Description of several chemical structure file formats used by computer programs developed at Molecular Design Limited

By A. Dalby, J. Nourse, W. D. Hounshell, Ann. K. I. Gushurst, D. Grier, B. A. Leland, J. Laufer. 1992

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Citations in the corpus

PubChem Substance and Compound databases (2015, methodology): “The records can be exported in several formats, including SDF (11), large and small images, SMILES (12–14), InChI (15–18), XML and either text or binary ASN.1.”
REFMAC5 dictionary: organization of prior chemical knowledge and guidelines for its use. (2004, methodology): “Future versions of the dictionary will contain tools to use popular computational chemical ®le formats such as SMILES (Weininger, 1988) and MDL MOLFILES (Dalby et al., 1992).”
Ambiguity of non-systematic chemical identifiers within and between small-molecule databases (2015, unknown): “We focused on compound records that had associated chemical structures in the form of MOL files [27].”
Combining Machine Learning Systems and Multiple Docking Simulation Packages to Improve Docking Prediction Reliability for Network Pharmacology (2013, methodology): “Users can upload a reasonable number of test compound structures in 1D, 2D, or 3D, and the screening pipeline accepts most common formats, such as MDL SDF [35], Sybyl Mol2 [36] and Daylight SMILES [37].”
PubChem: Integrated Platform of Small Molecules and Biological Activities (2008, methodology): “These formats include SDF, image, small image, SMILES, InChI, XML, and either text or binary ASN.1.”
The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching (2017, background): “The format forms the core of the larger CTfile family which was originally developed by MDL Information Systems [73].”
AceDRG: a stereochemical description generator for ligands (2017, methodology): “The current version of AceDRG accepts CCD mmCIF, SMILES string, SDF MOL (Dalby et al. , 1992) and SYBYL MOL2 (Clark et al. , 1989) ﬁle formats.”
ClassyFire: automated chemical classification with a comprehensive, computable taxonomy (2016, background): “Classification results can also be downloaded in a JSON [40], SDF [41], or CSV [42] format.”
JLigand: a graphical tool for the CCP4 template-restraint library (2012, methodology): “In particular, SDF (Dalby et al., 1992), SYBYL mol2 (Tripos, 2005) and PDB files, as well as SMILE strings (Weininger, 1988; Greaves et al., 1999), can be used as input files for LibCheck.”