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    Shruthi Viswanath, PhD

    TitlePostdoctoral Scholar
    SchoolUCSF School of Pharmacy
    Address1700 4th Street
    San Francisco CA 94158
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      Collapse Biography 
      Collapse Education and Training
      University of Texas at AustinPh. D.Computer Science2014
      National Institute of Technology KarnatakaB. TechInformation Technology2008
      Collapse Awards and Honors
      UT Austin2008 - 2009Microelectronics and Computer Development Fellowship
      UT Austin2008 - 2008Phi Kappa Phi Honor Society
      UT Austin2008 - 2008Deans Award for Excellence
      NITK2005 - 2008Institute of Engineers Certificate of Merit
      NITK2008 - 2008Institute Gold Medal, Best Outgoing Student of Information Technology
      IIT Kanpur2006 - 2006Summer UG Research Grant for Excellence

      Collapse Overview 
      Collapse Overview
      I am a postdoctoral scholar in the laboratory of Prof Andrej Sali at UCSF. My research is focused in two directions: (a) methods and (b) applications of integrative modeling for determining the structure of macromolecular complexes. Using integrative modeling we are working to determine the structure of the yeast spindle pole body, a gigadalton cell organelle involved in nucleating microtubules in yeast. Towards this aim, we are modeling the (1) structure of the SPB core and (2) its interaction with the gamma tubulin subcomplex. We work with experimental collaborators combining FRET, EM, SAXS, X-ray and proteomics data in an integrative structure determination approach. I also work on the methods side of integrative modeling. To this end, I develop (1) improved validation protocols for modeling and (2) better ways to represent proteins in integrative models.

      Collapse Interests
      Computational structural biology, protein-protein docking, integrative modeling, cell biology, machine learning, computational statistics, protein structure prediction.

      Collapse Bibliographic 
      Collapse Publications
      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
      List All   |   Timeline
      1. Lensink MF, Velankar S, Kryshtafovych A, Huang SY, Schneidman-Duhovny D, Sali A, Segura J, Fernandez-Fuentes N, Viswanath S, Elber R, Grudinin S, Popov P, Neveu E, Lee H, Baek M, Park S, Heo L, Rie Lee G, Seok C, Qin S, Zhou HX, Ritchie DW, Maigret B, Devignes MD, Ghoorah A, Torchala M, Chaleil RA, Bates PA, Ben-Zeev E, Eisenstein M, Negi SS, Weng Z, Vreven T, Pierce BG, Borrman TM, Yu J, Ochsenbein F, Guerois R, Vangone A, Rodrigues JP, van Zundert G, Nellen M, Xue L, Karaca E, Melquiond AS, Visscher K, Kastritis PL, Bonvin AM, Xu X, Qiu L, Yan C, Li J, Ma Z, Cheng J, Zou X, Shen Y, Peterson LX, Kim HR, Roy A, Han X, Esquivel-Rodriguez J, Kihara D, Yu X, Bruce NJ, Fuller JC, Wade RC, Anishchenko I, Kundrotas PJ, Vakser IA, Imai K, Yamada K, Oda T, Nakamura T, Tomii K, Pallara C, Romero-Durana M, Jiménez-García B, Moal IH, Férnandez-Recio J, Joung JY, Kim JY, Joo K, Lee J, Kozakov D, Vajda S, Mottarella S, Hall DR, Beglov D, Mamonov A, Xia B, Bohnuud T, Del Carpio CA, Ichiishi E, Marze N, Kuroda D, Roy Burman SS, Gray JJ, Chermak E, Cavallo L, Oliva R, Tovchigrechko A, Wodak SJ, et al. Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment. Proteins. 2016 Apr 28. PMID: 27122118.
        View in: PubMed
      2. Viswanath S, Dominguez L, Foster LS, Straub JE, Elber R. Extension of a protein docking algorithm to membranes and applications to amyloid precursor protein dimerization. Proteins. 2015 Dec; 83(12):2170-85. PMID: 26404856.
        View in: PubMed
      3. Luo J, Cimermancic P, Viswanath S, Ebmeier CC, Kim B, Dehecq M, Raman V, Greenberg CH, Pellarin R, Sali A, Taatjes DJ, Hahn S, Ranish J. Architecture of the Human and Yeast General Transcription and DNA Repair Factor TFIIH. Mol Cell. 2015 Sep 3; 59(5):794-806. PMID: 26340423; PMCID: PMC4560838 [Available on 09/03/16].
      4. Viswanath S, Ravikant DV, Elber R. DOCK/PIERR: web server for structure prediction of protein-protein complexes. Methods Mol Biol. 2014; 1137:199-207. PMID: 24573483.
        View in: PubMed
      5. Viswanath S, Kreuzer SM, Cardenas AE, Elber R. Analyzing milestoning networks for molecular kinetics: definitions, algorithms, and examples. J Chem Phys. 2013 Nov 7; 139(17):174105. PMID: 24206285; PMCID: PMC3838425.
      6. Viswanath S, Ravikant DV, Elber R. Improving ranking of models for protein complexes with side chain modeling and atomic potentials. Proteins. 2013 Apr; 81(4):592-606. PMID: 23180599.
        View in: PubMed
      7. Shruthi Viswanath, Chengyong Yang. . Color call improvement in next generation sequencing using multi-class support vector machines. Color call improvement in next generation sequencing using multi-class support vector machines. 2012; 13(8):A3.
      8. K Chandrasekaran, Prarthana A.G. and Shruthi Viswanath. . Requirements Driven Modeling of Autonomic Systems,. Requirements Driven Modeling of Autonomic Systems. 2008; 175-180.
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