Search Results - "Kamisetty, Hetunandan"

Robust and accurate prediction of residue-residue interactions across protein interfaces using evolutionary information by Ovchinnikov, Sergey, Kamisetty, Hetunandan, Baker, David

“…Do the amino acid sequence identities of residues that make contact across protein interfaces covary during evolution? If so, such covariance could be used to…”
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Assessing the utility of coevolution-based residue–residue contact predictions in a sequence- and structure-rich era by Kamisetty, Hetunandan, Ovchinnikov, Sergey, Baker, David

“…Recently developed methods have shown considerable promise in predicting residue–residue contacts in protein 3D structures using evolutionary covariance…”
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Protein structure determination using metagenome sequence data by Ovchinnikov, Sergey, Park, Hahnbeom, Varghese, Neha, Huang, Po-Ssu, Pavlopoulos, Georgios A., Kim, David E., Kamisetty, Hetunandan, Kyrpides, Nikos C., Baker, David

“…Despite decades of work by structural biologists, there are still ~5200 protein families with unknown structure outside the range of comparative modeling. We…”
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Learning generative models for protein fold families by Balakrishnan, Sivaraman, Kamisetty, Hetunandan, Carbonell, Jaime G., Lee, Su-In, Langmead, Christopher James

“…We introduce a new approach to learning statistical models from multiple sequence alignments (MSA) of proteins. Our method, called GREMLIN (Generative…”
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Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing by Whitehead, Timothy A, Chevalier, Aaron, Song, Yifan, Dreyfus, Cyrille, Fleishman, Sarel J, De Mattos, Cecilia, Myers, Chris A, Kamisetty, Hetunandan, Blair, Patrick, Wilson, Ian A, Baker, David

“…To increase the affinity of designed protein inhibitors for influenza hemagglutinin, Whitehead et al . use yeast display and deep sequencing to measure the…”
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Computation and Functional Studies Provide a Model for the Structure of the Zinc Transporter hZIP4 by Antala, Sagar, Ovchinnikov, Sergey, Kamisetty, Hetunandan, Baker, David, Dempski, Robert E.

“…Members of the Zrt and Irt protein (ZIP) family are a central participant in transition metal homeostasis as they function to increase the cytosolic…”
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Large-scale determination of previously unsolved protein structures using evolutionary information by Ovchinnikov, Sergey, Kinch, Lisa, Park, Hahnbeom, Liao, Yuxing, Pei, Jimin, Kim, David E, Kamisetty, Hetunandan, Grishin, Nick V, Baker, David

“…The prediction of the structures of proteins without detectable sequence similarity to any protein of known structure remains an outstanding scientific…”
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An efficient randomized algorithm for contact-based NMR backbone resonance assignment by Kamisetty, Hetunandan, Bailey-Kellogg, Chris, Pandurangan, Gopal

“…Motivation: Backbone resonance assignment is a critical bottleneck in studies of protein structure, dynamics and interactions by nuclear magnetic resonance…”
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Origins of coevolution between residues distant in protein 3D structures by Anishchenko, Ivan, Ovchinnikov, Sergey, Kamisetty, Hetunandan, Baker, David

“…Residue pairs that directly coevolve in protein families are generally close in protein 3D structures. Here we study the exceptions to this general…”
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Accounting for conformational entropy in predicting binding free energies of protein-protein interactions by Kamisetty, Hetunandan, Ramanathan, Arvind, Bailey-Kellogg, Chris, Langmead, Christopher James

“…Protein‐protein interactions are governed by the change in free energy upon binding, ΔG = ΔH − TΔS. These interactions are often marginally stable, so one must…”
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Learning sequence determinants of protein:protein interaction specificity with sparse graphical models by Kamisetty, Hetunandan, Ghosh, Bornika, Langmead, Christopher James, Bailey-Kellogg, Chris

“…In studying the strength and specificity of interaction between members of two protein families, key questions center on which pairs of possible partners…”
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Learning generative models of molecular dynamics by Razavian, Narges Sharif, Kamisetty, Hetunandan, Langmead, Christopher J

“…We introduce three algorithms for learning generative models of molecular structures from molecular dynamics simulations. The first algorithm learns a…”
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Free energy estimates of all-atom protein structures using generalized belief propagation by Kamisetty, Hetunandan, Xing, Eric P, Langmead, Christopher J

“…We present a technique for approximating the free energy of protein structures using generalized belief propagation (GBP). The accuracy and utility of these…”
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Match-Tensor: a Deep Relevance Model for Search by Jaech, Aaron, Kamisetty, Hetunandan, Ringger, Eric, Clarke, Charlie

“…The application of Deep Neural Networks for ranking in search engines may obviate the need for the extensive feature engineering common to current…”
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