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| OpenEye OEChem | |
|---|---|
| Name | OEChem |
| Developer | OpenEye Scientific Software |
| Latest release | (proprietary) |
| Written in | C++ |
| Operating system | Windows, Linux, macOS |
| Genre | Cheminformatics toolkit |
| License | Commercial |
OpenEye OEChem is a commercial cheminformatics toolkit produced by OpenEye Scientific Software for molecular manipulation, representation, and analysis. The toolkit is used in pharmaceutical research, computational chemistry, and structural biology by organizations such as Pfizer, Novartis, Roche, GlaxoSmithKline, and Merck & Co.. It interoperates with software and institutions like Schrödinger, Academic Research Consortium, Lawrence Berkeley National Laboratory, Argonne National Laboratory, and European Bioinformatics Institute.
OEChem provides APIs for chemical perception, atom typing, substructure search, and molecular property calculation for use in workflows at companies including AstraZeneca, Bayer, Eli Lilly and Company, Takeda Pharmaceutical Company, and Sanofi. It supports integration with visualization and modeling platforms developed by groups such as UCSF, Stanford University, Massachusetts Institute of Technology, Harvard University, and California Institute of Technology. The toolkit complements computational engines like AutoDock Vina, GROMACS, AMBER, CHARMM, and NAMD and is often used alongside data resources including Protein Data Bank, ChEMBL, PubChem, DrugBank, and ZINC15.
Development began in the late 1990s amid growth in cheminformatics at companies and labs such as Sun Microsystems Laboratories, IBM Research, Microsoft Research, Bell Labs, and Los Alamos National Laboratory. OEChem evolved through contributions informed by standards from organizations like IUPAC, InChI Trust, OpenBabel Project, MDL Information Systems, and Chemical Abstracts Service. The toolkit's roadmap has been influenced by collaborations with academic groups at University of Cambridge, University of Oxford, ETH Zurich, Max Planck Society, and Imperial College London and by industry consortia including Bioinformatics Open Source Conference participants and members of The Royal Society.
Key features include atom and bond manipulation, stereochemistry handling, aromaticity models, and tautomer enumeration leveraged in projects at Genentech, Regeneron Pharmaceuticals, Illumina, Thermo Fisher Scientific, and Agilent Technologies. The API supports substructure search, SMARTS pattern matching, molecular descriptor calculation, and fingerprinting used in cheminformatics pipelines at Novartis Institutes for BioMedical Research, Boehringer Ingelheim, Bristol-Myers Squibb, Vertex Pharmaceuticals, and Celgene. It also implements canonicalization, SMILES parsing, and molecular hashing routines paralleling efforts by Daylight Chemical Information Systems, OpenEye Scientific Software (company), RDKit contributors, ChemAxon, and BIOVIA for tasks in virtual screening and lead optimization practiced at Merck KGaA, Lilly Research Laboratories, and Johnson & Johnson.
OEChem reads and writes formats used by community resources and commercial packages such as SDF, MOL2, PDB, SMILES, and InChI strings managed by InChI Trust. It interfaces with conversion tools and libraries developed by Open Babel, RDKit, ChemAxon, Dialogues on Open Data, and standards bodies like The International Union of Pure and Applied Chemistry to maintain compatibility with datasets from European Molecular Biology Laboratory, National Institutes of Health, Wellcome Trust, Bill & Melinda Gates Foundation, and Defense Advanced Research Projects Agency.
Distributed under commercial licensing tailored for academia and industry, OEChem licensing negotiates with institutions like Massachusetts General Hospital, Johns Hopkins University, University of California, San Francisco, Cold Spring Harbor Laboratory, and Scripps Research. Supported on major platforms including Linux, macOS, and Windows Server environments used at supercomputing centers like Oak Ridge National Laboratory, Lawrence Livermore National Laboratory, National Center for Supercomputing Applications, ServiceNow, and corporate clusters at Google, Amazon Web Services, and Microsoft Azure.
OEChem is applied in virtual screening, lead discovery, ADMET prediction, and patent analysis workflows at pharmaceutical and biotech firms such as Amgen, Biogen, Illumina Ventures, Regeneron, and Genmab. It underpins scaffold hopping, similarity searching, and library design in collaborations with institutions like Cold Spring Harbor, Scripps Institution of Oceanography, Weill Cornell Medicine, Yale University, and Columbia University. The toolkit is also incorporated into cheminformatics curricula and training at University of California, Berkeley, Princeton University, Cornell University, Duke University, and Johns Hopkins Bloomberg School of Public Health.
OEChem integrates with other OpenEye toolkits for tasks involving docking, scoring, and molecular mechanics used in pipelines with FRED, HYBRID, OMEGA, ROCS, and SZYBKI at research groups including Scripps Research Institute, Fred Hutchinson Cancer Research Center, Dana-Farber Cancer Institute, Memorial Sloan Kettering Cancer Center, and Vanderbilt University Medical Center. Cross-toolkit workflows connect to visualization platforms and cheminformatics services provided by organizations such as MolSoft, Schrödinger, LLC, Accelrys, OpenEye Scientific Software (company), and repositories like GitHub for reproducible research and collaborative development.
Category:Cheminformatics software