| Year |
Citation |
Score |
| 2023 |
Mulvaney T, Kretsch RC, Elliott L, Beton JG, Kryshtafovych A, Rigden DJ, Das R, Topf M. CASP15 cryo-EM protein and RNA targets: Refinement and analysis using experimental maps. Proteins. 91: 1935-1951. PMID 37994556 DOI: 10.1002/prot.26644 |
0.333 |
|
| 2023 |
Das R, Kretsch RC, Simpkin AJ, Mulvaney T, Pham P, Rangan R, Bu F, Keegan RM, Topf M, Rigden DJ, Miao Z, Westhof E. Assessment of three-dimensional RNA structure prediction in CASP15. Proteins. PMID 37876231 DOI: 10.1002/prot.26602 |
0.319 |
|
| 2023 |
Mulvaney T, Kretsch RC, Elliott L, Beton J, Kryshtafovych A, Rigden DJ, Das R, Topf M. CASP15 cryoEM protein and RNA targets: refinement and analysis using experimental maps. Biorxiv : the Preprint Server For Biology. PMID 37609268 DOI: 10.1101/2023.08.07.552287 |
0.322 |
|
| 2023 |
Kretsch RC, Andersen ES, Bujnicki JM, Chiu W, Das R, Luo B, Masquida B, McRae EKS, Schroeder GM, Su Z, Wedekind JE, Xu L, Zhang K, Zheludev IN, Moult J, et al. RNA target highlights in CASP15: Evaluation of predicted models by structure providers. Proteins. PMID 37466021 DOI: 10.1002/prot.26550 |
0.346 |
|
| 2023 |
Kryshtafovych A, Antczak M, Szachniuk M, Zok T, Kretsch RC, Rangan R, Pham P, Das R, Robin X, Studer G, Durairaj J, Eberhardt J, Sweeney A, Topf M, Schwede T, et al. New prediction categories in CASP15. Proteins. PMID 37306011 DOI: 10.1002/prot.26515 |
0.307 |
|
| 2023 |
Das R, Kretsch RC, Simpkin A, Mulvaney T, Pham P, Rangan R, Bu F, Keegan R, Topf M, Rigden D, Miao Z, Westhof E. Assessment of three-dimensional RNA structure prediction in CASP15. Biorxiv : the Preprint Server For Biology. PMID 37162955 DOI: 10.1101/2023.04.25.538330 |
0.314 |
|
| 2023 |
Watkins AM, Das R. RNA 3D Modeling with FARFAR2, Online. Methods in Molecular Biology (Clifton, N.J.). 2586: 233-249. PMID 36705908 DOI: 10.1007/978-1-0716-2768-6_14 |
0.36 |
|
| 2022 |
Wayment-Steele HK, Kladwang W, Watkins AM, Kim DS, Tunguz B, Reade W, Demkin M, Romano J, Wellington-Oguri R, Nicol JJ, Gao J, Onodera K, Fujikawa K, Mao H, Vandewiele G, ... ... Das R, et al. Deep learning models for predicting RNA degradation via dual crowdsourcing. Nature Machine Intelligence. 4: 1174-1184. PMID 36567960 DOI: 10.1038/s42256-022-00571-8 |
0.307 |
|
| 2022 |
Wayment-Steele HK, Kladwang W, Strom AI, Lee J, Treuille A, Becka A, Das R. RNA secondary structure packages evaluated and improved by high-throughput experiments. Nature Methods. PMID 36192461 DOI: 10.1038/s41592-022-01605-0 |
0.336 |
|
| 2022 |
Kim DS, Watkins A, Bidstrup E, Lee J, Topkar V, Kofman C, Schwarz KJ, Liu Y, Pintilie G, Roney E, Das R, Jewett MC. Three-dimensional structure-guided evolution of a ribosome with tethered subunits. Nature Chemical Biology. PMID 35836020 DOI: 10.1038/s41589-022-01064-w |
0.328 |
|
| 2022 |
Alford RF, Leaver-Fay A, Jeliazkov JR, O'Meara MJ, DiMaio FP, Park H, Shapovalov MV, Renfrew PD, Mulligan VK, Kappel K, Labonte JW, Pacella MS, Bonneau R, Bradley P, Dunbrack RL, ... Das R, et al. Correction to "The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design". Journal of Chemical Theory and Computation. PMID 35667008 DOI: 10.1021/acs.jctc.2c00500 |
0.781 |
|
| 2021 |
Le KH, Adolf-Bryfogle J, Klima JC, Lyskov S, Labonte J, Bertolani S, Burman SSR, Leaver-Fay A, Weitzner B, Maguire J, Rangan R, Adrianowycz MA, Alford RF, Adal A, Nance ML, ... ... Das R, et al. PyRosetta Jupyter Notebooks Teach Biomolecular Structure Prediction and Design. Biophysicist (Rockville, Md.). 2: 108-122. PMID 35128343 DOI: 10.35459/tbp.2019.000147 |
0.804 |
|
| 2021 |
Koehler Leman J, Lyskov S, Lewis SM, Adolf-Bryfogle J, Alford RF, Barlow K, Ben-Aharon Z, Farrell D, Fell J, Hansen WA, Harmalkar A, Jeliazkov J, Kuenze G, Krys JD, Ljubetič A, ... ... Das R, et al. Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks. Nature Communications. 12: 6947. PMID 34845212 DOI: 10.1038/s41467-021-27222-7 |
0.774 |
|
| 2021 |
Wayment-Steele HK, Kladwang W, Watkins AM, Kim DS, Tunguz B, Reade W, Demkin M, Romano J, Wellington-Oguri R, Nicol JJ, Gao J, Onodera K, Fujikawa K, Mao H, Vandewiele G, ... ... Das R, et al. Predictive models of RNA degradation through dual crowdsourcing. Arxiv. PMID 34671698 |
0.336 |
|
| 2021 |
Wayment-Steele HK, Kim DS, Choe CA, Nicol JJ, Wellington-Oguri R, Watkins AM, Parra Sperberg RA, Huang PS, Participants E, Das R. Correction to 'Theoretical basis for stabilizing messenger RNA through secondary structure design'. Nucleic Acids Research. PMID 34591967 DOI: 10.1093/nar/gkab911 |
0.528 |
|
| 2021 |
Wayment-Steele HK, Kim DS, Choe CA, Nicol JJ, Wellington-Oguri R, Watkins AM, Parra Sperberg RA, Huang PS, Participants E, Das R. Theoretical basis for stabilizing messenger RNA through secondary structure design. Nucleic Acids Research. PMID 34520542 DOI: 10.1093/nar/gkab764 |
0.526 |
|
| 2021 |
Townshend RJL, Eismann S, Watkins AM, Rangan R, Karelina M, Das R, Dror RO. Geometric deep learning of RNA structure. Science (New York, N.Y.). 373: 1047-1051. PMID 34446608 DOI: 10.1126/science.abe5650 |
0.308 |
|
| 2021 |
Su Z, Zhang K, Kappel K, Li S, Palo MZ, Pintilie GD, Rangan R, Luo B, Wei Y, Das R, Chiu W. Cryo-EM structures of full-length Tetrahymena ribozyme at 3.1 Å resolution. Nature. PMID 34381213 DOI: 10.1038/s41586-021-03803-w |
0.305 |
|
| 2021 |
Rangan R, Watkins AM, Chacon J, Kretsch R, Kladwang W, Zheludev IN, Townley J, Rynge M, Thain G, Das R. De novo 3D models of SARS-CoV-2 RNA elements from consensus experimental secondary structures. Nucleic Acids Research. PMID 33693814 DOI: 10.1093/nar/gkab119 |
0.31 |
|
| 2021 |
Rangan R, Watkins AM, Chacon J, Kretsch R, Kladwang W, Zheludev IN, Townley J, Rynge M, Thain G, Das R. De novo 3D models of SARS-CoV-2 RNA elements from consensus experimental secondary structures. Nucleic Acids Research. PMID 33693814 DOI: 10.1093/nar/gkab119 |
0.31 |
|
| 2020 |
Wayment-Steele HK, Kim DS, Choe CA, Nicol JJ, Wellington-Oguri R, Sperberg RAP, Huang PS, Das R. Theoretical basis for stabilizing messenger RNA through secondary structure design. Biorxiv : the Preprint Server For Biology. PMID 32869022 DOI: 10.1101/2020.08.22.262931 |
0.511 |
|
| 2020 |
Palka C, Forino N, Hentschel J, Das R, Stone MD. Folding heterogeneity in the essential human telomerase RNA three-way junction. Rna (New York, N.Y.). PMID 32817241 DOI: 10.1261/Rna.077255.120 |
0.358 |
|
| 2020 |
Kappel K, Zhang K, Su Z, Watkins AM, Kladwang W, Li S, Pintilie G, Topkar VV, Rangan R, Zheludev IN, Yesselman JD, Chiu W, Das R. Accelerated cryo-EM-guided determination of three-dimensional RNA-only structures. Nature Methods. 17: 699-707. PMID 32616928 DOI: 10.1038/S41592-020-0878-9 |
0.421 |
|
| 2020 |
Watkins AM, Rangan R, Das R. FARFAR2: Improved De Novo Rosetta Prediction of Complex Global RNA Folds. Structure (London, England : 1993). PMID 32531203 DOI: 10.1016/J.Str.2020.05.011 |
0.434 |
|
| 2020 |
Leman JK, Weitzner BD, Lewis SM, Adolf-Bryfogle J, Alam N, Alford RF, Aprahamian M, Baker D, Barlow KA, Barth P, Basanta B, Bender BJ, Blacklock K, Bonet J, Boyken SE, ... ... Das R, et al. Macromolecular modeling and design in Rosetta: recent methods and frameworks. Nature Methods. PMID 32483333 DOI: 10.1038/S41592-020-0848-2 |
0.707 |
|
| 2020 |
Kladwang W, Topkar V, Liu B, Rangan R, Hodges T, Keane S, Al-Hashimi HM, Das R. Anomalous reverse transcription through chemical modifications in polyadenosine stretches. Biochemistry. PMID 32407625 DOI: 10.1021/Acs.Biochem.0C00020 |
0.36 |
|
| 2020 |
Rangan R, Zheludev IN, Das R. RNA genome conservation and secondary structure in SARS-CoV-2 and SARS-related viruses: a first look. Rna (New York, N.Y.). PMID 32398273 DOI: 10.1261/Rna.076141.120 |
0.333 |
|
| 2020 |
Miao Z, Adamiak RW, Antczak M, Boniecki MJ, Bujnicki JM, Chen SJ, Cheng CY, Cheng Y, Chou FC, Das R, Dokholyan NV, Ding F, Geniesse C, Jiang Y, Joshi A, et al. RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers. Rna (New York, N.Y.). PMID 32371455 DOI: 10.1261/Rna.075341.120 |
0.429 |
|
| 2020 |
Jain N, Blauch LR, Szymanski MR, Das R, Tang SKY, Yin YW, Fire AZ. Transcription polymerase-catalyzed emergence of novel RNA replicons. Science (New York, N.Y.). PMID 32217750 DOI: 10.1126/Science.Aay0688 |
0.332 |
|
| 2019 |
Zhang K, Li S, Kappel K, Pintilie G, Su Z, Mou TC, Schmid MF, Das R, Chiu W. Cryo-EM structure of a 40 kDa SAM-IV riboswitch RNA at 3.7 Å resolution. Nature Communications. 10: 5511. PMID 31796736 DOI: 10.1038/S41467-019-13494-7 |
0.375 |
|
| 2019 |
Magnus M, Kappel K, Das R, Bujnicki JM. RNA 3D structure prediction guided by independent folding of homologous sequences. Bmc Bioinformatics. 20: 512. PMID 31640563 DOI: 10.1186/S12859-019-3120-Y |
0.408 |
|
| 2019 |
Li X, Liu S, Zhang L, Issaian A, Hill RC, Espinosa S, Shi S, Cui Y, Kappel K, Das R, Hansen KC, Zhou ZH, Zhao R. A unified mechanism for intron and exon definition and back-splicing. Nature. PMID 31485080 DOI: 10.1038/S41586-019-1523-6 |
0.327 |
|
| 2019 |
Yesselman JD, Eiler D, Carlson ED, Gotrik MR, d'Aquino AE, Ooms AN, Kladwang W, Carlson PD, Shi X, Costantino DA, Herschlag D, Lucks JB, Jewett MC, Kieft JS, Das R. Computational design of three-dimensional RNA structure and function. Nature Nanotechnology. PMID 31427748 DOI: 10.1038/S41565-019-0517-8 |
0.583 |
|
| 2019 |
Koirala D, Shao Y, Koldobskaya Y, Fuller JR, Watkins AM, Shelke SA, Pilipenko EV, Das R, Rice PA, Piccirilli JA. A conserved RNA structural motif for organizing topology within picornaviral internal ribosome entry sites. Nature Communications. 10: 3629. PMID 31399592 DOI: 10.1038/S41467-019-11585-Z |
0.326 |
|
| 2019 |
Yesselman JD, Denny SK, Bisaria N, Herschlag D, Greenleaf WJ, Das R. Sequence-dependent RNA helix conformational preferences predictably impact tertiary structure formation. Proceedings of the National Academy of Sciences of the United States of America. PMID 31375637 DOI: 10.1073/Pnas.1901530116 |
0.597 |
|
| 2019 |
Wu MJ, Andreasson JO, Kladwang W, Greenleaf WJ, Das R. Automated design of diverse stand-alone riboswitches. Acs Synthetic Biology. PMID 31298841 DOI: 10.1021/Acssynbio.9B00142 |
0.42 |
|
| 2019 |
Koodli RV, Keep B, Coppess KR, Portela F, Das R. EternaBrain: Automated RNA design through move sets and strategies from an Internet-scale RNA videogame. Plos Computational Biology. 15: e1007059. PMID 31247029 DOI: 10.1371/Journal.Pcbi.1007059 |
0.415 |
|
| 2019 |
Wayment-Steele H, Wu M, Gotrik M, Das R. Evaluating riboswitch optimality. Methods in Enzymology. 623: 417-450. PMID 31239056 DOI: 10.1016/Bs.Mie.2019.05.028 |
0.337 |
|
| 2019 |
Watkins AM, Rangan R, Das R. Using Rosetta for RNA homology modeling. Methods in Enzymology. 623: 177-207. PMID 31239046 DOI: 10.1016/Bs.Mie.2019.05.026 |
0.496 |
|
| 2019 |
Huang L, Wang J, Watkins AM, Das R, Lilley DMJ. Structure and ligand binding of the glutamine-II riboswitch. Nucleic Acids Research. PMID 31216023 DOI: 10.1093/Nar/Gkz539 |
0.344 |
|
| 2019 |
Jarmoskaite I, Denny SK, Vaidyanathan PP, Becker WR, Andreasson JOL, Layton CJ, Kappel K, Shivashankar V, Sreenivasan R, Das R, Greenleaf WJ, Herschlag D. A Quantitative and Predictive Model for RNA Binding by Human Pumilio Proteins. Molecular Cell. PMID 31078383 DOI: 10.1016/J.Molcel.2019.04.012 |
0.599 |
|
| 2019 |
Kappel K, Jarmoskaite I, Vaidyanathan PP, Greenleaf WJ, Herschlag D, Das R. Blind tests of RNA-protein binding affinity prediction. Proceedings of the National Academy of Sciences of the United States of America. PMID 30962376 DOI: 10.1073/Pnas.1819047116 |
0.6 |
|
| 2019 |
Boeynaems S, Holehouse AS, Weinhardt V, Kovacs D, Van Lindt J, Larabell C, Van Den Bosch L, Das R, Tompa PS, Pappu RV, Gitler AD. Spontaneous driving forces give rise to protein-RNA condensates with coexisting phases and complex material properties. Proceedings of the National Academy of Sciences of the United States of America. PMID 30926670 DOI: 10.1073/Pnas.1821038116 |
0.346 |
|
| 2018 |
Hartwick EW, Costantino DA, MacFadden A, Nix JC, Tian S, Das R, Kieft JS. Ribosome-induced RNA conformational changes in a viral 3'-UTR sense and regulate translation levels. Nature Communications. 9: 5074. PMID 30498211 DOI: 10.1038/S41467-018-07542-X |
0.372 |
|
| 2018 |
Kappel K, Das R. Sampling Native-like Structures of RNA-Protein Complexes through Rosetta Folding and Docking. Structure (London, England : 1993). PMID 30416038 DOI: 10.1016/J.Str.2018.10.001 |
0.412 |
|
| 2018 |
Kappel K, Liu S, Larsen KP, Skiniotis G, Puglisi EV, Puglisi JD, Zhou ZH, Zhao R, Das R. De novo computational RNA modeling into cryo-EM maps of large ribonucleoprotein complexes. Nature Methods. 15: 947-954. PMID 30377372 DOI: 10.1038/S41592-018-0172-2 |
0.399 |
|
| 2018 |
Yesselman JD, Tian S, Liu X, Shi L, Li JB, Das R. Updates to the RNA mapping database (RMDB), version 2. Nucleic Acids Research. 46: D375-D379. PMID 30053264 DOI: 10.1093/Nar/Gkx873 |
0.388 |
|
| 2018 |
Denny SK, Bisaria N, Yesselman JD, Das R, Herschlag D, Greenleaf WJ. High-Throughput Investigation of Diverse Junction Elements in RNA Tertiary Folding. Cell. PMID 29961580 DOI: 10.1016/J.Cell.2018.05.038 |
0.609 |
|
| 2018 |
Zettl T, Das R, Harbury PAB, Herschlag D, Lipfert J, Mathew RS, Shi X. Recording and Analyzing Nucleic Acid Distance Distributions with X-Ray Scattering Interferometry (XSI). Current Protocols in Nucleic Acid Chemistry. 73: e54. PMID 29927110 DOI: 10.1002/Cpnc.54 |
0.68 |
|
| 2018 |
Watkins AM, Geniesse C, Kladwang W, Zakrevsky P, Jaeger L, Das R. Blind prediction of noncanonical RNA structure at atomic accuracy. Science Advances. 4: eaar5316. PMID 29806027 DOI: 10.1126/Sciadv.Aar5316 |
0.465 |
|
| 2018 |
Chen L, Roake CM, Freund A, Batista PJ, Tian S, Yin YA, Gajera CR, Lin S, Lee B, Pech MF, Venteicher AS, Das R, Chang HY, Artandi SE. An Activity Switch in Human Telomerase Based on RNA Conformation and Shaped by TCAB1. Cell. PMID 29804836 DOI: 10.1016/J.Cell.2018.04.039 |
0.32 |
|
| 2018 |
Gracia B, Al-Hashimi HM, Bisaria N, Das R, Herschlag D, Russell R. Hidden Structural Modules in a Cooperative RNA Folding Transition. Cell Reports. 22: 3240-3250. PMID 29562180 DOI: 10.1016/J.Celrep.2018.02.101 |
0.583 |
|
| 2018 |
Tian S, Kladwang W, Das R. Allosteric mechanism of theadenine riboswitch resolved by four-dimensional chemical mapping. Elife. 7. PMID 29446752 DOI: 10.7554/Elife.29602 |
0.375 |
|
| 2018 |
Palka C, Das R, Tzfati Y, Stone M. Investigating the Function of Conformational Heterogeneity in Telomerase RNA using Multi-dimensional Chemical Mapping and Single-Molecule Spectroscopy Biophysical Journal. 114: 215a. DOI: 10.1016/J.Bpj.2017.11.1201 |
0.331 |
|
| 2017 |
Leppek K, Das R, Barna M. Functional 5' UTR mRNA structures in eukaryotic translation regulation and how to find them. Nature Reviews. Molecular Cell Biology. PMID 29165424 DOI: 10.1038/Nrm.2017.103 |
0.378 |
|
| 2017 |
Moretti R, Lyskov S, Das R, Meiler J, Gray JJ. Web-accessible molecular modeling with Rosetta: The Rosetta Online Server That Includes Everyone (ROSIE). Protein Science : a Publication of the Protein Society. PMID 28960691 DOI: 10.1002/Pro.3313 |
0.69 |
|
| 2017 |
Cheng CY, Kladwang W, Yesselman JD, Das R. RNA structure inference through chemical mapping after accidental or intentional mutations. Proceedings of the National Academy of Sciences of the United States of America. PMID 28851837 DOI: 10.1073/Pnas.1619897114 |
0.354 |
|
| 2017 |
Tian S, Das R. Primerize-2D: automated primer design for RNA multidimensional chemical mapping. Bioinformatics (Oxford, England). 33: 1405-1406. PMID 28453672 DOI: 10.1093/Bioinformatics/Btw814 |
0.409 |
|
| 2017 |
Alford RF, Leaver-Fay A, Jeliazkov JR, O'Meara MJ, DiMaio FP, Park H, Shapovalov MV, Renfrew PD, Mulligan VK, Kappel K, Labonte JW, Pacella MS, Bonneau R, Bradley P, Dunbrack RL, ... Das R, et al. The Rosetta all-atom energy function for macromolecular modeling and design. Journal of Chemical Theory and Computation. PMID 28430426 DOI: 10.1021/Acs.Jctc.7B00125 |
0.787 |
|
| 2017 |
Miao Z, Adamiak RW, Antczak M, Batey RT, Becka AJ, Biesiada M, Boniecki MJ, Bujnicki J, Chen SJ, Cheng CY, Chou FC, Ferré-D'Amaré AR, Das R, Dawson WK, Feng D, et al. RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme. Rna (New York, N.Y.). PMID 28138060 DOI: 10.1261/Rna.060368.116 |
0.442 |
|
| 2017 |
Parks JW, Kappel K, Das R, Stone MD. Single-molecule FRET-Rosetta reveals RNA structural rearrangements during human telomerase catalysis. Rna (New York, N.Y.). 23: 175-188. PMID 28096444 DOI: 10.1261/Rna.058743.116 |
0.414 |
|
| 2017 |
Kappel K, Jarmoskaite I, Vaidyanathan PP, Greenleaf WJ, Herschlag D, Das R. Blind Predictions of RNA/Protein Relative Binding Affinities Biophysical Journal. 112. DOI: 10.1016/J.Bpj.2016.11.434 |
0.6 |
|
| 2016 |
Yesselman JD, Das R. Modeling Small Noncanonical RNA Motifs with the Rosetta FARFAR Server. Methods in Molecular Biology (Clifton, N.J.). 1490: 187-198. PMID 27665600 DOI: 10.1007/978-1-4939-6433-8_12 |
0.418 |
|
| 2016 |
Chou FC, Kladwang W, Kappel K, Das R. Blind tests of RNA nearest-neighbor energy prediction. Proceedings of the National Academy of Sciences of the United States of America. PMID 27402765 DOI: 10.1073/Pnas.1523335113 |
0.41 |
|
| 2016 |
Tian S, Das R. RNA structure through multidimensional chemical mapping. Quarterly Reviews of Biophysics. 49: e7. PMID 27266715 DOI: 10.1017/S0033583516000020 |
0.395 |
|
| 2016 |
Anderson-Lee J, Fisker E, Kosaraju V, Wu M, Kong J, Lee J, Lee M, Zada M, Treuille A, Das R. Principles for Predicting RNA Secondary Structure Design Difficulty. Journal of Molecular Biology. PMID 26902426 DOI: 10.1016/J.Jmb.2015.11.013 |
0.433 |
|
| 2016 |
Chou FC, Echols N, Terwilliger TC, Das R. RNA Structure Refinement Using the ERRASER-Phenix Pipeline. Methods in Molecular Biology (Clifton, N.J.). 1320: 269-82. PMID 26227049 DOI: 10.1007/978-1-4939-2763-0_17 |
0.402 |
|
| 2016 |
Denny S, Bisaria N, Yesselman J, Das R, Herschlag D, Greenleaf W. High Throughput Characterization of RNA Tertiary Elements Biophysical Journal. 110: 363a. DOI: 10.1016/J.Bpj.2015.11.1957 |
0.581 |
|
| 2015 |
Cordero P, Das R. Rich RNA Structure Landscapes Revealed by Mutate-and-Map Analysis. Plos Computational Biology. 11: e1004473. PMID 26566145 DOI: 10.1371/Journal.Pcbi.1004473 |
0.414 |
|
| 2015 |
Kumar R, Rai AK, Das D, Das R, Kumar RS, Sarma A, Sharma S, Kataki AC, Ramteke A. Alcohol and Tobacco Increases Risk of High Risk HPV Infection in Head and Neck Cancer Patients: Study from North-East Region of India. Plos One. 10: e0140700. PMID 26473489 DOI: 10.1371/journal.pone.0140700 |
0.417 |
|
| 2015 |
Yu Cheng C, Chou FC, Kladwang W, Tian S, Cordero P, Das R. Correction: Consistent global structures of complex RNA states through multidimensional chemical mapping. Elife. 4. PMID 26196348 DOI: 10.7554/Elife.10095 |
0.336 |
|
| 2015 |
Cheng CY, Chou FC, Kladwang W, Tian S, Cordero P, Das R. Consistent global structures of complex RNA states through multidimensional chemical mapping. Elife. 4: e07600. PMID 26035425 DOI: 10.7554/Elife.07600 |
0.335 |
|
| 2015 |
Tian S, Yesselman JD, Cordero P, Das R. Primerize: automated primer assembly for transcribing non-coding RNA domains. Nucleic Acids Research. 43: W522-6. PMID 25999345 DOI: 10.1093/Nar/Gkv538 |
0.384 |
|
| 2015 |
Yesselman JD, Das R. RNA-Redesign: a web server for fixed-backbone 3D design of RNA. Nucleic Acids Research. 43: W498-501. PMID 25964298 DOI: 10.1093/Nar/Gkv465 |
0.429 |
|
| 2015 |
Lee S, Kim H, Tian S, Lee T, Yoon S, Das R. Automated band annotation for RNA structure probing experiments with numerous capillary electrophoresis profiles. Bioinformatics (Oxford, England). 31: 2808-15. PMID 25943472 DOI: 10.1093/Bioinformatics/Btv282 |
0.398 |
|
| 2015 |
Miao Z, Adamiak RW, Blanchet MF, Boniecki M, Bujnicki JM, Chen SJ, Cheng C, Chojnowski G, Chou FC, Cordero P, Cruz JA, Ferré-D'Amaré AR, Das R, Ding F, Dokholyan NV, et al. RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures. Rna (New York, N.Y.). 21: 1066-84. PMID 25883046 DOI: 10.1261/Rna.049502.114 |
0.444 |
|
| 2015 |
Cheng CY, Chou FC, Das R. Modeling complex RNA tertiary folds with Rosetta. Methods in Enzymology. 553: 35-64. PMID 25726460 DOI: 10.1016/Bs.Mie.2014.10.051 |
0.46 |
|
| 2015 |
Xue S, Tian S, Fujii K, Kladwang W, Das R, Barna M. RNA regulons in Hox 5' UTRs confer ribosome specificity to gene regulation. Nature. 517: 33-8. PMID 25409156 DOI: 10.1038/Nature14010 |
0.303 |
|
| 2014 |
Lipfert J, Skinner GM, Keegstra JM, Hensgens T, Jager T, Dulin D, Köber M, Yu Z, Donkers SP, Chou FC, Das R, Dekker NH. Double-stranded RNA under force and torque: similarities to and striking differences from double-stranded DNA. Proceedings of the National Academy of Sciences of the United States of America. 111: 15408-13. PMID 25313077 DOI: 10.1073/Pnas.1407197111 |
0.605 |
|
| 2014 |
Treuille A, Das R. Scientific rigor through videogames. Trends in Biochemical Sciences. 39: 507-9. PMID 25300714 DOI: 10.1016/J.Tibs.2014.08.005 |
0.341 |
|
| 2014 |
Tian S, Cordero P, Kladwang W, Das R. High-throughput mutate-map-rescue evaluates SHAPE-directed RNA structure and uncovers excited states. Rna (New York, N.Y.). 20: 1815-26. PMID 25183835 DOI: 10.1261/Rna.044321.114 |
0.382 |
|
| 2014 |
Chou FC, Lipfert J, Das R. Blind predictions of DNA and RNA tweezers experiments with force and torque Plos Computational Biology. 10: e1003756. PMID 25102226 DOI: 10.1371/Journal.Pcbi.1003756 |
0.639 |
|
| 2014 |
Kladwang W, Mann TH, Becka A, Tian S, Kim H, Yoon S, Das R. Standardization of RNA chemical mapping experiments. Biochemistry. 53: 3063-5. PMID 24766159 DOI: 10.1021/Bi5003426 |
0.361 |
|
| 2014 |
Beauchamp KA, Pande VS, Das R. Bayesian energy landscape tilting: Towards concordant models of molecular ensembles Biophysical Journal. 106: 1381-1390. PMID 24655513 DOI: 10.1016/J.Bpj.2014.02.009 |
0.373 |
|
| 2014 |
Lipfert J, Doniach S, Das R, Herschlag D. Understanding nucleic acid-ion interactions. Annual Review of Biochemistry. 83: 813-41. PMID 24606136 DOI: 10.1146/Annurev-Biochem-060409-092720 |
0.764 |
|
| 2014 |
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, Das R. Structure determination of noncanonical RNA motifs guided by ¹H NMR chemical shifts. Nature Methods. 11: 413-6. PMID 24584194 DOI: 10.1038/Nmeth.2876 |
0.394 |
|
| 2014 |
Lee J, Kladwang W, Lee M, Cantu D, Azizyan M, Kim H, Limpaecher A, Yoon S, Treuille A, Das R. RNA design rules from a massive open laboratory. Proceedings of the National Academy of Sciences of the United States of America. 111: 2122-7. PMID 24469816 DOI: 10.1073/Pnas.1313039111 |
0.425 |
|
| 2014 |
Kryshtafovych A, Moult J, Bales P, Bazan JF, Biasini M, Burgin A, Chen C, Cochran FV, Craig TK, Das R, Fass D, Garcia-Doval C, Herzberg O, Lorimer D, Luecke H, et al. Challenging the state of the art in protein structure prediction: Highlights of experimental target structures for the 10th Critical Assessment of Techniques for Protein Structure Prediction Experiment CASP10. Proteins. 82: 26-42. PMID 24318984 DOI: 10.1002/Prot.24489 |
0.38 |
|
| 2014 |
Seetin MG, Kladwang W, Bida JP, Das R. Massively parallel RNA chemical mapping with a reduced bias MAP-seq protocol. Methods in Molecular Biology (Clifton, N.J.). 1086: 95-117. PMID 24136600 DOI: 10.1007/978-1-62703-667-2_6 |
0.355 |
|
| 2014 |
Cordero P, Kladwang W, VanLang CC, Das R. The mutate-and-map protocol for inferring base pairs in structured RNA. Methods in Molecular Biology (Clifton, N.J.). 1086: 53-77. PMID 24136598 DOI: 10.1007/978-1-62703-667-2_4 |
0.34 |
|
| 2014 |
Beauchamp K, Pande V, Das R. Inferring Structural Ensembles from Noisy Experiments and Molecular Dynamics: Correcting Force Field Bias with Bayesian Energy Landscape Tilting Biophysical Journal. 106: 406a. DOI: 10.1016/J.Bpj.2013.11.2286 |
0.332 |
|
| 2013 |
Das R. Atomic-accuracy prediction of protein loop structures through an RNA-inspired Ansatz. Plos One. 8: e74830. PMID 24204571 DOI: 10.1371/Journal.Pone.0074830 |
0.479 |
|
| 2013 |
Drew K, Renfrew PD, Craven TW, Butterfoss GL, Chou FC, Lyskov S, Bullock BN, Watkins A, Labonte JW, Pacella M, Kilambi KP, Leaver-Fay A, Kuhlman B, Gray JJ, Bradley P, ... ... Das R, et al. Adding diverse noncanonical backbones to rosetta: enabling peptidomimetic design. Plos One. 8: e67051. PMID 23869206 DOI: 10.1371/Journal.Pone.0067051 |
0.807 |
|
| 2013 |
Kim H, Cordero P, Das R, Yoon S. HiTRACE-Web: an online tool for robust analysis of high-throughput capillary electrophoresis. Nucleic Acids Research. 41: W492-8. PMID 23761448 DOI: 10.1093/Nar/Gkt501 |
0.401 |
|
| 2013 |
Lyskov S, Chou FC, Conchúir SÓ, Der BS, Drew K, Kuroda D, Xu J, Weitzner BD, Renfrew PD, Sripakdeevong P, Borgo B, Havranek JJ, Kuhlman B, Kortemme T, Bonneau R, ... ... Das R, et al. Serverification of molecular modeling applications: the Rosetta Online Server that Includes Everyone (ROSIE). Plos One. 8: e63906. PMID 23717507 DOI: 10.1371/Journal.Pone.0063906 |
0.813 |
|
| 2013 |
Adams PD, Baker D, Brunger AT, Das R, DiMaio F, Read RJ, Richardson DC, Richardson JS, Terwilliger TC. Advances, interactions, and future developments in the CNS, Phenix, and Rosetta structural biology software systems. Annual Review of Biophysics. 42: 265-87. PMID 23451892 DOI: 10.1146/Annurev-Biophys-083012-130253 |
0.511 |
|
| 2013 |
Chou FC, Sripakdeevong P, Dibrov SM, Hermann T, Das R. Correcting pervasive errors in RNA crystallography through enumerative structure prediction. Nature Methods. 10: 74-6. PMID 23202432 DOI: 10.1038/Nmeth.2262 |
0.389 |
|
| 2013 |
Molski MA, Goodman JL, Chou FC, Baker D, Das R, Schepartz A. Remodeling a β-peptide bundle Chemical Science. 4: 319-324. DOI: 10.1039/C2Sc21117C |
0.381 |
|
| 2012 |
Cordero P, Lucks JB, Das R. An RNA Mapping DataBase for curating RNA structure mapping experiments. Bioinformatics (Oxford, England). 28: 3006-8. PMID 22976082 DOI: 10.1093/Bioinformatics/Bts554 |
0.383 |
|
| 2012 |
Cordero P, Kladwang W, VanLang CC, Das R. Quantitative dimethyl sulfate mapping for automated RNA secondary structure inference. Biochemistry. 51: 7037-9. PMID 22913637 DOI: 10.1021/Bi3008802 |
0.427 |
|
| 2012 |
Kladwang W, Hum J, Das R. Ultraviolet shadowing of RNA can cause significant chemical damage in seconds. Scientific Reports. 2: 517. PMID 22816040 DOI: 10.1038/Srep00517 |
0.315 |
|
| 2012 |
Frederiksen JK, Li NS, Das R, Herschlag D, Piccirilli JA. Metal-ion rescue revisited: biochemical detection of site-bound metal ions important for RNA folding. Rna (New York, N.Y.). 18: 1123-41. PMID 22539523 DOI: 10.1261/Rna.028738.111 |
0.537 |
|
| 2012 |
Cruz JA, Blanchet MF, Boniecki M, Bujnicki JM, Chen SJ, Cao S, Das R, Ding F, Dokholyan NV, Flores SC, Huang L, Lavender CA, Lisi V, Major F, Mikolajczak K, et al. RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction. Rna (New York, N.Y.). 18: 610-25. PMID 22361291 DOI: 10.1261/Rna.031054.111 |
0.432 |
|
| 2012 |
Kladwang W, Chou FC, Das R. Automated RNA structure prediction uncovers a kink-turn linker in double glycine riboswitches. Journal of the American Chemical Society. 134: 1404-7. PMID 22192063 DOI: 10.1021/Ja2093508 |
0.44 |
|
| 2011 |
Sripakdeevong P, Kladwang W, Das R. An enumerative stepwise ansatz enables atomic-accuracy RNA loop modeling. Proceedings of the National Academy of Sciences of the United States of America. 108: 20573-8. PMID 22143768 DOI: 10.1073/Pnas.1106516108 |
0.458 |
|
| 2011 |
Kladwang W, VanLang CC, Cordero P, Das R. A two-dimensional mutate-and-map strategy for non-coding RNA structure. Nature Chemistry. 3: 954-62. PMID 22109276 DOI: 10.1038/Nchem.1176 |
0.408 |
|
| 2011 |
Kladwang W, VanLang CC, Cordero P, Das R. Understanding the errors of SHAPE-directed RNA structure modeling. Biochemistry. 50: 8049-56. PMID 21842868 DOI: 10.1021/Bi200524N |
0.429 |
|
| 2011 |
Beauchamp KA, Ensign DL, Das R, Pande VS. Quantitative comparison of villin headpiece subdomain simulations and triplet-triplet energy transfer experiments Proceedings of the National Academy of Sciences of the United States of America. 108: 12734-12739. PMID 21768345 DOI: 10.1073/Pnas.1010880108 |
0.344 |
|
| 2011 |
Das R. Four small puzzles that Rosetta doesn't solve. Plos One. 6: e20044. PMID 21625446 DOI: 10.1371/Journal.Pone.0020044 |
0.484 |
|
| 2011 |
Rocca-Serra P, Bellaousov S, Birmingham A, Chen C, Cordero P, Das R, Davis-Neulander L, Duncan CD, Halvorsen M, Knight R, Leontis NB, Mathews DH, Ritz J, Stombaugh J, Weeks KM, et al. Sharing and archiving nucleic acid structure mapping data. Rna (New York, N.Y.). 17: 1204-12. PMID 21610212 DOI: 10.1261/Rna.2753211 |
0.337 |
|
| 2011 |
Kladwang W, Cordero P, Das R. A mutate-and-map strategy accurately infers the base pairs of a 35-nucleotide model RNA. Rna (New York, N.Y.). 17: 522-34. PMID 21239468 DOI: 10.1261/Rna.2516311 |
0.377 |
|
| 2011 |
Leaver-Fay A, Tyka M, Lewis SM, Lange OF, Thompson J, Jacak R, Kaufman K, Renfrew PD, Smith CA, Sheffler W, Davis IW, Cooper S, Treuille A, Mandell DJ, Richter F, ... ... Das R, et al. ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. Methods in Enzymology. 487: 545-74. PMID 21187238 DOI: 10.1016/B978-0-12-381270-4.00019-6 |
0.746 |
|
| 2010 |
Kladwang W, Das R. A mutate-and-map strategy for inferring base pairs in structured nucleic acids: proof of concept on a DNA/RNA helix. Biochemistry. 49: 7414-6. PMID 20677780 DOI: 10.1021/Bi101123G |
0.359 |
|
| 2010 |
Fleishman SJ, Corn JE, Strauch EM, Whitehead TA, Andre I, Thompson J, Havranek JJ, Das R, Bradley P, Baker D. Rosetta in CAPRI rounds 13-19. Proteins. 78: 3212-8. PMID 20597089 DOI: 10.1002/Prot.22784 |
0.791 |
|
| 2010 |
Das R, Karanicolas J, Baker D. Atomic accuracy in predicting and designing noncanonical RNA structure. Nature Methods. 7: 291-4. PMID 20190761 DOI: 10.1038/Nmeth.1433 |
0.72 |
|
| 2009 |
Das R, André I, Shen Y, Wu Y, Lemak A, Bansal S, Arrowsmith CH, Szyperski T, Baker D. Simultaneous prediction of protein folding and docking at high resolution. Proceedings of the National Academy of Sciences of the United States of America. 106: 18978-83. PMID 19864631 DOI: 10.1073/Pnas.0904407106 |
0.706 |
|
| 2009 |
Raman S, Vernon R, Thompson J, Tyka M, Sadreyev R, Pei J, Kim D, Kellogg E, DiMaio F, Lange O, Kinch L, Sheffler W, Kim BH, Das R, Grishin NV, et al. Structure prediction for CASP8 with all-atom refinement using Rosetta. Proteins. 77: 89-99. PMID 19701941 DOI: 10.1002/Prot.22540 |
0.798 |
|
| 2009 |
Kim J, Yu S, Shim B, Kim H, Min H, Chung EY, Das R, Yoon S. A robust peak detection method for RNA structure inference by high-throughput contact mapping. Bioinformatics (Oxford, England). 25: 1137-44. PMID 19246511 DOI: 10.1093/Bioinformatics/Btp110 |
0.342 |
|
| 2009 |
Schwede T, Sali A, Honig B, Levitt M, Berman HM, Jones D, Brenner SE, Burley SK, Das R, Dokholyan NV, Dunbrack RL, Fidelis K, Fiser A, Godzik A, Huang YJ, et al. Outcome of a workshop on applications of protein models in biomedical research. Structure (London, England : 1993). 17: 151-9. PMID 19217386 DOI: 10.1016/J.Str.2008.12.014 |
0.617 |
|
| 2009 |
Das R, Baker D. Prospects for de novo phasing with de novo protein models. Acta Crystallographica. Section D, Biological Crystallography. 65: 169-75. PMID 19171972 DOI: 10.1107/S0907444908020039 |
0.481 |
|
| 2009 |
Jonikas MA, Radmer RJ, Laederach A, Das R, Pearlman S, Herschlag D, Altman RB. Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters. Rna (New York, N.Y.). 15: 189-99. PMID 19144906 DOI: 10.1261/Rna.1270809 |
0.613 |
|
| 2009 |
Blum B, Jordan MI, Kim DE, Das R, Bradley P, Baker D. Feature selection methods for improving protein structure prediction with Rosetta Advances in Neural Information Processing Systems 20 - Proceedings of the 2007 Conference. |
0.515 |
|
| 2008 |
Laederach A, Das R, Vicens Q, Pearlman SM, Brenowitz M, Herschlag D, Altman RB. Semiautomated and rapid quantification of nucleic acid footprinting and structure mapping experiments. Nature Protocols. 3: 1395-401. PMID 18772866 DOI: 10.1038/Nprot.2008.134 |
0.52 |
|
| 2008 |
Das R, Baker D. Macromolecular modeling with rosetta. Annual Review of Biochemistry. 77: 363-82. PMID 18410248 DOI: 10.1146/Annurev.Biochem.77.062906.171838 |
0.589 |
|
| 2008 |
Das R, Kudaravalli M, Jonikas M, Laederach A, Fong R, Schwans JP, Baker D, Piccirilli JA, Altman RB, Herschlag D. Structural inference of native and partially folded RNA by high-throughput contact mapping. Proceedings of the National Academy of Sciences of the United States of America. 105: 4144-9. PMID 18322008 DOI: 10.1073/Pnas.0709032105 |
0.629 |
|
| 2007 |
Qian B, Raman S, Das R, Bradley P, McCoy AJ, Read RJ, Baker D. High-resolution structure prediction and the crystallographic phase problem. Nature. 450: 259-64. PMID 17934447 DOI: 10.1038/Nature06249 |
0.746 |
|
| 2007 |
Das R, Qian B, Raman S, Vernon R, Thompson J, Bradley P, Khare S, Tyka MD, Bhat D, Chivian D, Kim DE, Sheffler WH, Malmström L, Wollacott AM, Wang C, et al. Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home. Proteins. 69: 118-28. PMID 17894356 DOI: 10.1002/Prot.21636 |
0.759 |
|
| 2007 |
Das R, Baker D. Automated de novo prediction of native-like RNA tertiary structures. Proceedings of the National Academy of Sciences of the United States of America. 104: 14664-9. PMID 17726102 DOI: 10.1073/Pnas.0703836104 |
0.539 |
|
| 2007 |
Lipfert J, Das R, Chu VB, Kudaravalli M, Boyd N, Herschlag D, Doniach S. Structural transitions and thermodynamics of a glycine-dependent riboswitch from Vibrio cholerae. Journal of Molecular Biology. 365: 1393-406. PMID 17118400 DOI: 10.1016/J.Jmb.2006.10.022 |
0.786 |
|
| 2006 |
Russell R, Das R, Suh H, Travers KJ, Laederach A, Engelhardt MA, Herschlag D. The paradoxical behavior of a highly structured misfolded intermediate in RNA folding. Journal of Molecular Biology. 363: 531-44. PMID 16963081 DOI: 10.1016/J.Jmb.2006.08.024 |
0.562 |
|
| 2005 |
Das R, Travers KJ, Bai Y, Herschlag D. Determining the Mg2+ stoichiometry for folding an RNA metal ion core. Journal of the American Chemical Society. 127: 8272-3. PMID 15941246 DOI: 10.1021/Ja051422H |
0.581 |
|
| 2005 |
Das R, Laederach A, Pearlman SM, Herschlag D, Altman RB. SAFA: semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments. Rna (New York, N.Y.). 11: 344-54. PMID 15701734 DOI: 10.1261/Rna.7214405 |
0.573 |
|
| 2005 |
Bai Y, Das R, Millett IS, Herschlag D, Doniach S. Probing counterion modulated repulsion and attraction between nucleic acid duplexes in solution. Proceedings of the National Academy of Sciences of the United States of America. 102: 1035-40. PMID 15647360 DOI: 10.1073/Pnas.0404448102 |
0.692 |
|
| 2004 |
Andresen K, Das R, Park HY, Smith H, Kwok LW, Lamb JS, Kirkland EJ, Herschlag D, Finkelstein KD, Pollack L. Spatial distribution of competing ions around DNA in solution. Physical Review Letters. 93: 248103. PMID 15697865 DOI: 10.1103/Physrevlett.93.248103 |
0.493 |
|
| 2004 |
Takamoto K, Das R, He Q, Doniach S, Brenowitz M, Herschlag D, Chance MR. Principles of RNA compaction: insights from the equilibrium folding pathway of the P4-P6 RNA domain in monovalent cations. Journal of Molecular Biology. 343: 1195-206. PMID 15491606 DOI: 10.1016/J.Jmb.2004.08.080 |
0.663 |
|
| 2003 |
Das R, Kwok LW, Millett IS, Bai Y, Mills TT, Jacob J, Maskel GS, Seifert S, Mochrie SG, Thiyagarajan P, Doniach S, Pollack L, Herschlag D. The fastest global events in RNA folding: electrostatic relaxation and tertiary collapse of the Tetrahymena ribozyme. Journal of Molecular Biology. 332: 311-9. PMID 12948483 DOI: 10.1016/S0022-2836(03)00854-4 |
0.711 |
|
| 2003 |
Das R, Mills TT, Kwok LW, Maskel GS, Millett IS, Doniach S, Finkelstein KD, Herschlag D, Pollack L. Counterion distribution around DNA probed by solution X-ray scattering. Physical Review Letters. 90: 188103. PMID 12786045 DOI: 10.1103/Physrevlett.90.188103 |
0.621 |
|
| 2003 |
Bartley LE, Zhuang X, Das R, Chu S, Herschlag D. Exploration of the transition state for tertiary structure formation between an RNA helix and a large structured RNA. Journal of Molecular Biology. 328: 1011-26. PMID 12729738 DOI: 10.1016/S0022-2836(03)00272-9 |
0.747 |
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