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| About Markus Sitzmann (NCI) |
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Markus Sitzmann obtained his Ph.D. in 2004 at the Computer-Chemistry-Center of the University of Erlangen-Nuremberg in Germany. His Ph.D. research focused on the development of methods for computer-assisted planning of organic synthesis. In August 2004, he joined the CADD group at the Laboratory of Medicinal Chemistry, National Cancer Institute in Frederick, NIH as a postdoctoral fellow. At the CADD Group, his work is focused on chemical information processing as well as on developing computer-based techniques for finding novel lead structures or the chemical refinement of promising candidates. He is one of the developers of the Chemical Structure Lookup Service (CSLS) which is currently one of the largest, publicly available small-molecule structure collections.
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| About Igor V. Filippov (NCI) |
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Igor Filippov studied at the Moscow Institute of Physics and Technology (B.Sc. 1996) and the Ohio State University (Ph.D. 2002). The topic of his graduate research was Discrete Light Cone Quantization which involved computer modeling of energy spectra of subatomic particles. Currently he is working in the Computer-Aided Drug Design group at the Laboratory of Medicinal Chemistry, NCI/SAIC-Frederick Inc., developing software for chemoinformatics projects such as the Chemical Structure Lookup Service (CSLS, http://cactus.nci.nih.gov/lookup/) and Optical Structure Recognition Application (OSRA, http://cactus.nci.nih.gov/osra/).
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A Highly Annotated SD file of all Ligand Occurrences in the PDB
Igor V. Filippov and Markus Sitzmann, National Cancer Institute
We report on the generation of a highly annotated SD file of all ligand occurrences in the PDB. The starting point for this project was the consolidated ligand structure files recently made available on the download page of the Ligand Expo web site. The chemoinformatics toolkit CACTVS was used for the initial conversion from PDB to SD format. Care was taken to determine the correct chemical connectivity of each ligand as best as possible, through both plausibility checks and comparison with other PDB-ligand databases. The resulting SD file was annotated with numerous data extracted from the original full-entry PDB files. These annotations include "standard" properties such as resolution, year of publication, etc.; but also annotations less commonly found in secondary PDB ligand collections, such as beamline, sample temperature during collection, average ligand B values, and refinement software used. The structures have also been annotated with their presence or absence in other well-known ligand databases: BindingDB, Binding MOAD, PDBBind, sc-PDB, and the close-contact subset of MSD Ligenv. These and other annotations are intended to not only provide a convenient single source of structures and associated data that is amenable to fine-grained filtering to extract well-defined subsets for specific modeling and analysis tasks; but also to allow one to easily test for possible correlations of structural properties (such as conformational energies) with parameters that may have had an influence on the quality of the ligand structure along the crystallographic "pipeline" from crystallization through collection and refinement to deposition.
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