membrane insertion and the kinetics of enzyme reactions. It has also been used to effectively study protein interactions, including protein-protein complex formation involving either induced-fit or rigid-body mechanisms, and protein-lipid complexes. A new web-based bioinformatics resource, the Protein Circular Dichroism Data Bank (PCDDB), has been created which enables archiving, access and analyses of CD and SRCD spectra and supporting metadata, now making this information publicly available. To summarize, the developing method of SRCD spectroscopy has the potential for playing an important role in new types of studies of protein conformations and their complexes.

The Protein Circular Dichroism Data Bank (PCDDB) - First Release of a New Resource for Spectroscopic Data Sharing

The Protein Circular Dichroism Data Bank (PCDDB) has been designed as a resource for the deposition of circular dichroism (CD) spectroscopic data and accompanying meta-data, with links to sequence and structure data bases and citation references. A key aim of the PCDDB is to provide a repository for spectroscopic data in a comparable manner to that of the long-established Protein Data Bank (PDB), which contains three-dimensional structures of proteins and their associated crystallographic, NMR or cryo-EM data. The PCDDB will be a searchable data bank of CD spectra, with associated tools and protocols for spectral matching, analysis and back-calculations available as part of the overall resource. In addition, validation software will be available for verification of the quality of the CD data deposited, in order to maintain a high standard of data incorporated into this resource. The PCDDB will accommodate both conventional (lab-based) CD data and synchrotron radiation circular dichroism (SRCD) data. It will provide for easy wide-spread dissemination of research results and a facility for data sharing, as a simple means of fulfilling granting body requirements. The first release of the Protein Circular Dichroism Data Bank was made publicly-available in September 2009. The first entries were of the 71 proteins that comprise the SP175 reference database (Lees et al., Bioinformatics 22:1955; 2006). In the current release, users can download and access these data files. In the full beta release, due in late 2009/early 2010, users will be able to deposit their own spectra, which will be validated before being made openly available on line. The PCDDB can be accessed through the website http://pcddb.cryst.bbk.ac.uk.(Supported by a grant to BAW and RWJ from the BBSRC Bioinformatics and Biological Resources Fund).

Protein circular dichroism data bank (PCDDB): Data bank and website design

The Protein Circular Dichroism Data Bank (PCDDB) is a new deposition data bank for validated circular dichroism spectra of biomacromolecules. Its aim is to be a resource for the structural biology and bioinformatics communities, providing open access and archiving facilities for circular dichroism and synchrotron radiation circular dichroism spectra. It is named in parallel with the Protein Data Bank (PDB), a long-existing valuable reference data bank for protein crystal and NMR structures. In this article, we discuss the design of the data bank structure and the deposition website located at http://pcddb.cryst.bbk.ac.uk. Our aim is to produce a flexible and comprehensive archive, which enables user-friendly spectral deposition and searching. In the case of a protein whose crystal structure and sequence are known, the PCDDB entry will be linked to the appropriate PDB and sequence data bank files, respectively. It is anticipated that the PCDDB will provide a readily accessible biophysical catalogue of information on folded proteins that may be of value in structural genomics programs, for quality control and archiving in industrial and academic labs, as a resource for programs developing spectroscopic structural analysis methods, and in bioinformatics studies.

The Protein Circular Dichroism Data Bank (PCDDB): A bioinformatics and spectroscopic resource

This article describes the development and creation of the Protein Circular Dichroism Data Bank (PCDDB), a deposition and searchable data bank for validated circular dichroism spectra located at http://pcddb.cryst.bbk.ac.uk/.