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26 results on '"Sripakdeevong, Parin"'

2. 274 Development of CTX112 a next generation allogeneic multiplexed CRISPR-edited CART cell therapy with disruptions of the TGFBR2 and Regnase-1 genes for improved manufacturing and potency

Author

Kalaitzidis, Demetrios, primary, Ghonime, Mohammed, additional, Chain, Robert, additional, Jaishankar, Nivedita, additional, Settipane, Davis, additional, Padalia, Zinkal, additional, Zakas, Lauren, additional, Kuppuraju, Meghna, additional, Tetteh, Paul, additional, Dequeant, Mary-Lee, additional, Karnik, Sushant, additional, Massilamany, Chandirasegaran, additional, McEwan, Brigid, additional, Dar, Henia, additional, Allen, Melanie, additional, Serwer, Laura, additional, Nguyen, Thao, additional, Butler-Gauthier, Melanie, additional, Sripakdeevong, Parin, additional, Nagar, Shashwat, additional, Tang, Yin, additional, Flanagan, Nicole, additional, Huang, Elaine, additional, Phuyal, Shashwant, additional, Dunn, Andrew, additional, Koch, Elizabeth, additional, Sula, Erisa, additional, Waldman, Jacob, additional, Zhang, Maria Lei, additional, Loaiza, Cristian, additional, Thorstensen, Erin, additional, Steiger, Keith, additional, Schum, Katie, additional, Urbaez, Kayla, additional, Ma, Anna, additional, Weaver, Annie Yang, additional, Finch, Christopher, additional, Cohen, Sarah, additional, Morrow, PK, additional, Benton, Mark, additional, and Terrett, Jonathan, additional

Published
2023
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3. Serverification of Molecular Modeling Applications: the Rosetta Online Server that Includes Everyone (ROSIE)

Author

Lyskov, Sergey, Chou, Fang-Chieh, Conchúir, Shane Ó, Der, Bryan S., Drew, Kevin, Kuroda, Daisuke, Xu, Jianqing, Weitzner, Brian D., Renfrew, P. Douglas, Sripakdeevong, Parin, Borgo, Benjamin, Havranek, James J., Kuhlman, Brian, Kortemme, Tanja, Bonneau, Richard, Gray, Jeffrey J., and Das, Rhiju

Subjects
Quantitative Biology - Quantitative Methods, Quantitative Biology - Biomolecules
Abstract

The Rosetta molecular modeling software package provides experimentally tested and rapidly evolving tools for the 3D structure prediction and high-resolution design of proteins, nucleic acids, and a growing number of non-natural polymers. Despite its free availability to academic users and improving documentation, use of Rosetta has largely remained confined to developers and their immediate collaborators due to the code's difficulty of use, the requirement for large computational resources, and the unavailability of servers for most of the Rosetta applications. Here, we present a unified web framework for Rosetta applications called ROSIE (Rosetta Online Server that Includes Everyone). ROSIE provides (a) a common user interface for Rosetta protocols, (b) a stable application programming interface for developers to add additional protocols, (c) a flexible back-end to allow leveraging of computer cluster resources shared by RosettaCommons member institutions, and (d) centralized administration by the RosettaCommons to ensure continuous maintenance. This paper describes the ROSIE server infrastructure, a step-by-step 'serverification' protocol for use by Rosetta developers, and the deployment of the first nine ROSIE applications by six separate developer teams: Docking, RNA de novo, ERRASER, Antibody, Sequence Tolerance, Supercharge, Beta peptide design, NCBB design, and VIP redesign. As illustrated by the number and diversity of these applications, ROSIE offers a general and speedy paradigm for serverification of Rosetta applications that incurs negligible cost to developers and lowers barriers to Rosetta use for the broader biological community. ROSIE is available at http://rosie.rosettacommons.org.

Published
2013
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4. Correcting pervasive errors in RNA crystallography through enumerative structure prediction

Author

Chou, Fang-Chieh, Sripakdeevong, Parin, Dibrov, Sergey M., Hermann, Thomas, and Das, Rhiju

Subjects
Quantitative Biology - Biomolecules
Abstract

Three-dimensional RNA models fitted into crystallographic density maps exhibit pervasive conformational ambiguities, geometric errors and steric clashes. To address these problems, we present enumerative real-space refinement assisted by electron density under Rosetta (ERRASER), coupled to Python-based hierarchical environment for integrated 'xtallography' (PHENIX) diffraction-based refinement. On 24 data sets, ERRASER automatically corrects the majority of MolProbity-assessed errors, improves the average Rfree factor, resolves functionally important discrepancies in noncanonical structure and refines low-resolution models to better match higher-resolution models.

Published
2011
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5. Can biopolymer structures be sampled enumeratively? Atomic-accuracy RNA loop modeling by a stepwise ansatz

Author

Sripakdeevong, Parin, Kladwang, Wipapat, and Das, Rhiju

Subjects
Quantitative Biology - Biomolecules
Abstract

Atomic-accuracy structure prediction of macromolecules is a long-sought goal of computational biophysics. Accurate modeling should be achievable by optimizing a physically realistic energy function but is presently precluded by incomplete sampling of a biopolymer's many degrees of freedom. We present herein a working hypothesis, called the "stepwise ansatz", for recursively constructing well-packed atomic-detail models in small steps, enumerating several million conformations for each monomer and covering all build-up paths. By implementing the strategy in Rosetta and making use of high-performance computing, we provide first tests of this hypothesis on a benchmark of fifteen RNA loop modeling problems drawn from riboswitches, ribozymes, and the ribosome, including ten cases that were not solvable by prior knowledge based modeling approaches. For each loop problem, this deterministic stepwise assembly (SWA) method either reaches atomic accuracy or exposes flaws in Rosetta's all-atom energy function, indicating the resolution of the conformational sampling bottleneck. To our knowledge, SWA is the first enumerative, ab initio build-up method to systematically outperform existing Monte Carlo and knowledge-based methods for 3D structure prediction. As a rigorous experimental test, we have applied SWA to a small RNA motif of previously unknown structure, the C7.2 tetraloop/tetraloop-receptor, and stringently tested this blind prediction with nucleotide-resolution structure mapping data.

Published
2011

6. Why Can't We Predict RNA Structure At Atomic Resolution?

Author

Beauchamp, Kyle, Sripakdeevong, Parin, and Das, Rhiju

Subjects
Quantitative Biology - Biomolecules, Physics - Biological Physics, Physics - Chemical Physics
Abstract

No existing algorithm can start with arbitrary RNA sequences and return the precise, three-dimensional structures that ensures their biological function. This chapter outlines current algorithms for automated RNA structure prediction (including our own FARNA-FARFAR), highlights their successes, and dissects their limitations, using a tetraloop and the sarcin/ricin motif as examples. The barriers to future advances are considered in light of three particular challenges: improving computational sampling, reducing reliance on experimentally solved structures, and avoiding coarse-grained representations of atomic-level interactions. To help meet these challenges and better understand the current state of the field, we propose an ongoing community-wide CASP-style experiment for evaluating the performance of current structure prediction algorithms., Comment: K. Beauchamp & P. Sripakdeevong are equally contributing authors. Submission for book: RNA 3D Structure Analysis and Prediction, editors: N. Leontis & E. Westhof

Published
2011

7. Parameter scaling in a novel measure of quantum-classical difference for decohering chaotic systems

Author

Wiebe, Nathan, Sripakdeevong, Parin, Gammal, Arnaldo, and Pattanayak, Arjendu K.

Subjects
Quantum Physics
Abstract

In this paper we introduce a diagnostic for measuring the quantum-classical difference for open quantum systems, which is the normalized size of the quantum terms in the Master equation for Wigner function evolution. For a driven Duffing oscillator, this measure shows remarkably precise scaling over long time-scales with the parameter $\zeta_0=\hbar^2/D$. We also see that, independent of $\zeta_0$ the dynamics follows a similar pattern. For small $\zeta_0$ all of our curves collapses to essentially a single curve when scaled by the maximum value of the quantum-classical difference. In both limits of large and small $\zeta_0$ we see a saturation effect in the size of the quantum-classical difference; that is, the instantaneous difference between quantum and classical evolutions cannot be either too small or too large., Comment: 4 pages, submitted at Physical Review

Published
2009

8. Data from AACR Project GENIE: Powering Precision Medicine through an International Consortium

Author

André, Fabrice, primary, Arnedos, Monica, primary, Baras, Alexander S., primary, Baselga, José, primary, Bedard, Philippe L., primary, Berger, Michael F., primary, Bierkens, Mariska, primary, Calvo, Fabien, primary, Cerami, Ethan, primary, Chakravarty, Debyani, primary, Dang, Kristen K., primary, Davidson, Nancy E., primary, Del Vecchio Fitz, Catherine, primary, Dogan, Semih, primary, DuBois, Raymond N., primary, Ducar, Matthew D., primary, Futreal, P. Andrew, primary, Gao, Jianjiong, primary, Garcia, Francisco, primary, Gardos, Stu, primary, Gocke, Christopher D., primary, Gross, Benjamin E., primary, Guinney, Justin, primary, Heins, Zachary J., primary, Hintzen, Stephanie, primary, Horlings, Hugo, primary, Hudeček, Jan, primary, Hyman, David M., primary, Kamel-Reid, Suzanne, primary, Kandoth, Cyriac, primary, Kinyua, Walter, primary, Kumari, Priti, primary, Kundra, Ritika, primary, Ladanyi, Marc, primary, Lefebvre, Céline, primary, LeNoue-Newton, Michele L., primary, Lepisto, Eva M., primary, Levy, Mia A., primary, Lindeman, Neal I., primary, Lindsay, James, primary, Liu, David, primary, Lu, Zhibin, primary, MacConaill, Laura E., primary, Maurer, Ian, primary, Maxwell, David S., primary, Meijer, Gerrit A., primary, Meric-Bernstam, Funda, primary, Micheel, Christine M., primary, Miller, Clinton, primary, Mills, Gordon, primary, Moore, Nathanael D., primary, Nederlof, Petra M., primary, Omberg, Larsson, primary, Orechia, John A., primary, Park, Ben Ho, primary, Pugh, Trevor J., primary, Reardon, Brendan, primary, Rollins, Barrett J., primary, Routbort, Mark J., primary, Sawyers, Charles L., primary, Schrag, Deborah, primary, Schultz, Nikolaus, primary, Shaw, Kenna R Mills, primary, Shivdasani, Priyanka, primary, Siu, Lillian L., primary, Solit, David B., primary, Sonke, Gabe S., primary, Soria, Jean Charles, primary, Sripakdeevong, Parin, primary, Stickle, Natalie H., primary, Stricker, Thomas P., primary, Sweeney, Shawn M., primary, Taylor, Barry S., primary, ten Hoeve, Jelle J., primary, Thomas, Stacy B., primary, Van Allen, Eliezer M., primary, Van 'T Veer, Laura J., primary, van de Velde, Tony, primary, van Tinteren, Harm, primary, Velculescu, Victor E., primary, Virtanen, Carl, primary, Voest, Emile E., primary, Wang, Lucy L., primary, Wathoo, Chetna, primary, Watt, Stuart, primary, Yu, Celeste, primary, Yu, Thomas V., primary, Yu, Emily, primary, Zehir, Ahmet, primary, and Zhang, Hongxin, primary

Published
2023
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9. Table S3 from AACR Project GENIE: Powering Precision Medicine through an International Consortium

Author

André, Fabrice, primary, Arnedos, Monica, primary, Baras, Alexander S., primary, Baselga, José, primary, Bedard, Philippe L., primary, Berger, Michael F., primary, Bierkens, Mariska, primary, Calvo, Fabien, primary, Cerami, Ethan, primary, Chakravarty, Debyani, primary, Dang, Kristen K., primary, Davidson, Nancy E., primary, Del Vecchio Fitz, Catherine, primary, Dogan, Semih, primary, DuBois, Raymond N., primary, Ducar, Matthew D., primary, Futreal, P. Andrew, primary, Gao, Jianjiong, primary, Garcia, Francisco, primary, Gardos, Stu, primary, Gocke, Christopher D., primary, Gross, Benjamin E., primary, Guinney, Justin, primary, Heins, Zachary J., primary, Hintzen, Stephanie, primary, Horlings, Hugo, primary, Hudeček, Jan, primary, Hyman, David M., primary, Kamel-Reid, Suzanne, primary, Kandoth, Cyriac, primary, Kinyua, Walter, primary, Kumari, Priti, primary, Kundra, Ritika, primary, Ladanyi, Marc, primary, Lefebvre, Céline, primary, LeNoue-Newton, Michele L., primary, Lepisto, Eva M., primary, Levy, Mia A., primary, Lindeman, Neal I., primary, Lindsay, James, primary, Liu, David, primary, Lu, Zhibin, primary, MacConaill, Laura E., primary, Maurer, Ian, primary, Maxwell, David S., primary, Meijer, Gerrit A., primary, Meric-Bernstam, Funda, primary, Micheel, Christine M., primary, Miller, Clinton, primary, Mills, Gordon, primary, Moore, Nathanael D., primary, Nederlof, Petra M., primary, Omberg, Larsson, primary, Orechia, John A., primary, Park, Ben Ho, primary, Pugh, Trevor J., primary, Reardon, Brendan, primary, Rollins, Barrett J., primary, Routbort, Mark J., primary, Sawyers, Charles L., primary, Schrag, Deborah, primary, Schultz, Nikolaus, primary, Shaw, Kenna R Mills, primary, Shivdasani, Priyanka, primary, Siu, Lillian L., primary, Solit, David B., primary, Sonke, Gabe S., primary, Soria, Jean Charles, primary, Sripakdeevong, Parin, primary, Stickle, Natalie H., primary, Stricker, Thomas P., primary, Sweeney, Shawn M., primary, Taylor, Barry S., primary, ten Hoeve, Jelle J., primary, Thomas, Stacy B., primary, Van Allen, Eliezer M., primary, Van 'T Veer, Laura J., primary, van de Velde, Tony, primary, van Tinteren, Harm, primary, Velculescu, Victor E., primary, Virtanen, Carl, primary, Voest, Emile E., primary, Wang, Lucy L., primary, Wathoo, Chetna, primary, Watt, Stuart, primary, Yu, Celeste, primary, Yu, Thomas V., primary, Yu, Emily, primary, Zehir, Ahmet, primary, and Zhang, Hongxin, primary

Published
2023
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10. Supplemental Methods, Supplemental Tables 1-2, Supplemental Figures 1-4 from AACR Project GENIE: Powering Precision Medicine through an International Consortium

Author

André, Fabrice, primary, Arnedos, Monica, primary, Baras, Alexander S., primary, Baselga, José, primary, Bedard, Philippe L., primary, Berger, Michael F., primary, Bierkens, Mariska, primary, Calvo, Fabien, primary, Cerami, Ethan, primary, Chakravarty, Debyani, primary, Dang, Kristen K., primary, Davidson, Nancy E., primary, Del Vecchio Fitz, Catherine, primary, Dogan, Semih, primary, DuBois, Raymond N., primary, Ducar, Matthew D., primary, Futreal, P. Andrew, primary, Gao, Jianjiong, primary, Garcia, Francisco, primary, Gardos, Stu, primary, Gocke, Christopher D., primary, Gross, Benjamin E., primary, Guinney, Justin, primary, Heins, Zachary J., primary, Hintzen, Stephanie, primary, Horlings, Hugo, primary, Hudeček, Jan, primary, Hyman, David M., primary, Kamel-Reid, Suzanne, primary, Kandoth, Cyriac, primary, Kinyua, Walter, primary, Kumari, Priti, primary, Kundra, Ritika, primary, Ladanyi, Marc, primary, Lefebvre, Céline, primary, LeNoue-Newton, Michele L., primary, Lepisto, Eva M., primary, Levy, Mia A., primary, Lindeman, Neal I., primary, Lindsay, James, primary, Liu, David, primary, Lu, Zhibin, primary, MacConaill, Laura E., primary, Maurer, Ian, primary, Maxwell, David S., primary, Meijer, Gerrit A., primary, Meric-Bernstam, Funda, primary, Micheel, Christine M., primary, Miller, Clinton, primary, Mills, Gordon, primary, Moore, Nathanael D., primary, Nederlof, Petra M., primary, Omberg, Larsson, primary, Orechia, John A., primary, Park, Ben Ho, primary, Pugh, Trevor J., primary, Reardon, Brendan, primary, Rollins, Barrett J., primary, Routbort, Mark J., primary, Sawyers, Charles L., primary, Schrag, Deborah, primary, Schultz, Nikolaus, primary, Shaw, Kenna R Mills, primary, Shivdasani, Priyanka, primary, Siu, Lillian L., primary, Solit, David B., primary, Sonke, Gabe S., primary, Soria, Jean Charles, primary, Sripakdeevong, Parin, primary, Stickle, Natalie H., primary, Stricker, Thomas P., primary, Sweeney, Shawn M., primary, Taylor, Barry S., primary, ten Hoeve, Jelle J., primary, Thomas, Stacy B., primary, Van Allen, Eliezer M., primary, Van 'T Veer, Laura J., primary, van de Velde, Tony, primary, van Tinteren, Harm, primary, Velculescu, Victor E., primary, Virtanen, Carl, primary, Voest, Emile E., primary, Wang, Lucy L., primary, Wathoo, Chetna, primary, Watt, Stuart, primary, Yu, Celeste, primary, Yu, Thomas V., primary, Yu, Emily, primary, Zehir, Ahmet, primary, and Zhang, Hongxin, primary

Published
2023
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11. Supplemental File 1 from AACR Project GENIE: Powering Precision Medicine through an International Consortium

Author

André, Fabrice, primary, Arnedos, Monica, primary, Baras, Alexander S., primary, Baselga, José, primary, Bedard, Philippe L., primary, Berger, Michael F., primary, Bierkens, Mariska, primary, Calvo, Fabien, primary, Cerami, Ethan, primary, Chakravarty, Debyani, primary, Dang, Kristen K., primary, Davidson, Nancy E., primary, Del Vecchio Fitz, Catherine, primary, Dogan, Semih, primary, DuBois, Raymond N., primary, Ducar, Matthew D., primary, Futreal, P. Andrew, primary, Gao, Jianjiong, primary, Garcia, Francisco, primary, Gardos, Stu, primary, Gocke, Christopher D., primary, Gross, Benjamin E., primary, Guinney, Justin, primary, Heins, Zachary J., primary, Hintzen, Stephanie, primary, Horlings, Hugo, primary, Hudeček, Jan, primary, Hyman, David M., primary, Kamel-Reid, Suzanne, primary, Kandoth, Cyriac, primary, Kinyua, Walter, primary, Kumari, Priti, primary, Kundra, Ritika, primary, Ladanyi, Marc, primary, Lefebvre, Céline, primary, LeNoue-Newton, Michele L., primary, Lepisto, Eva M., primary, Levy, Mia A., primary, Lindeman, Neal I., primary, Lindsay, James, primary, Liu, David, primary, Lu, Zhibin, primary, MacConaill, Laura E., primary, Maurer, Ian, primary, Maxwell, David S., primary, Meijer, Gerrit A., primary, Meric-Bernstam, Funda, primary, Micheel, Christine M., primary, Miller, Clinton, primary, Mills, Gordon, primary, Moore, Nathanael D., primary, Nederlof, Petra M., primary, Omberg, Larsson, primary, Orechia, John A., primary, Park, Ben Ho, primary, Pugh, Trevor J., primary, Reardon, Brendan, primary, Rollins, Barrett J., primary, Routbort, Mark J., primary, Sawyers, Charles L., primary, Schrag, Deborah, primary, Schultz, Nikolaus, primary, Shaw, Kenna R Mills, primary, Shivdasani, Priyanka, primary, Siu, Lillian L., primary, Solit, David B., primary, Sonke, Gabe S., primary, Soria, Jean Charles, primary, Sripakdeevong, Parin, primary, Stickle, Natalie H., primary, Stricker, Thomas P., primary, Sweeney, Shawn M., primary, Taylor, Barry S., primary, ten Hoeve, Jelle J., primary, Thomas, Stacy B., primary, Van Allen, Eliezer M., primary, Van 'T Veer, Laura J., primary, van de Velde, Tony, primary, van Tinteren, Harm, primary, Velculescu, Victor E., primary, Virtanen, Carl, primary, Voest, Emile E., primary, Wang, Lucy L., primary, Wathoo, Chetna, primary, Watt, Stuart, primary, Yu, Celeste, primary, Yu, Thomas V., primary, Yu, Emily, primary, Zehir, Ahmet, primary, and Zhang, Hongxin, primary

Published
2023
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16. Abstract 3616: Fix the fixation: effect of formalin fixation on targeted sequencing, variant calling and gene expression

Author

Alla, Ravi, primary, Luo, Shujun, additional, Helman, Elena, additional, Boyle, Sean M., additional, Clark, Michael J., additional, Scott, Kirk, additional, Sripakdeevong, Parin, additional, Karbelashvili, Mirian, additional, Church, Deanna M., additional, Snyder, Michael, additional, West, John, additional, and Chen, Richard, additional

Published
2016
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17. Abstract 3169: The benefits and burdens of assaying matched normal tissue when sequencing cancer genomes

Author

Helman, Elena, primary, Clark, Michael J., additional, Alla, Ravi, additional, Boyle, Sean M., additional, Luo, Shujun, additional, Virk, Selene, additional, Church, Deanna, additional, Sripakdeevong, Parin, additional, Harris, Jason, additional, karbelashvili, Mirian, additional, Haudenschild, Christian, additional, West, John, additional, and Chen, Richard, additional

Published
2016
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18. Abstract 3899: Integrating RNA/DNA analysis with a comprehensive cancer panel to improve interpretations of stage four metastatic renal cell carcinoma

Author

Boyle, Sean M., primary, Clark, Michael J., additional, Helman, Elena, additional, Parker, Alexander S., additional, Ho, Thai, additional, Luo, Shujun, additional, Kirk, Scott, additional, Sripakdeevong, Parin, additional, Karbelashvili, Mirian, additional, Church, Deanna M., additional, Snyder, Michael, additional, West, John, additional, and Chen, Rich, additional

Published
2015
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19. Abstract 4744: Solving genomic assay trade-offs with an optimized, extended cancer gene panel for research and clinical applications

Author

Clark, Michael J., primary, Boyle, Sean M., additional, Helman, Elena, additional, Luo, Shujun, additional, Bartha, Gabor, additional, Morra, Massimo, additional, Patwardhan, Anil, additional, Haudenschild, Christian, additional, Karbelashvili, Mirian, additional, Sripakdeevong, Parin, additional, Harris, Jason, additional, Church, Deanna, additional, Chervitz, Stephen, additional, West, John, additional, and Chen, Richard, additional

Published
2015
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20. Abstract 1457: Genomic characterization of a PDX model of T-DM1-resistant HER2+ invasive ductal carcinoma using augmented exome sequencing

Author

Helman, Elena, primary, Wick, Michael J., additional, Clark, Michael J., additional, Gamez, Lizette, additional, Boyle, Sean, additional, Papadopoulos, Kyriakos P., additional, Luo, Shujun, additional, Tolcher, Anthony W., additional, Sripakdeevong, Parin, additional, Karbelashvili, Mirian, additional, Church, Deanna, additional, Chen, Richard, additional, and West, John, additional

Published
2015
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21. The detection of clinically relevant cancer mutations using a high depth, augmented, comprehensive cancer gene panel.

Author

Clark, Michael James, primary, Helman, Elena, additional, Boyle, Sean, additional, Luo, Shujun, additional, Church, Deanna, additional, Harris, Jason, additional, Karbelashvili, Mirian, additional, Chervitz, Stephen, additional, Sripakdeevong, Parin, additional, Bartha, Gabor, additional, Patwardhan, Anil Jayant, additional, West, John, additional, and Chen, Richard, additional

Published
2015
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22. Structure determination of noncanonical RNA motifs guided by 1H NMR chemical shifts

Author

Sripakdeevong, Parin, primary, Cevec, Mirko, additional, Chang, Andrew T, additional, Erat, Michèle C, additional, Ziegeler, Melanie, additional, Zhao, Qin, additional, Fox, George E, additional, Gao, Xiaolian, additional, Kennedy, Scott D, additional, Kierzek, Ryszard, additional, Nikonowicz, Edward P, additional, Schwalbe, Harald, additional, Sigel, Roland K O, additional, Turner, Douglas H, additional, and Das, Rhiju, additional

Published
2014
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23. Serverification of Molecular Modeling Applications: The Rosetta Online Server That Includes Everyone (ROSIE)

Author

Lyskov, Sergey, primary, Chou, Fang-Chieh, additional, Conchúir, Shane Ó., additional, Der, Bryan S., additional, Drew, Kevin, additional, Kuroda, Daisuke, additional, Xu, Jianqing, additional, Weitzner, Brian D., additional, Renfrew, P. Douglas, additional, Sripakdeevong, Parin, additional, Borgo, Benjamin, additional, Havranek, James J., additional, Kuhlman, Brian, additional, Kortemme, Tanja, additional, Bonneau, Richard, additional, Gray, Jeffrey J., additional, and Das, Rhiju, additional

Published
2013
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24. RNA-Puzzles: A CASP-like evaluation of RNA three-dimensional structure prediction

Author

Cruz, José Almeida, primary, Blanchet, Marc-Frédérick, additional, Boniecki, Michal, additional, Bujnicki, Janusz M., additional, Chen, Shi-Jie, additional, Cao, Song, additional, Das, Rhiju, additional, Ding, Feng, additional, Dokholyan, Nikolay V., additional, Flores, Samuel Coulbourn, additional, Huang, Lili, additional, Lavender, Christopher A., additional, Lisi, Véronique, additional, Major, François, additional, Mikolajczak, Katarzyna, additional, Patel, Dinshaw J., additional, Philips, Anna, additional, Puton, Tomasz, additional, Santalucia, John, additional, Sijenyi, Fredrick, additional, Hermann, Thomas, additional, Rother, Kristian, additional, Rother, Magdalena, additional, Serganov, Alexander, additional, Skorupski, Marcin, additional, Soltysinski, Tomasz, additional, Sripakdeevong, Parin, additional, Tuszynska, Irina, additional, Weeks, Kevin M., additional, Waldsich, Christina, additional, Wildauer, Michael, additional, Leontis, Neocles B., additional, and Westhof, Eric, additional

Published
2012
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25. Structure determination of noncanonical RNA motifs guided by 1H NMR chemical shifts.

Author

Sripakdeevong, Parin, Cevec, Mirko, Chang, Andrew T, Erat, Michèle C, Ziegeler, Melanie, Zhao, Qin, Fox, George E, Gao, Xiaolian, Kennedy, Scott D, Kierzek, Ryszard, Nikonowicz, Edward P, Schwalbe, Harald, Sigel, Roland K O, Turner, Douglas H, and Das, Rhiju

Subjects
*NON-coding RNA, *MOLECULAR structure of RNA, *MOLECULAR structure of catalytic RNA, *PROTEIN folding, *CHEMICAL shift (Nuclear magnetic resonance), *NUCLEAR magnetic resonance spectroscopy
Abstract

Structured noncoding RNAs underlie fundamental cellular processes, but determining their three-dimensional structures remains challenging. We demonstrate that integrating 1H NMR chemical shift data with Rosetta de novo modeling can be used to consistently determine high-resolution RNA structures. On a benchmark set of 23 noncanonical RNA motifs, including 11 'blind' targets, chemical-shift Rosetta for RNA (CS-Rosetta-RNA) recovered experimental structures with high accuracy (0.6-2.0 Å all-heavy-atom r.m.s. deviation) in 18 cases. [ABSTRACT FROM AUTHOR]

Published
2014
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26. Structure determination of noncanonical RNA motifs guided by ¹H NMR chemical shifts.

Author

Sripakdeevong P, Cevec M, Chang AT, Erat MC, Ziegeler M, Zhao Q, Fox GE, Gao X, Kennedy SD, Kierzek R, Nikonowicz EP, Schwalbe H, Sigel RK, Turner DH, and Das R

Subjects
Animals, Nuclear Magnetic Resonance, Biomolecular methods, Nucleotide Motifs, RNA, Untranslated chemistry
Abstract

Structured noncoding RNAs underlie fundamental cellular processes, but determining their three-dimensional structures remains challenging. We demonstrate that integrating ¹H NMR chemical shift data with Rosetta de novo modeling can be used to consistently determine high-resolution RNA structures. On a benchmark set of 23 noncanonical RNA motifs, including 11 'blind' targets, chemical-shift Rosetta for RNA (CS-Rosetta-RNA) recovered experimental structures with high accuracy (0.6-2.0 Å all-heavy-atom r.m.s. deviation) in 18 cases.

Published
2014
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