Shruthi Viswanath, PhD

TitlePostdoctoral Scholar
InstitutionUniversity of California San Francisco
Address1700 4th Street
San Francisco CA 94158
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    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.

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    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.
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    1. Viswanath S, Chemmama IE, Cimermancic P, Sali A. Assessing Exhaustiveness of Stochastic Sampling for Integrative Modeling of Macromolecular Structures. Biophys J. 2017 Dec 05; 113(11):2344-2353. PMID: 29211988.
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    2. Webb B, Viswanath S, Bonomi M, Pellarin R, Greenberg CH, Saltzberg D, Sali A. Integrative structure modeling with the Integrative Modeling Platform. Protein Sci. 2018 Jan; 27(1):245-258. PMID: 28960548.
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    3. Viswanath S, Bonomi M, Kim SJ, Klenchin VA, Taylor KC, Yabut KC, Umbreit NT, Van Epps HA, Meehl J, Jones MH, Russel D, Velazquez-Muriel JA, Winey M, Rayment I, Davis TN, Sali A, Muller EG. The molecular architecture of the yeast spindle pole body core determined by Bayesian integrative modeling. Mol Biol Cell. 2017 Nov 07; 28(23):3298-3314. PMID: 28814505.
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    4. 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. Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment. Proteins. 2016 09; 84 Suppl 1:323-48. PMID: 27122118.
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    5. 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; PMCID: PMC4715591 [Available on 12/01/16].
    6. 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 03; 59(5):794-806. PMID: 26340423; PMCID: PMC4560838.
    7. 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.
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    8. Viswanath S, Kreuzer SM, Cardenas AE, Elber R. Analyzing milestoning networks for molecular kinetics: definitions, algorithms, and examples. J Chem Phys. 2013 Nov 07; 139(17):174105. PMID: 24206285; PMCID: PMC3838425.
    9. 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.
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    10. Shruthi Viswanath, Chengyong Yang.BMC Bioinformatics. Color call improvement in next generation sequencing using multi-class support vector machines. 2012; 13(8):A3.
    11. K Chandrasekaran, Prarthana A.G. and Shruthi Viswanath.Proceedings of the International Conference on Computer Networks and Security (ICCNS). Requirements Driven Modeling of Autonomic Systems. 2008; 175-180.
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