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61-535: The PDB is a key in areas of structural biology , such as structural genomics . Most major scientific journals and some funding agencies now require scientists to submit their structure data to the PDB. Many other databases use protein structures deposited in the PDB. For example, SCOP and CATH classify protein structures, while PDBsum provides a graphic overview of PDB entries using information from other sources, such as Gene Ontology . Two forces converged to initiate

122-549: A numeric character reference . Consider the Chinese character "中", whose numeric code in Unicode is hexadecimal 4E2D, or decimal 20,013. A user whose keyboard offers no method for entering this character could still insert it in an XML document encoded either as &#20013; or &#x4e2d; . Similarly, the string "I <3 Jörg" could be encoded for inclusion in an XML document as I &lt;3 J&#xF6;rg . &#0;

183-413: A diffraction pattern . These experiments led to the development of X-ray crystallography , and its usage in exploring biological structures. In 1951, Rosalind Franklin and Maurice Wilkins used X-ray diffraction patterns to capture the first image of deoxyribonucleic acid (DNA). Francis Crick and James Watson modeled the double helical structure of DNA using this same technique in 1953 and received

244-586: A common format to make them available for geometric and graphical evaluation. By 1971, one of Meyer's programs, SEARCH, enabled researchers to remotely access information from the database to study protein structures offline. SEARCH was instrumental in enabling networking, thus marking the functional beginning of the PDB. The Protein Data Bank was announced in October 1971 in Nature New Biology as

305-594: A growing number of proteins are determined by cryo-electron microscopy . For PDB structures determined by X-ray diffraction that have a structure factor file, their electron density map may be viewed. The data of such structures may be viewed on the three PDB websites. Historically, the number of structures in the PDB has grown at an approximately exponential rate, with 100 registered structures in 1982, 1,000 structures in 1993, 10,000 in 1999, 100,000 in 2014, and 200,000 in January 2023. The file format initially used by

366-504: A joint venture between Cambridge Crystallographic Data Centre , UK and Brookhaven National Laboratory, US. Upon Hamilton's death in 1973, Tom Koetzle took over direction of the PDB for the subsequent 20 years. In January 1994, Joel Sussman of Israel's Weizmann Institute of Science was appointed head of the PDB. In October 1998, the PDB was transferred to the Research Collaboratory for Structural Bioinformatics (RCSB);

427-448: A list of syntax rules provided in the specification. Some key points in the fairly lengthy list include: The definition of an XML document excludes texts that contain violations of well-formedness rules; they are simply not XML. An XML processor that encounters such a violation is required to report such errors and to cease normal processing. This policy, occasionally referred to as " draconian error handling", stands in notable contrast to

488-522: A mechanism whereby an XML processor can reliably, without any prior knowledge, determine which encoding is being used. Encodings other than UTF-8 and UTF-16 are not necessarily recognized by every XML parser (and in some cases not even UTF-16, even though the standard mandates it to also be recognized). XML provides escape facilities for including characters that are problematic to include directly. For example: There are five predefined entities : All permitted Unicode characters may be represented with

549-555: A more compact non-XML syntax; the two syntaxes are isomorphic and James Clark 's conversion tool— Trang —can convert between them without loss of information. RELAX NG has a simpler definition and validation framework than XML Schema, making it easier to use and implement. It also has the ability to use datatype framework plug-ins ; a RELAX NG schema author, for example, can require values in an XML document to conform to definitions in XML Schema Datatypes. Schematron

610-506: A rich datatyping system and allow for more detailed constraints on an XML document's logical structure. XSDs also use an XML-based format, which makes it possible to use ordinary XML tools to help process them. xs:schema element that defines a schema: RELAX NG (Regular Language for XML Next Generation) was initially specified by OASIS and is now a standard (Part 2: Regular-grammar-based validation of ISO/IEC 19757 – DSDL ). RELAX NG schemas may be written in either an XML based syntax or

671-950: A unique identifier for biomolecules, because several structures for the same molecule—in different environments or conformations—may be contained in PDB with different PDB IDs.) The structure files may be viewed using one of several free and open source computer programs , including Jmol , Pymol , VMD , Molstar and Rasmol . Other non-free, shareware programs include ICM-Browser, MDL Chime , UCSF Chimera , Swiss-PDB Viewer, StarBiochem (a Java-based interactive molecular viewer with integrated search of protein databank), Sirius , and VisProt3DS (a tool for Protein Visualization in 3D stereoscopic view in anaglyph and other modes), and Discovery Studio . The RCSB PDB website contains an extensive list of both free and commercial molecule visualization programs and web browser plugins. Structural biology Structural biology , as defined by

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732-421: A validity error must be able to report it, but may continue normal processing. A DTD is an example of a schema or grammar . Since the initial publication of XML 1.0, there has been substantial work in the area of schema languages for XML. Such schema languages typically constrain the set of elements that may be used in a document, which attributes may be applied to them, the order in which they may appear, and

793-527: A vocabulary to refer to the constructs within an XML document, but does not provide any guidance on how to access this information. A variety of APIs for accessing XML have been developed and used, and some have been standardized. Existing APIs for XML processing tend to fall into these categories: Stream-oriented facilities require less memory and, for certain tasks based on a linear traversal of an XML document, are faster and simpler than other alternatives. Tree-traversal and data-binding APIs typically require

854-506: Is bioinformatics to look for patterns among the diverse sequences that give rise to particular shapes. Researchers often can deduce aspects of the structure of integral membrane proteins based on the membrane topology predicted by hydrophobicity analysis . See protein structure prediction . Structural biologists have made significant contributions towards understanding the molecular components and mechanisms underlying human diseases. For example, cryo-EM and ssNMR have been used to study

915-461: Is a lexical , event-driven API in which a document is read serially and its contents are reported as callbacks to various methods on a handler object of the user's design. SAX is fast and efficient to implement, but difficult to use for extracting information at random from the XML, since it tends to burden the application author with keeping track of what part of the document is being processed. It

976-456: Is a markup language and file format for storing, transmitting, and reconstructing arbitrary data. It defines a set of rules for encoding documents in a format that is both human-readable and machine-readable . The World Wide Web Consortium 's XML 1.0 Specification of 1998 and several other related specifications —all of them free open standards —define XML. The design goals of XML emphasize simplicity, generality, and usability across

1037-726: Is a language for making assertions about the presence or absence of patterns in an XML document. It typically uses XPath expressions. Schematron is now a standard (Part 3: Rule-based validation of ISO/IEC 19757 – DSDL ). DSDL (Document Schema Definition Languages) is a multi-part ISO/IEC standard (ISO/IEC 19757) that brings together a comprehensive set of small schema languages, each targeted at specific problems. DSDL includes RELAX NG full and compact syntax, Schematron assertion language, and languages for defining datatypes, character repertoire constraints, renaming and entity expansion, and namespace-based routing of document fragments to different validators. DSDL schema languages do not have

1098-578: Is an XML industry data standard. XML is used extensively to underpin various publishing formats. One of the applications of XML is in the transfer of Operational meteorology (OPMET) information based on IWXXM standards. The material in this section is based on the XML Specification . This is not an exhaustive list of all the constructs that appear in XML; it provides an introduction to the key constructs most often encountered in day-to-day use. XML documents consist entirely of characters from

1159-498: Is better suited to situations in which certain types of information are always handled the same way, no matter where they occur in the document. Pull parsing treats the document as a series of items read in sequence using the iterator design pattern . This allows for writing of recursive descent parsers in which the structure of the code performing the parsing mirrors the structure of the XML being parsed, and intermediate parsed results can be used and accessed as local variables within

1220-509: Is commonly used to analyze the dynamic movements of biological molecules. In 1975, the first simulation of a biological folding process using MD was published in Nature. Recently, protein structure prediction was significantly improved by a new machine learning method called AlphaFold . Some claim that computational approaches are starting to lead the field of structural biology research. Biomolecules are too small to see in detail even with

1281-442: Is not permitted because the null character is one of the control characters excluded from XML, even when using a numeric character reference. An alternative encoding mechanism such as Base64 is needed to represent such characters. Comments may appear anywhere in a document outside other markup. Comments cannot appear before the XML declaration. Comments begin with <!-- and end with --> . For compatibility with SGML ,

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1342-623: Is of great interest to biologists because macromolecules carry out most of the functions of cells , and it is only by coiling into specific three-dimensional shapes that they are able to perform these functions. This architecture, the " tertiary structure " of molecules, depends in a complicated way on each molecule's basic composition, or " primary structure ." At lower resolutions, tools such as FIB-SEM tomography have allowed for greater understanding of cells and their organelles in 3-dimensions, and how each hierarchical level of various extracellular matrices contributes to function (for example in bone). In

1403-447: The HIV envelope allows the virus to evade human immune responses. Structural biology is also an important component of drug discovery . Scientists can identify targets using genomics, study those targets using structural biology, and develop drugs that are suited for those targets. Specifically, ligand- NMR , mass spectrometry , and X-ray crystallography are commonly used techniques in

1464-509: The Internet . It is a textual data format with strong support via Unicode for different human languages . Although the design of XML focuses on documents, the language is widely used for the representation of arbitrary data structures , such as those used in web services . Several schema systems exist to aid in the definition of XML-based languages, while programmers have developed many application programming interfaces (APIs) to aid

1525-466: The Journal of Structural Biology , deals with structural analysis of living material (formed, composed of, and/or maintained and refined by living cells) at every level of organization. Early structural biologists throughout the 19th and early 20th centuries were primarily only able to study structures to the limit of the naked eye's visual acuity and through magnifying glasses and light microscopes. In

1586-458: The Unicode repertoire. Except for a small number of specifically excluded control characters , any character defined by Unicode may appear within the content of an XML document. XML includes facilities for identifying the encoding of the Unicode characters that make up the document, and for expressing characters that, for one reason or another, cannot be used directly. Unicode code points in

1647-410: The infoset augmentation facility and attribute defaults. RELAX NG and Schematron intentionally do not provide these. A cluster of specifications closely related to XML have been developed, starting soon after the initial publication of XML 1.0. It is frequently the case that the term "XML" is used to refer to XML together with one or more of these other technologies that have come to be seen as part of

1708-576: The 20th century, a variety of experimental techniques were developed to examine the 3D structures of biological molecules. The most prominent techniques are X-ray crystallography , nuclear magnetic resonance , and electron microscopy . Through the discovery of X-rays and its applications to protein crystals, structural biology was revolutionized, as now scientists could obtain the three-dimensional structures of biological molecules in atomic detail. Likewise, NMR spectroscopy allowed information about protein structure and dynamics to be obtained. Finally, in

1769-415: The 21st century, electron microscopy also saw a drastic revolution with the development of more coherent electron sources, aberration correction for electron microscopes, and reconstruction software that enabled the successful implementation of high resolution cryo-electron microscopy, thereby permitting the study of individual proteins and molecular complexes in three-dimensions at angstrom resolution. With

1830-650: The Nobel Prize in Medicine along with Wilkins in 1962. Pepsin crystals were the first proteins to be crystallized for use in X-ray diffraction, by Theodore Svedberg who received the 1962 Nobel Prize in Chemistry. The first tertiary protein structure , that of myoglobin , was published in 1958 by John Kendrew . During this time, modeling of protein structures was done using balsa wood or wire models. With

1891-485: The PDB comprised: Most structures are determined by X-ray diffraction, but about 7% of structures are determined by protein NMR . When using X-ray diffraction, approximations of the coordinates of the atoms of the protein are obtained, whereas using NMR, the distance between pairs of atoms of the protein is estimated. The final conformation of the protein is obtained from NMR by solving a distance geometry problem. After 2013,

Protein Data Bank - Misplaced Pages Continue

1952-546: The PDB was called the PDB file format. The original format was restricted by the width of computer punch cards to 80 characters per line. Around 1996, the "macromolecular Crystallographic Information file" format, mmCIF, which is an extension of the CIF format was phased in. mmCIF became the standard format for the PDB archive in 2014. In 2019, the wwPDB announced that depositions for crystallographic methods would only be accepted in mmCIF format. An XML version of PDB, called PDBML,

2013-653: The PDB: a small but growing collection of sets of protein structure data determined by X-ray diffraction; and the newly available (1968) molecular graphics display, the Brookhaven RAster Display (BRAD), to visualize these protein structures in 3-D. In 1969, with the sponsorship of Walter Hamilton at the Brookhaven National Laboratory , Edgar Meyer ( Texas A&M University ) began to write software to store atomic coordinate files in

2074-429: The XML core. Some other specifications conceived as part of the "XML Core" have failed to find wide adoption, including XInclude , XLink , and XPointer . The design goals of XML include, "It shall be easy to write programs which process XML documents." Despite this, the XML specification contains almost no information about how programmers might go about doing such processing. The XML Infoset specification provides

2135-555: The XML processor inserts in the DTD itself and in the XML document wherever they are referenced, like character escapes. DTD technology is still used in many applications because of its ubiquity. A newer schema language, described by the W3C as the successor of DTDs, is XML Schema , often referred to by the initialism for XML Schema instances, XSD (XML Schema Definition). XSDs are far more powerful than DTDs in describing XML languages. They use

2196-517: The aggregation of amyloid fibrils, which are associated with Alzheimer's disease , Parkinson's disease , and type II diabetes . In addition to amyloid proteins, scientists have used cryo-EM to produce high resolution models of tau filaments in the brain of Alzheimer's patients which may help develop better treatments in the future. Structural biology tools can also be used to explain interactions between pathogens and hosts. For example, structural biology tools have enabled virologists to understand how

2257-434: The allowable parent/child relationships. The oldest schema language for XML is the document type definition (DTD), inherited from SGML. DTDs have the following benefits: DTDs have the following limitations: Two peculiar features that distinguish DTDs from other schema types are the syntactic support for embedding a DTD within XML documents and for defining entities , which are arbitrary fragments of text or markup that

2318-621: The base language for communication protocols such as SOAP and XMPP . It is one of the message exchange formats used in the Asynchronous JavaScript and XML (AJAX) programming technique. Many industry data standards, such as Health Level 7 , OpenTravel Alliance , FpML , MISMO , and National Information Exchange Model are based on XML and the rich features of the XML schema specification. In publishing, Darwin Information Typing Architecture

2379-401: The behavior of programs that process HTML , which are designed to produce a reasonable result even in the presence of severe markup errors. XML's policy in this area has been criticized as a violation of Postel's law ("Be conservative in what you send; be liberal in what you accept"). The XML specification defines a valid XML document as a well-formed XML document which also conforms to

2440-423: The case of C1 characters, this restriction is a backwards incompatibility; it was introduced to allow common encoding errors to be detected. The code point U+0000 (Null) is the only character that is not permitted in any XML 1.1 document. The Unicode character set can be encoded into bytes for storage or transmission in a variety of different ways, called "encodings". Unicode itself defines encodings that cover

2501-429: The data structure and contain metadata . What is within the tags is data, encoded in the way the XML standard specifies. An additional XML schema (XSD) defines the necessary metadata for interpreting and validating XML. (This is also referred to as the canonical schema.) An XML document that adheres to basic XML rules is "well-formed"; one that adheres to its schema is "valid." IETF RFC 7303 (which supersedes

Protein Data Bank - Misplaced Pages Continue

2562-658: The development of nuclear magnetic resonance (NMR). Currently, solid-state NMR is widely used in the field of structural biology to determine the structure and dynamic nature of proteins ( protein NMR ). In 1990, Richard Henderson produced the first three-dimensional, high resolution image of bacteriorhodopsin using cryogenic electron microscopy (cryo-EM). Since then, cryo-EM has emerged as an increasingly popular technique to determine three-dimensional, high resolution structures of biological images. More recently, computational methods have been developed to model and study biological structures. For example, molecular dynamics (MD)

2623-486: The development of these three techniques, the field of structural biology expanded and also became a branch of molecular biology , biochemistry , and biophysics concerned with the molecular structure of biological macromolecules (especially proteins , made up of amino acids , RNA or DNA , made up of nucleotides , and membranes , made up of lipids ), how they acquire the structures they have, and how alterations in their structures affect their function. This subject

2684-442: The direct use of almost any Unicode character in element names, attributes, comments, character data, and processing instructions (other than the ones that have special symbolic meaning in XML itself, such as the less-than sign, "<"). The following is a well-formed XML document including Chinese , Armenian and Cyrillic characters: The XML specification defines an XML document as a well-formed text, meaning that it satisfies

2745-449: The drug discovery process. For example, researchers have used structural biology to better understand Met , a protein encoded by a protooncogene that is an important drug target in cancer . Similar research has been conducted for HIV targets to treat people with AIDS . Researchers are also developing new antimicrobials for mycobacterial infections using structure-driven drug discovery. XML Extensible Markup Language ( XML )

2806-523: The entire repertoire; well-known ones include UTF-8 (which the XML standard recommends using, without a BOM ) and UTF-16 . There are many other text encodings that predate Unicode, such as ASCII and various ISO/IEC 8859 ; their character repertoires are in every case subsets of the Unicode character set. XML allows the use of any of the Unicode-defined encodings and any other encodings whose characters also appear in Unicode. XML also provides

2867-498: The following ranges are valid in XML 1.0 documents: XML 1.1 extends the set of allowed characters to include all the above, plus the remaining characters in the range U+0001–U+001F. At the same time, however, it restricts the use of C0 and C1 control characters other than U+0009 (Horizontal Tab), U+000A (Line Feed), U+000D (Carriage Return), and U+0085 (Next Line) by requiring them to be written in escaped form (for example U+0001 must be written as &#x01; or its equivalent). In

2928-480: The four members of wwPDB can act as deposition, data processing and distribution centers for PDB data. The data processing refers to the fact that wwPDB staff review and annotate each submitted entry. The data are then automatically checked for plausibility (the source code for this validation software has been made available to the public at no charge). The PDB database is updated weekly ( UTC +0 Wednesday), along with its holdings list. As of 10 January 2023,

2989-708: The functions performing the parsing, or passed down (as function parameters) into lower-level functions, or returned (as function return values) to higher-level functions. Examples of pull parsers include Data::Edit::Xml in Perl , StAX in the Java programming language, XMLPullParser in Smalltalk , XMLReader in PHP , ElementTree.iterparse in Python , SmartXML in Red , System.Xml.XmlReader in

3050-484: The invention of modeling software such as CCP4 in the late 1970s, modeling is now done with computer assistance. Recent developments in the field have included the generation of X-ray free electron lasers , allowing analysis of the dynamics and motion of biological molecules, and the use of structural biology in assisting synthetic biology . In the late 1930s and early 1940s, the combination of work done by Isidor Rabi , Felix Bloch , and Edward Mills Purcell led to

3111-535: The most advanced light microscopes . The methods that structural biologists use to determine their structures generally involve measurements on vast numbers of identical molecules at the same time. These methods include: Most often researchers use them to study the " native states " of macromolecules. But variations on these methods are also used to watch nascent or denatured molecules assume or reassume their native states. See protein folding . A third approach that structural biologists take to understanding structure

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3172-550: The older RFC 3023 ), provides rules for the construction of media types for use in XML message. It defines three media types: application/xml ( text/xml is an alias), application/xml-external-parsed-entity ( text/xml-external-parsed-entity is an alias) and application/xml-dtd . They are used for transmitting raw XML files without exposing their internal semantics . RFC 7303 further recommends that XML-based languages be given media types ending in +xml , for example, image/svg+xml for SVG . Further guidelines for

3233-459: The past few years it has also become possible to predict highly accurate physical molecular models to complement the experimental study of biological structures. Computational techniques such as molecular dynamics simulations can be used in conjunction with empirical structure determination strategies to extend and study protein structure, conformation and function. In 1912 Max Von Laue directed X-rays at crystallized copper sulfate generating

3294-449: The processing of XML data. The main purpose of XML is serialization , i.e. storing, transmitting, and reconstructing arbitrary data. For two disparate systems to exchange information, they need to agree upon a file format. XML standardizes this process. It is therefore analogous to a lingua franca for representing information. As a markup language , XML labels, categorizes, and structurally organizes information. XML tags represent

3355-487: The rules of a Document Type Definition (DTD). In addition to being well formed, an XML document may be valid . This means that it contains a reference to a Document Type Definition (DTD), and that its elements and attributes are declared in that DTD and follow the grammatical rules for them that the DTD specifies. XML processors are classified as validating or non-validating depending on whether or not they check XML documents for validity. A processor that discovers

3416-469: The string "--" (double-hyphen) is not allowed inside comments; this means comments cannot be nested. The ampersand has no special significance within comments, so entity and character references are not recognized as such, and there is no way to represent characters outside the character set of the document encoding. An example of a valid comment: <!--no need to escape <code> & such in comments--> XML 1.0 (Fifth Edition) and XML 1.1 support

3477-601: The transfer was completed in June 1999. The new director was Helen M. Berman of Rutgers University (one of the managing institutions of the RCSB, the other being the San Diego Supercomputer Center at UC San Diego ). In 2003, with the formation of the wwPDB, the PDB became an international organization. The founding members are PDBe (Europe), RCSB (US), and PDBj (Japan). The BMRB joined in 2006. Each of

3538-530: The use of XML in a networked context appear in RFC 3470 , also known as IETF BCP 70, a document covering many aspects of designing and deploying an XML-based language. XML has come into common use for the interchange of data over the Internet. Hundreds of document formats using XML syntax have been developed, including RSS , Atom , Office Open XML , OpenDocument , SVG , COLLADA , and XHTML . XML also provides

3599-472: The use of much more memory, but are often found more convenient for use by programmers; some include declarative retrieval of document components via the use of XPath expressions. XSLT is designed for declarative description of XML document transformations, and has been widely implemented both in server-side packages and Web browsers. XQuery overlaps XSLT in its functionality, but is designed more for searching of large XML databases . Simple API for XML (SAX)

3660-426: The vendor support of XML Schemas yet, and are to some extent a grassroots reaction of industrial publishers to the lack of utility of XML Schemas for publishing . Some schema languages not only describe the structure of a particular XML format but also offer limited facilities to influence processing of individual XML files that conform to this format. DTDs and XSDs both have this ability; they can for instance provide

3721-399: Was described in 2005. The structure files can be downloaded in any of these three formats, though an increasing number of structures do not fit the legacy PDB format. Individual files are easily downloaded into graphics packages from Internet URLs : The " 4hhb " is the PDB identifier. Each structure published in PDB receives a four-character alphanumeric identifier, its PDB ID. (This is not

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