Sai Kumar Ramadugu

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Protein folding is scientifically and computationally challenging problem. The early phases of protein folding are interesting due to various events like nascent secondary structure formation, hydrophobic collapse leading to formation of non-native or meta-stable conformations. These events occur within a very short time span of 100 ns as compared to total(More)
In this study, we present a general-purpose methodology for deriving the three-dimensional (3D) arrangement of multivalent transmembrane complexes in the presence of their ligands. Specifically, we predict the most likely families of structures of the experimentally intractable trimeric asialoglycoprotein receptor (ASGP-R), which consists of human hepatic(More)
In this article, we characterize the behavior of water on the surface of a diverse group of carbohydrates and attempt to determine the role of saccharide size, linkage, and branching as well as secondary structure on the dynamics and structure of water at the surface. In order to better understand the similarities and differences in the behavior of the(More)
An Advanced Cyberinfrastructure Research and Education Facilitator (ACI-REF) works directly with researchers to advance the computing- and data-intensive aspects of their research, helping them to make effective use of Cyberinfrastructure (CI). The University of Oklahoma (OU) is leading a national "virtual residency" program to prepare ACI-REFs to provide(More)
The carbohydrate binding protein, Cyanovirin-N, obtained from cyanobacteria, consists of high-affinity and low-affinity binding domains. To avoid the formation of a domain swapped structure in solution and also to better focus on the binding of carbohydrates at the high-affinity site, the Ghirlanda group (Biochemistry, 46, 2007, 9199-9207) engineered the(More)
The utilization of substoichiometric amounts of commercially available nickel(II) triflate as an activator in the reagent-controlled glycosylation reaction for the stereoselective construction of biologically relevant targets containing 1,2-cis-2-amino glycosidic linkages is reported. This straightforward and accessible methodology is mild, operationally(More)
The current thesis presents work on the structure and dynamics of oligosaccharides and polysaccharides as well as the free energetics of carbohydrate-protein interactions. By applying various computational tools such as molecular dynamics simulations, our in-house fast sugar structure prediction software, replica exchange molecular dynamics, homology(More)
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