SCIENTIFIC/COLLABORATIVE ACTIVITIES Summary: 5 seminars, 4+ collaborations, 3+ prospective students - “Modelling protein interactomes” seminars for KMUTT, BIOTEC, Kasetsart, Mahidol, and Ramathibodi. - Collaboration with Dr. Duangdao on protein-DNA 3 D modelling (described next); RNA folding/protein RNA structure prediction. - Collaboration with Dr. Sissades on CYP 450 side effect and toxicity prediction; porting our docking code to GPUs. - Collaboration with Dr. Sukathida on neuraminidase mutant structure binding to drugs; Dr. Sukathida has two students who will potentially go to the US. - Collaboration with Drs. Supa and Chak at Kasetsart on influenza vaccine design; student Nipa will potentially return to the US. - Predicted hybrid enzyme structure ranking for Somchai; functional annotation ongoing. - Met with several researchers and students and discussed computational biology topics; 2+ students interested in pursuing studies or doing a postdoc in my group.
TECHNICAL ACTIVITIES Protein-DNA 3 D modelling server: > 90% complete. Given a protein sequence, and optional DNA sequence, predict protein-DNA complex at atomic resolution. - Installed Linux on desktop/server. - Downloaded all the RAMP/Protinfo program and source files. - Installation of all software in the RAMP/Protinfo suite. - Modified source code for server/FORTRAN compatability. * - Update protein-DNA complexes on the fly and clean – slow. * - Protein-DNA complex reconstruction and emailing. - Expansive design paradigm: will include new protein-DNA complexes as they are available in the PDB, can easily expand to RNA. - RAMP/Protinfo software is now available in house for all sorts of modelling purposes. - Papers with Duangdao; need to benchmark elegantly in paper 1. - Paper 1: A webserver for three-dimensional atomic resolution protein-DNA complex prediction. - Paper 2+: Applications of atomic resolution protein-DNA complex models (inducer/repressor/operator prediction, mutational analyses, multiprotein-DNA complexes).
CALENDAR OF ACTIVITIES dec 02 am meeting with Drs. Duangdao and Supawadee's group dec 02 pm meeting with Dr. Kanyawim dec 08 am lunch with Dr. Prasit dec 14 am talk with Dr. Somchai (from Dr. Lily's lab) on protein design dec 14 pm meeting with Dr. Yongyuth dec 15 pm meeting with Dr. Duangdao and student Wit on RNA folding dec 16 am obtain work permit photo and medical certificate dec 18 am KMUTT seminar "Modelling interactomes" from 10 -1130 a dec 18 am meeting with Drs. Morakot and Supaporn (4 -5 p) dec 21 am BIOTEC seminar "Modelling interactomes" from 9 -10 a dec 21 pm meeting with KMUTT researcher dec 22 pm meeting with Dr. Sissades and student – started collaboration on drug side effect and toxicity predictions based on CYP 450 interactions dec 22 pm first month report dec 23 pm meeting with Somchai (from Dr. Lily's lab) on protein design dec 29 am meeting with Dr. Sissades and students - started second collaboration on porting Samudrala flexible docking code to GPUs jan 08 ** meeting with Dr. Wasun Chantratita and students at Ramathibodi Hospital jan 13 ** seminar "Modelling protein interactomes" and meeting with Drs. Supa Hannongbua and Chak Sangma at Kasetsart University jan 19 ** seminar "Modelling protein interactomes" at Mahidol University Microbiology Dept jan 22 ** meeting at BIOTEC jan ? ? ** seminar "Modelling protein interactomes" at Ramathibodi Hospital
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