This article was accepted into the corpus but its outbound wikilinks were never NER-processed — typical at the deepest BFS hop or when the run's entity cap was reached. No expansion funnel to show.
| MOL file | |
|---|---|
| Name | MOL file |
| Extension | .mol |
| Mime | chemical/x-mdl-molfile |
| Type | Chemical file format |
| Developer | Accelrys; originally Molecular Design Limited |
| Released | 1980s |
MOL file The MOL file is a plain-text chemical file format used to represent single molecules with atom and bond lists, coordinates, and simple metadata. It serves as an interchange format among cheminformatics, molecular modeling, and computational chemistry packages such as Accelrys, OpenEye Scientific Software, Schrödinger, Inc., ChemAxon, and RDKit-based workflows. The format underpins many data pipelines in cheminformatics projects associated with institutions like PubChem and ChEMBL and integrates with standards from organizations such as IUPAC and the American Chemical Society.
The MOL file encodes a molecule as a connection table with explicit Cartesian coordinates for atoms, indexed bonds, and limited stereochemistry flags. It emerged as a staple format alongside related formats used by repositories like Protein Data Bank for small molecules and by commercial systems such as Chemical Abstracts Service. Practitioners in pharmaceutical companies including Novartis, Pfizer, and Roche frequently exchange MOL files during hit identification and lead optimization campaigns. The format’s simplicity enables interoperability with scientific toolkits from academic groups at institutions like University of Cambridge and Massachusetts Institute of Technology.
Development traces to Molecular Design Limited and later stewardship by companies such as MDL Information Systems and Accelrys during the 1980s and 1990s. The format evolved alongside graphical editors like ISIS/Draw and later tools produced by Symyx Technologies and BIOVIA. Adoption grew as cheminformatics matured in laboratories at organizations including GlaxoSmithKline and research centers like European Bioinformatics Institute. Over time, extensions and conventions were introduced to represent stereochemical descriptors, isotopes, and reaction centric data used by initiatives like Enamine and datasets in ZINC database.
A MOL-format file is structured in discrete blocks: a header block, a counts line, atom block, bond block, and optional property blocks. The header typically contains a molecule name and program or user comments; commercial editors such as ChemDraw and MarvinSketch populate these fields. The counts line provides atom and bond counts used by parsers in libraries like OpenBabel and RDKit. Each atom line supplies Cartesian coordinates (x, y, z), an atomic symbol, and flags conforming to conventions influenced by standards from IUPAC. Bond lines cite the indices of connected atoms, bond order, and stereochemical attributes; these are recognized by engines such as GAMESS and Gaussian. Optional property lines beginning with "M " convey additional keyed values adopted by data curation groups at National Institutes of Health-funded projects.
Atom records carry element symbols drawn from the periodic table used by laboratories like Lawrence Berkeley National Laboratory and databases curated by National Center for Biotechnology Information. Coordinates are usually in Ångström units as used in structural biology at European Molecular Biology Laboratory. Bond records indicate single, double, triple, or aromatic bond orders with stereo flags compatible with stereochemical representations in systems developed at Stanford University and University of California, San Francisco. Charge, isotope, and radical information can be embedded via explicit property lines exploited by cheminformatics platforms such as ChemAxon and OpenEye Scientific Software. Metadata fields are commonly leveraged by cheminformatics pipelines in industry consortia like PharmaNet and academic collaborations with repositories such as ChEMBL.
Several related formats expand or encapsulate the MOL connection table. The SDF (Structure-Data File) format bundles multiple MOL records with keyed data fields and is widely used by databases like PubChem and ZINC database. The V2000 and V3000 are two major MOL dialects: V3000 adds more expressive features recognized by modern editors such as ChemDraw and toolkits like OpenBabel. Other alternative representations include SMILES used by projects at Daylight Chemical Information Systems and InChI strings standardized by IUPAC and InChI Trust; these are often stored alongside MOL records in data exchanges among organizations like Cambridge Crystallographic Data Centre.
MOL files are used for tasks including molecular visualization, virtual screening workflows, conformer generation, force-field parameter assignment, and QSAR model building by academic groups at Harvard University and industry labs at AstraZeneca. Major cheminformatics toolkits—OpenBabel, RDKit, CDK—provide read/write support and conversion utilities. Commercial suites such as Schrödinger, Inc.’s Maestro, Accelrys’ Discovery Studio, and ChemAxon’s Marvin implement full parsing and GUI integration. Public repositories like PubChem ingest MOL or SDF submissions, and electronic lab notebooks developed by companies like Benchling interoperate with MOL files for structure storage.
Critiques focus on expressiveness and ambiguity: the format does not fully capture reaction mechanisms, macromolecular assemblies as handled by Protein Data Bank, or complex stereochemical conventions promulgated in some IUPAC recommendations. The V2000 variant has fixed field widths that constrain large molecules, prompting migration to V3000 in workflows at Pfizer and Novartis. Lack of formal versioning and optional extensions can cause interoperability issues between tools from vendors including BIOVIA and open-source projects like OpenBabel. Finally, compressed binary alternatives and graph-based standards used in initiatives at Google and Microsoft offer more efficient storage for very large datasets, which has motivated community discussions at conferences organized by International Union of Crystallography.
Category:Chemical file formats