221:, they could grow very large and were often compressed. Some tools, such as Jmol and KiNG, could read PDB files in gzipped format. The wwPDB maintained the specifications of the PDB file format and its XML alternative, PDBML. There was a fairly major change in PDB format specification (to version 3.0) in August 2007, and a remediation of many file problems in the existing database. The typical file extension for a PDB file was
156:(CML) is an open standard for representing molecular and other chemical data. The open source project includes XML Schema, source code for parsing and working with CML data, and an active community. The articles Tools for Working with Chemical Markup Language and XML for Chemistry and Biosciences discusses CML in more detail. CML data files are accepted by many tools, including
25:
726:
is a free and open-source Python library for parsing, storing, and converting various file formats commonly used by quantum chemistry, molecular dynamics, and plane-wave density-functional-theory software programs. It also supports a flexible framework for generating input files for various software
662:(SDF) files. They are text files that adhere to a strict format for representing multiple chemical structure records and associated data fields. The format was originally developed and published by Molecular Design Limited (MDL). MOL is another file format from MDL. It is documented in Chapter 4 of
282:
file) are largely unique to CHARMM. The CARD format is fixed-column-width, resembles the PDB format, and is used exclusively for storing atomic coordinates. The PSF file contains atomic connectivity information (which describes atomic bonds) and is required before beginning a simulation. The typical
780:
This project started in
January 1994, and was first announced during the Chemistry workshop at the First WWW International Conference, held at CERN in May 1994. ... The first version of an Internet draft was published during May–October 1994, and the second revised version during April–September
259:
as well as position at a given point in the simulation trajectory. It does not allow for the storage of connectivity information, which in GROMACS is obtained from separate molecule and system topology files. The typical file extension for a GROMACS file is
645:
The MDL number contains a unique identification number for each reaction and variation. The format is RXXXnnnnnnnn. R indicates a reaction, XXX indicates which database contains the reaction record. The numeric portion, nnnnnnnn, is an 8-digit number.
1568:'s The Distributed Structure-Searchable Toxicity (DSSTox) Database Network is a project of EPA's Computational Toxicology Program. The database provides SDF molecular files with a focus on carcinogenic and otherwise toxic substances.
1545:
eMolecules is a commercial database for molecular data. The data includes a two-dimensional structure diagram and a smiles string for each compound. eMolecules supports fast substructure searching based on parts of the molecular
1857:
Rzepa, H. S.; Murray-Rust, P.; Whitaker, B. J. (1998). "The
Application of Chemical Multipurpose Internet Mail Extensions (Chemical MIME) Internet Standards to Electronic Mail and World Wide Web Information Exchange".
90:
is commonly used for proteins but is also used for other types of molecules. There are many other types which are detailed below. Various software systems are available to convert from one format to another.
1515:
and tar.gz formats to register chemical MIME types on a web server. Programs can then register as viewer, editor or processor for these formats so that full support for chemical MIME types is available.
85:
is a simple format that usually gives the number of atoms in the first line, a comment on the second, followed by a number of lines with atomic symbols (or atomic numbers) and cartesian coordinates. The
1524:
Here is a short list of sources of freely available molecular data. There are many more resources than listed here out there on the
Internet. Links to these sources are given in the references below.
217:
Some PDB files contained an optional section describing atom connectivity as well as position. Because these files were sometimes used to describe macromolecular assemblies or molecules represented in
637:
is a simple format that usually gives the number of atoms in the first line, a comment on the second, followed by a number of lines with atomic symbols (or atomic numbers) and cartesian coordinates.
321:
software can use OpenBabel to import and export a number of file formats. However, by default, it uses the GPR format. This file is composed of several parts, separated by a tag (
1353:
687:
are freely available open source tools specifically designed for converting between file formats. Their chemical expert systems support a large atom type conversion tables.
1606:
734:
A number of tools intended for viewing and editing molecular structures are able to read in files in a number of formats and write them out in other formats. The tools
1487:
1461:
669:
PubChem also has XML and ASN1 file formats, which are export options from the PubChem online database. They are both text based (ASN1 is most often a binary format).
303:
The
General Simulation Data (GSD) file format created for efficient reading / writing of generic particle simulations, primarily - but not restricted to - those from
371:. Based on SMILES, it incorporates a complete syntax for specifying relative stereochemistry. SLN has a rich query syntax that allows for the specification of
1542:) is an excellent source of protein and nucleic acid molecular coordinate data. The data is three-dimensional and provided in Protein Data Bank (PDB) format.
447:
781:
1995. A paper presented to the CPEP (Committee on
Printed and Electronic Publications) at the IUPAC meeting in August 1996 is available for discussion.
46:
33:
1535:
database is a huge source of chemical data. All of the data is in two-dimensions. Data includes SDF, SMILES, PubChem XML, and PubChem ASN1 formats.
278:
molecular dynamics package can read and write a number of standard chemical and biochemical file formats; however, the CARD (coordinate) and PSF (
1552:
is a commercial data base for molecular data. The search results include a two-dimensional structure diagram and a mole file for many compounds.
203:
192:
1565:
1419:
937:
1961:
1788:
Weininger, David (1988). "SMILES, a
Chemical Language and Information System: 1: Introduction to Methodology and Encoding Rules".
177:
87:
184:
and thus limited to a maximum number of atoms, residues, and chains; this resulted in splitting very large structures such as
2012:
1753:
Brooks, B.M.; et al. (1983). "CHARMM: A program for macromolecular energy, minimization, and dynamics calculations".
214:. In 2014, the PDB format was officially replaced with mmCIF, and newer PDB structures may not have PDB files available.
1529:
307:. The package also contains a python module that reads and writes HOOMD schema gsd files with an easy to use syntax.
239:. Some molecular modeling tools wrote nonstandard PDB-style files that adapted the basic format to their own needs.
70:
is a type of data file which is used specifically for depicting molecular data. One of the most widely used is the
38:
1990:
1596:
739:
107:
and many formats have been created, with varying degrees of documentation. The format is indicated in three ways:
1601:
980:
971:
255:
simulations, so it allows for additional numerical precision and optionally retains information about particle
153:
81:
files. They are text files that represent multiple chemical structure records and associated data fields. The
1970:
1957:
1657:"KING (Kinemage, Next Generation): A versatile interactive molecular and scientific visualization program"
1555:
1512:
1188:
1158:
1140:
655:
364:
218:
75:
71:
247:
The GROMACS file format family was created for use with the molecular simulation software package
1805:
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252:
181:
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1735:
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1926:
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1797:
1762:
1725:
1717:
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for molecules. SMILES strings include connectivity but do not include 2D or 3D coordinates.
375:
queries. The syntax also supports the specification of combinatorial libraries of ChemDraw.
1885:
634:
207:
196:
188:
into multiple files. For example, the E. coli 70S was represented as 4 PDB files in 2009:
82:
1974:
1730:
1705:
1681:
1656:
728:
457:
211:
2006:
451:
368:
100:
1774:
1809:
1899:
1631:
120:(usually 3 letters). This is widely used, but fragile as common suffixes such as
1578:
1332:
1611:
710:
For example, to convert the file epinephrine.sdf in SDF to CML use the command
251:. It closely resembles the PDB format but was designed for storing output from
138:
where the format information is included in the file. Examples are CIF and CML.
1314:
735:
157:
1558:
1583:
1371:
751:
747:
743:
680:
165:
1940:
1739:
1690:
24:
1998:: CADD Group Chemoinformatics Tools and User Services (CACTUS). July 2009.
1766:
460:
are not represented. Other atoms are represented by their element symbols
1721:
1278:
603:
318:
256:
185:
1931:
1914:
1801:
180:
is an obsolete format for protein structures developed in 1972. It is a
1985:
1532:
575:
552:
534:
406:
394:
248:
1871:
210:, 3I1O, and 3I1P. In 2014, they were consolidated into a single file,
1587:
723:
684:
275:
1672:
672:
There are a large number of other formats listed in the table below
308:
1844:
1591:
1259:
727:
packages. For a complete list of supported formats, please go to
802:
786:
773:
755:
161:
1995:
1833:
1483:
976:
18:
943:
1539:
1503:
For Linux/Unix, configuration files are available as a "
16:
File format that stores chemical formulae and structures
1822:
1986:"Resolve a structure identifier as SDF, CML, MRV, PDB"
132:
are used by many systems, including non-chemical ones.
1886:"Package Search Results for "chemical-mime" | Debian"
729:
https://iodata.readthedocs.io/en/latest/formats.html
715:
obabel -i sdf epinephrine.sdf -o cml epinephrine.cml
1354:
Simplified molecular input line entry specification
654:One of the most widely used industry standards are
508:represents triple bonds. Branching is indicated by
772:"Chemical MIME" is a de facto approach for adding
1098:SPC format for spectral and chromatographic data
1240:IsoStar Library of Intermolecular Interactions
785:In 1998 the work was formally published in the
1706:"Remediation of the protein data bank archive"
110:
8:
1915:"Announcing the worldwide Protein Data Bank"
1900:"Why Use SourceForge? Features and Benefits"
1860:Journal of Chemical Information and Modeling
1790:Journal of Chemical Information and Modeling
448:simplified molecular input line entry system
99:Chemical information is usually provided as
1969:, San Leandro, California, United States:
512:. Rings are indicated by pairs of digits.
352:The proposed MIME type for this format is
1930:
1729:
1680:
1467:A line notation for biological molecules
940:, Crystallographic Information Framework
793:
519:
379:
49:of all important aspects of the article.
1622:
720:The resulting file is epinephrine.cml.
45:Please consider expanding the lead to
1612:NCI/CADD Chemical Identifier Resolver
7:
1277:Kinetic (Protein Structure) Images;
1559:Library of 3-D Molecular Structures
1262:Spectroscopic Data Exchange Format
144:added by a chemically aware server.
1913:Berman, H.M.; et al. (2003).
1566:US Environmental Protection Agency
14:
1704:Henrick, K.; et al. (2008).
1538:The worldwide Protein Data Bank (
1420:International Chemical Identifier
996:Compass program of the Takahashi
938:Crystallographic Information File
227:, although some older files used
1655:Chen, V.B.; et al. (2009).
1480:Pistoia Alliance XHELM XML file
1045:Gasteiger group CTX file format
111:§ The Chemical MIME Project
23:
1607:Software for molecular modeling
1358:A line notation for molecules.
1137:chemical/x-gaussian-checkpoint
1030:Chemical Style Markup Language
37:may be too short to adequately
1490:including monomer definitions
1080:chemical/x-embl-dl-nucleotide
47:provide an accessible overview
1:
1716:(Database issue): D426–D433.
1823:MDL Information Systems 2005
1530:National Institute of Health
1311:chemical/x-macromodel-input
504:represents double bonds and
74:format, which is similar to
1845:The Chemical MIME Home Page
1350:chemical/x-daylight-smiles
1161:Cube (Wavefunction) Format
776:types to chemical streams.
2029:
1847:(accessed 2013-January-24)
1441:JSDraw native file format
1185:chemical/x-gaussian-input
676:Converting between formats
428:Query for amide/sulfamide
418:Query showing R sidechain
1919:Nature Structural Biology
1597:Chemistry Development Kit
1203:chemical/x-gcg8-sequence
1155:chemical/x-gaussian-cube
1064:Chemical eXchange Format
956:CrystalMaker Data format
859:chemical/x-cactvs-binary
766:The Chemical MIME Project
740:Chemistry Development Kit
283:file extensions used are
1602:Chemical Markup Language
1520:Sources of chemical data
1295:MacMolecule File Format
1206:Protein Sequence Format
1118:chemical/x-gamess-input
1095:chemical/x-galactic-spc
981:Chemical Markup Language
972:Chemical Markup Language
762:fit into this category.
178:Protein Data Bank Format
172:Protein Data Bank Format
154:Chemical Markup Language
149:Chemical Markup Language
88:Protein Data Bank Format
1971:MDL Information Systems
1958:MDL Information Systems
1403:SketchEl XML DataSheet
1329:chemical/x-mdl-molfile
1292:chemical/x-macmolecule
1083:EMBL Nucleotide Format
877:ChemDraw eXchange file
1710:Nucleic Acids Research
1368:chemical/x-mdl-sdfile
783:
354:application/x-ghemical
95:Distinguishing formats
2013:Chemical file formats
1767:10.1002/jcc.540040211
1400:chemical/x-datasheet
1008:chemical/x-crossfire
892:MSI Cerius II format
836:chemical/x-cache-csf
778:
660:Structure Data Format
136:self-describing files
77:Structure Data Format
1632:"wwPDB: File Format"
1385:chemical/x-sketchel
1317:Molecular Mechanics
1274:chemical/x-kinemage
1256:chemical/x-jcamp-dx
1121:GAMESS Input format
919:chemical/x-chemdraw
839:CAChe MolStruct CSF
650:Other common formats
400:CH:CH:CH:CH:CH:CH:@1
367:(SLN) is a chemical
313:Ghemical file format
68:chemical file format
1932:10.1038/nsb1203-980
1802:10.1021/ci00057a005
1556:New York University
1372:Structure-Data File
1237:chemical/x-isostar
1218:chemical/x-genbank
993:chemical/x-compass
821:chemical/x-alchemy
656:chemical table file
382:
365:SYBYL Line Notation
360:SYBYL Line Notation
72:chemical table file
1722:10.1093/nar/gkm937
1505:chemical-mime-data
1438:chemical/x-jsdraw
1388:SketchEl Molecule
1143:Checkpoint Format
904:chemical/x-chem3d
889:chemical/x-cerius
658:formats, like the
515:Some examples are
450:, or SMILES, is a
380:
253:molecular dynamics
206:2016-10-16 at the
195:2016-10-05 at the
182:fixed-width format
142:chemical/MIME type
1872:10.1021/ci9803233
1667:(11): 2403–2409.
1494:
1493:
1477:chemical/x-xhelm
1460:Pistoia Alliance
1415:chemical/x-inchi
1221:ToGenBank Format
624:
623:
437:
436:
412:NH2CH(CH3)C(=O)OH
373:Markush structure
280:protein structure
64:
63:
2020:
1999:
1981:
1980:on June 30, 2007
1979:
1973:, archived from
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1896:
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1834:Mol2mol homepage
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1755:J. Comput. Chem
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1673:10.1002/pro.250
1661:Protein Science
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1061:chemical/x-cxf
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1042:chemical/x-ctx
1037:
1022:
1018:
1011:Crossfire file
1003:
988:
968:chemical/x-cml
963:
948:
934:chemical/x-cif
929:
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874:chemical/x-cdx
869:
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824:Alchemy Format
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635:XYZ file format
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32:This article's
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1963:CTFile Formats
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1951:External links
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1761:(2): 187–217.
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798:File extension
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758:, Mol2mol and
738:(based on the
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529:SMILES string
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458:Hydrogen atoms
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432:NHC=M1{M1:O,S}
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41:the key points
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1925:(12): 980.
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