Fwd: Chemistry Seminar Tuesday, 10/4/2016 Takayuki Kimura (Lustig) MS Final

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---------- Forwarded message ----------
From: Ngoc-Huong Nguyen <huongnng...@yahoo.com>
Date: Wed, Sep 28, 2016 at 8:34 PM
Subject: Fwd: Chemistry Seminar Tuesday, 10/4/2016 Takayuki Kimura (Lustig) MS Final
To: Biodiversity Club <biodiver...@gmail.com>




Ngoc-Huong Nguyen

Begin forwarded message:

From: SJSU Chemistry Club <chemistr...@gmail.com>
Date: September 28, 2016 at 8:03:59 PM PDT
To: "Chem Club (SAACS)" <chem-club-saacs@googlegroups.com>
Subject: Fwd: Chemistry Seminar Tuesday, 10/4/2016 Takayuki Kimura (Lustig) MS Final
Reply-To: chemistr...@gmail.com

Hello everyone, 

Please check out this seminar. RSVP here for participation points if you are a member: https://goo.gl/forms/rXAq0WXJHsnORr1o2

Best,
Nhi

---------- Forwarded message ----------
From: Roger Terrill <roger....@sjsu.edu>
Date: Wed, Sep 28, 2016 at 2:32 PM
Subject: Chemistry Seminar Tuesday, 10/4/2016 Takayuki Kimura (Lustig) MS Final
To: Chem Faculty <chem-facu...@sjsu.edu>, SJSU Chemistry Club <chemistr...@gmail.com>, sami....@sjsu.edu


CHEMISTRY Departmental Seminar

Mr. Takayuki Kimura

SJSU MS Candidate, Brooke Lustig Advisor

 

RNA-Protein Structure Classifiers Incorporated into Second-Generation Statistical Potentials

 

            Computational modeling of RNA-protein interactions remains an important endeavor.  However, exclusively all-atom approaches that model RNA-protein interactions via molecular dynamics are often problematic in their application.  One possible alternative is the implementation of hierarchical approaches, first efficiently exploring configurational space with a coarse-grained representation of the RNA and protein.  Subsequently, the lowest energy set of such coarse-grained models can be used as scaffolds for all-atom placements, a standard method in modeling protein 3D-structure. However, the coarse-grained modeling likely will require improved ribonucleotide-amino acid potentials as applied to coarse-grained structures.  As a first step we downloaded 1345 PDB files and clustered them with PISCES to obtain non-redundant complex data set.  The contacts were divided into nine types with DSSR according to the 3D structure of RNA and then 9 sets of potentials were calculated.  The potentials were applied to score fifty thousand poses generated by FTDock for twenty-one standard RNA-protein complexes.  The results compare favorably to existing RNA-protein potentials. Future research will optimize and test such combined potentials.

 

 

 

 

 

Tues, October 4 4:30 PM

Duncan Hall 250

For more information: Prof. Roger Terrill at 408-924-4970 / Roger....@sjsu.edu


--
Roger H. Terrill
Associate Professor of Chemistry
San Jose State University




--

Nhi Vo - President
Tina Nguyen - Vice President
Cuong Pham - Secretary
Tam Lam - Treasurer/General Manager
Irene Lin - Event Coordinator

Student Affiliates of the American Chemical Society/SAACS/Chemistry Club
Department of Chemistry, DH 20
San Jose State University
San Jose, CA  95192-0101

--
Nhi Vo - President
Tina Nguyen - Vice President
Cuong Pham - Secretary
Tam Lam - Treasurer/General Manager
Irene Lin - Event Coordinator
 
Student Affiliates of the American Chemical Society/SAACS/Chemistry Club
Department of Chemistry, DH 20
San Jose State University
San Jose, CA 95192-0101
(408) 924-4937
 
Facebook Page: https://www.facebook.com/groups/sjsuchemclub/
Google Group Page: https://groups.google.com/group/chem-club-saacs
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