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NLM Intramural Research Program (IRP) Seminars

We hold weekly seminars by NLM IRP members each Tuesday at 11 AM and selected Thursdays at 3 PM in the B2 Library, Building 38A. Visitors' presentations usually take place in the same room, but are scheduled on a different day of the week. If scheduling a visitor's presentation, please don't forget to book a seminar room.

To schedule a seminar, please click on the appropriate date in the calendar. Please follow this link to subscribe/unsubscribe to/from the NLM IRP seminar mailing list.



Questions about NLM IRP Seminars? Click here.



iCn3D viewer. Jiyao Wang's seminar on February 4, 2020. Illustration by Donald Bliss.

Upcoming Seminars

Zhi SunApril 13, 2021 at 11:00
PubChem3D: Conformer Generation with RDKit
“PubChem is an open archive for the biological activities of small molecules. It provides search and analysis tools to assist users in locating desired information. It consists of three primary databases: Substance, Compound, and BioAssay. For the Compound database, it currently contains over 100 million unique chemical structures extracted from contributed PubChem Substance records. PubChem3D provides theoretical 3-D conformer model description for each compound record, which is the foundation of the PubChem3D project. In addition to augmenting the existing similarity of 2-D chemical structure graphs. PubChem3D relates theoretical 3-D descriptions of chemical structures to experimental biological activities. To achieve this, PubChem team established theoretical conformer generation models which effectively compute and reproduce experimentally determined bioactive conformations. This is currently supported and maintained by commercial software packages and codes developed by PubChem. Conformer generation is of continuing interest in cheminformatics and particularly in computational drug discovery. It is also the basis of the PubChem3D project. In present work, we explore the use of RDKit, one of the leading small molecule conformer generation tools, for generating conformers in the PubChem3D project. The theoretical 3-D conformers were generated for over 30,000 small-molecule ligands in the Molecular Modeling Database (MMDB), whose 3-D structures were experimentally determined. The primary RDKit conformer generation parameters (the energy window size, force field variant, and ETKDG variant) are examined and optimized. Benchmark results indicate that the performance of RDKit tools is comparable to and even better than our current conformer generation algorithms, in obtaining low root-mean-squared distance (RMSD) conformers to the experimental structures. Therefore, RDKit can be a promising alternative to commercial software to establish new conformer models for the PubChem3D project. “

No seminar todayApril 15, 2021 at 15:00
No seminar today
Po-Ting LaiApril 20, 2021 at 11:00
TBD