571
Views
140
CrossRef citations to date
0
Altmetric
Original Articles

RNA2D3D: A program for Generating, Viewing, and Comparing 3-Dimensional Models of RNA

, &
Pages 669-683 | Received 22 Dec 2007, Published online: 24 Jul 2012

Keep up to date with the latest research on this topic with citation updates for this article.

Read on this site (9)

Krishna Kumar, Abhijit Chakraborty & Saikat Chakrabarti. (2021) PresRAT: a server for identification of bacterial small-RNA sequences and their targets with probable binding region. RNA Biology 18:8, pages 1152-1159.
Read now
Marcin Magnus, Dorota Matelska, Grzegorz Łach, Grzegorz Chojnowski, Michal J Boniecki, Elzbieta Purta, Wayne Dawson, Stanislaw Dunin-Horkawicz & Janusz M Bujnicki. (2014) Computational modeling of RNA 3D structures, with the aid of experimental restraints. RNA Biology 11:5, pages 522-536.
Read now
Yunjie Zhao, Zhou Gong & Yi Xiao. (2011) Improvements of the Hierarchical Approach for Predicting RNA Tertiary Structure. Journal of Biomolecular Structure and Dynamics 28:5, pages 815-826.
Read now
Zhou Gong, Yunjie Zhao & Yi Xiao. (2010) RNA Stability Under Different Combinations of Amber Force Fields and Solvation Models. Journal of Biomolecular Structure and Dynamics 28:3, pages 431-441.
Read now
K. Bhargavi, P. Kalyan Chaitanya, D. Ramasree, M. Vasavi, D.K. Murthy & V. Uma. (2010) Homology Modeling and Docking Studies of Human Bcl-2L10 Protein. Journal of Biomolecular Structure and Dynamics 28:3, pages 379-391.
Read now
A. Mahalakshmi & R. Shenbagarathai. (2010) Homology Modeling of Cry10Aa Toxin from B. thuringiensis israelensis and B. thuringiensis subsp. LDC-9. Journal of Biomolecular Structure and Dynamics 28:3, pages 363-378.
Read now
Shengli Zhang & Tianming Wang. (2010) A Complexity-based Method to Compare RNA Secondary Structures and its Application. Journal of Biomolecular Structure and Dynamics 28:2, pages 247-258.
Read now
M. Javad Aman, Hatice Karauzum, M. Gabriela Bowden & Tam Luong Nguyen. (2010) Structural Model of the Pre-pore Ring-like Structure of Panton-Valentine Leukocidin: Providing Dimensionality to Biophysical and Mutational Data. Journal of Biomolecular Structure and Dynamics 28:1, pages 1-12.
Read now

Articles from other publishers (131)

Roberta Rocca, Katia Grillone, Emanuele Liborio Citriniti, Gianmarco Gualtieri, Anna Artese, Pierosandro Tagliaferri, Pierfrancesco Tassone & Stefano Alcaro. (2023) Targeting non-coding RNAs: Perspectives and challenges of in-silico approaches. European Journal of Medicinal Chemistry 261, pages 115850.
Crossref
Weitong Lu, Tianyu Chen, Dexuan Xiao, Xin Qin, Yang Chen & Sirong Shi. (2023) Application and prospects of nucleic acid nanomaterials in tumor therapy. RSC Advances 13:37, pages 26288-26301.
Crossref
Xunxun Wang, Shixiong Yu, En Lou, Ya-Lan Tan & Zhi-Jie Tan. (2023) RNA 3D Structure Prediction: Progress and Perspective. Molecules 28:14, pages 5532.
Crossref
Franklin Ingrid Kamga Youmbi, Vianney Kengne Tchendji & Clémentin Tayou Djamegni. (2023) P-FARFAR2: A multithreaded greedy approach to sampling low-energy RNA structures in Rosetta FARFAR2. Computational Biology and Chemistry 104, pages 107878.
Crossref
Mengnan Zhao, Rujing Wang, Kunmeng Yang, Yuhong Jiang, Yachen Peng, Yuke Li, Zhen Zhang, Jianxun Ding & Sanjun Shi. (2023) Nucleic acid nanoassembly-enhanced RNA therapeutics and diagnosis. Acta Pharmaceutica Sinica B 13:3, pages 916-941.
Crossref
Raghvendra Pratap Singh, Atul K. Srivastava, Ying-Jie Yang, Geetanjali Manchanda, Ajay Kumar, Sachin T. Yerpude, Alok R. Rai & R.C. Dubey. (2023) Nucleic Acid Nanotechnology: Trends, Opportunities and Challenges. Current Pharmaceutical Biotechnology 24:1, pages 50-60.
Crossref
Valentina Abondano Perdomo & Taejin Kim. 2023. RNA Nanostructures. RNA Nanostructures 3 29 .
Yi Zhang, Yiduo Xiong & Yi Xiao. (2022) 3dDNA: A Computational Method of Building DNA 3D Structures. Molecules 27:18, pages 5936.
Crossref
Bingbing Xu, Yanda Zhu, Changchang Cao, Hao Chen, Qiongli Jin, Guangnan Li, Junfeng Ma, Siwy Ling Yang, Jieyu Zhao, Jianghui Zhu, Yiliang Ding, Xianyang Fang, Yongfeng Jin, Chun Kit Kwok, Aiming Ren, Yue Wan, Zhiye Wang, Yuanchao Xue, Huakun Zhang, Qiangfeng Cliff Zhang & Yu Zhou. (2022) Recent advances in RNA structurome. Science China Life Sciences 65:7, pages 1285-1324.
Crossref
Ibuki Kawamata. 2022. DNA Origami. DNA Origami 75 99 .
Allison N. Tran, Morgan Chandler, Justin Halman, Damian Beasock, Adam Fessler, Riley Q. McKeough, Phuong Anh Lam, Daniel P. Furr, Jian Wang, Edward Cedrone, Marina A. Dobrovolskaia, Nikolay V. Dokholyan, Susan R. Trammell & Kirill A. Afonin. (2022) Anhydrous Nucleic Acid Nanoparticles for Storage and Handling at Broad Range of Temperatures. Small 18:13.
Crossref
Ricardo Oliveira, Eva Pinho, Ana Luísa Sousa, Óscar Dias, Nuno Filipe Azevedo & Carina Almeida. (2022) Modelling aptamers with nucleic acid mimics (NAM): From sequence to three-dimensional docking. PLOS ONE 17:3, pages e0264701.
Crossref
Xianyang Fang, José Gallego & Yun-Xing Wang. 2022. Small Angle Scattering Part A: Methods for Structural Investigation. Small Angle Scattering Part A: Methods for Structural Investigation 479 529 .
Pritha Ghosh, Chandran Nithin, Astha Joshi, Filip Stefaniak, Tomasz K. Wirecki & Janusz M. Bujnicki. 2021. Ribozymes. Ribozymes 861 881 .
Daniel W. Binzel, Xin Li, Nicolas Burns, Eshan Khan, Wen-Jui Lee, Li-Ching Chen, Satheesh Ellipilli, Wayne Miles, Yuan Soon Ho & Peixuan Guo. (2021) Thermostability, Tunability, and Tenacity of RNA as Rubbery Anionic Polymeric Materials in Nanotechnology and Nanomedicine—Specific Cancer Targeting with Undetectable Toxicity. Chemical Reviews 121:13, pages 7398-7467.
Crossref
Harrison Ndung’u Mwangi, Edward Kirwa Muge, Peter Waiganjo Wagacha, Albert Ndakala & Francis Jackim Mulaa. (2021) Methods for Identifying Microbial Natural Product Compounds that Target Kinetoplastid RNA Structural Motifs by Homology and De Novo Modeled 18S rRNA. International Journal of Molecular Sciences 22:9, pages 4493.
Crossref
Sara Ibrahim Omar, Meng Zhao, Rohith Vedhthaanth Sekar, Sahar Arbabi Moghadam, Jack A. Tuszynski & Michael T. Woodside. (2021) Modeling the structure of the frameshift-stimulatory pseudoknot in SARS-CoV-2 reveals multiple possible conformers. PLOS Computational Biology 17:1, pages e1008603.
Crossref
Ujjwala Mandekar & Sunanda Khandait. 2021. Proceedings of Integrated Intelligence Enable Networks and Computing. Proceedings of Integrated Intelligence Enable Networks and Computing 371 382 .
Manoj Kumar Gupta, Gayatri Gouda, Ravindra Donde, Piyali Goswami, N. Rajesh, Pallabi Pati, Sushil Kumar Rathore, Ramakrishna Vadde & Lambodar Behera. 2021. Bioinformatics in Rice Research. Bioinformatics in Rice Research 209 237 .
Vladimir Reinharz, Roman Sarrazin-Gendron & Jérôme Waldispühl. 2021. RNA Bioinformatics. RNA Bioinformatics 17 42 .
Huiwen Wang & Yunjie Zhao. (2020) Methods and applications of RNA contact prediction*. Chinese Physics B 29:10, pages 108708.
Crossref
Yuhua Weng, Qianqian Huang, Chunhui Li, Yongfeng Yang, Xiaoxia Wang, Jie Yu, Yuanyu Huang & Xing-Jie Liang. (2020) Improved Nucleic Acid Therapy with Advanced Nanoscale Biotechnology. Molecular Therapy - Nucleic Acids 19, pages 581-601.
Crossref
Kai Xia, Jianlei Shen, Qian Li, Chunhai Fan & Hongzhou Gu. (2020) Near-Atomic Fabrication with Nucleic Acids. ACS Nano 14:2, pages 1319-1337.
Crossref
Lei Jin, Ya-Lan Tan, Yao Wu, Xunxun Wang, Ya-Zhou Shi & Zhi-Jie Tan. (2019) Structure folding of RNA kissing complexes in salt solutions: predicting 3D structure, stability, and folding pathway. RNA 25:11, pages 1532-1548.
Crossref
Satoshi Yamasaki, Takayuki Amemiya, Yukimitsu Yabuki, Katsuhisa Horimoto & Kazuhiko Fukui. (2019) ToGo-WF: prediction of RNA tertiary structures and RNA–RNA/protein interactions using the KNIME workflow. Journal of Computer-Aided Molecular Design 33:5, pages 497-507.
Crossref
Almudena Ponce-Salvatierra, Astha, Katarzyna Merdas, Chandran Nithin, Pritha Ghosh, Sunandan Mukherjee & Janusz M. Bujnicki. (2019) Computational modeling of RNA 3D structure based on experimental data. Bioscience Reports 39:2.
Crossref
Ruby Srivastava. 2019. Density Functional Theory. Density Functional Theory.
Y. Z. Wang, J. Li, S. Zhang, B. Huang, G. Yao & J. Zhang. (2019) An RNA Scoring Function for Tertiary Structure Prediction Based on Multi-Layer Neural Networks. Molecular Biology 53:1, pages 118-126.
Crossref
Pablo D. Dans, Diego Gallego, Alexandra Balaceanu, Leonardo Darré, Hansel Gómez & Modesto Orozco. (2019) Modeling, Simulations, and Bioinformatics at the Service of RNA Structure. Chem 5:1, pages 51-73.
Crossref
Effirul I. Ramlan & Mohd Firdaus-Raih. 2019. Encyclopedia of Bioinformatics and Computational Biology. Encyclopedia of Bioinformatics and Computational Biology 535 545 .
Maciej Antczak, Tomasz Zok, Maciej Osowiecki, Mariusz Popenda, Ryszard W. Adamiak & Marta Szachniuk. (2018) RNAfitme: a webserver for modeling nucleobase and nucleoside residue conformation in fixed-backbone RNA structures. BMC Bioinformatics 19:1.
Crossref
Jun Li, Wei Zhu, Jun Wang, Wenfei Li, Sheng Gong, Jian Zhang & Wei Wang. (2018) RNA3DCNN: Local and global quality assessments of RNA 3D structures using 3D deep convolutional neural networks. PLOS Computational Biology 14:11, pages e1006514.
Crossref
Sergio Cruz-León, Alvaro Vázquez-Mayagoitia, Simone Melchionna, Nadine Schwierz & Maria Fyta. (2018) Coarse-Grained Double-Stranded RNA Model from Quantum-Mechanical Calculations. The Journal of Physical Chemistry B 122:32, pages 7915-7928.
Crossref
Maciej Antczak, Mariusz Popenda, Tomasz Zok, Michal Zurkowski, Ryszard W Adamiak & Marta Szachniuk. (2018) New algorithms to represent complex pseudoknotted RNA structures in dot-bracket notation. Bioinformatics 34:8, pages 1304-1312.
Crossref
Simón Poblete, Sandro Bottaro & Giovanni Bussi. (2018) A nucleobase-centered coarse-grained representation for structure prediction of RNA motifs. Nucleic Acids Research 46:4, pages 1674-1683.
Crossref
Congcong Xu, Farzin Haque, Daniel L. Jasinski, Daniel W. Binzel, Dan Shu & Peixuan Guo. (2018) Favorable biodistribution, specific targeting and conditional endosomal escape of RNA nanoparticles in cancer therapy. Cancer Letters 414, pages 57-70.
Crossref
Mansi Arora & Deepak KaulMansi Arora & Deepak Kaul. 2018. Cancer RNome: Nature & Evolution. Cancer RNome: Nature & Evolution 287 313 .
Yuba R. Bhandari, Lixin Fan, Xianyang Fang, George F. Zaki, Eric A. Stahlberg, Wei Jiang, Charles D. Schwieters, Jason R. Stagno & Yun-Xing Wang. (2017) Topological Structure Determination of RNA Using Small-Angle X-Ray Scattering. Journal of Molecular Biology 429:23, pages 3635-3649.
Crossref
Wayne K Dawson, Michal Lazniewski & Dariusz Plewczynski. (2017) RNA structure interactions and ribonucleoprotein processes of the influenza A virus. Briefings in Functional Genomics.
Crossref
Jian Wang, Kangkun Mao, Yunjie Zhao, Chen Zeng, Jianjin Xiang, Yi Zhang & Yi Xiao. (2017) Optimization of RNA 3D structure prediction using evolutionary restraints of nucleotide–nucleotide interactions from direct coupling analysis. Nucleic Acids Research 45:11, pages 6299-6309.
Crossref
Li-Zhen SunDong ZhangShi-Jie Chen. (2017) Theory and Modeling of RNA Structure and Interactions with Metal Ions and Small Molecules. Annual Review of Biophysics 46:1, pages 227-246.
Crossref
Jaimie Marie Stewart, Hari K. K. Subramanian & Elisa Franco. (2017) Self-assembly of multi-stranded RNA motifs into lattices and tubular structures. Nucleic Acids Research 45:9, pages 5449-5457.
Crossref
David R. Bell, Sara Y. Cheng, Heber Salazar & Pengyu Ren. (2017) Capturing RNA Folding Free Energy with Coarse-Grained Molecular Dynamics Simulations. Scientific Reports 7:1.
Crossref
Jian Wang & Yi Xiao. (2017) Using 3dRNA for RNA 3‐D Structure Prediction and Evaluation. Current Protocols in Bioinformatics 57:1.
Crossref
Daniel Jasinski, Farzin Haque, Daniel W Binzel & Peixuan Guo. (2017) Advancement of the Emerging Field of RNA Nanotechnology. ACS Nano 11:2, pages 1142-1164.
Crossref
Kalle J. Hanhijärvi, Gabija Ziedaite, Dennis H. Bamford, Edward Hæggström & Minna M. Poranen. (2017) Single-molecule measurements of viral ssRNA packaging. RNA 23:1, pages 119-129.
Crossref
Taejin Kim, Wojciech K. Kasprzak & Bruce A. Shapiro. 2017. RNA Nanostructures. RNA Nanostructures 33 64 .
Rishabh Sharan, Eckart Bindewald, Wojciech K. Kasprzak & Bruce A. Shapiro. 2017. RNA Nanostructures. RNA Nanostructures 19 32 .
Dušan Turk. 2017. Protein Crystallography. Protein Crystallography 491 548 .
Shou-Jun Xiao. 2017. 3D DNA Nanostructure. 3D DNA Nanostructure 81 96 .
Lorena Parlea, Anu Puri, Wojciech Kasprzak, Eckart Bindewald, Paul Zakrevsky, Emily Satterwhite, Kenya Joseph, Kirill A. Afonin & Bruce A. Shapiro. (2016) Cellular Delivery of RNA Nanoparticles. ACS Combinatorial Science 18:9, pages 527-547.
Crossref
Jun Li, Jian Zhang, Jun Wang, Wenfei Li & Wei Wang. (2016) Structure Prediction of RNA Loops with a Probabilistic Approach. PLOS Computational Biology 12:8, pages e1005032.
Crossref
Yuba R. Bhandari, Wei Jiang, Eric A. Stahlberg, Jason R. Stagno & Yun-Xing Wang. (2016) Modeling RNA topological structures using small angle X-ray scattering. Methods 103, pages 18-24.
Crossref
Marcin Biesiada, Katarzyna Pachulska-Wieczorek, Ryszard W. Adamiak & Katarzyna J. Purzycka. (2016) RNAComposer and RNA 3D structure prediction for nanotechnology. Methods 103, pages 120-127.
Crossref
Wayne K Dawson & Janusz M Bujnicki. (2016) Computational modeling of RNA 3D structures and interactions. Current Opinion in Structural Biology 37, pages 22-28.
Crossref
Srinivas Somarowthu. (2016) Progress and Current Challenges in Modeling Large RNAs. Journal of Molecular Biology 428:5, pages 736-747.
Crossref
Kun Yan, Yasir Arfat, Dijie Li, Fan Zhao, Zhihao Chen, Chong Yin, Yulong Sun, Lifang Hu, Tuanmin Yang & Airong Qian. (2016) Structure Prediction: New Insights into Decrypting Long Noncoding RNAs. International Journal of Molecular Sciences 17:1, pages 132.
Crossref
Ya-Zhou Shi, Lei Jin, Feng-Hua Wang, Xiao-Long Zhu & Zhi-Jie Tan. (2015) Predicting 3D Structure, Flexibility, and Stability of RNA Hairpins in Monovalent and Divalent Ion Solutions. Biophysical Journal 109:12, pages 2654-2665.
Crossref
Corinna Theis, Craig L. Zirbel, Christian Höner zu Siederdissen, Christian Anthon, Ivo L. Hofacker, Henrik Nielsen & Jan Gorodkin. (2015) RNA 3D Modules in Genome-Wide Predictions of RNA 2D Structure. PLOS ONE 10:10, pages e0139900.
Crossref
Hosna Jabbari, Maral Aminpour & Carlo Montemagno. (2015) Computational Approaches to Nucleic Acid Origami. ACS Combinatorial Science 17:10, pages 535-547.
Crossref
Hui Li, Taek Lee, Thomas Dziubla, Fengmei Pi, Sijin Guo, Jing Xu, Chan Li, Farzin Haque, Xing-Jie Liang & Peixuan Guo. (2015) RNA as a stable polymer to build controllable and defined nanostructures for material and biomedical applications. Nano Today 10:5, pages 631-655.
Crossref
Liang Ding, Xingran Xue, Sal LaMarca, Mohammad Mohebbi, Abdul Samad, Russell L. Malmberg & Liming Cai. (2015) Accurate prediction of RNA nucleotide interactions with backbone k -tree model . Bioinformatics 31:16, pages 2660-2667.
Crossref
Xiaojun Xu & Shi-Jie Chen. (2015) Physics-based RNA structure prediction. Biophysics Reports 1:1, pages 2-13.
Crossref
Tristan Cragnolini, Yoann Laurin, Philippe Derreumaux & Samuela Pasquali. (2015) Coarse-Grained HiRE-RNA Model for ab Initio RNA Folding beyond Simple Molecules, Including Noncanonical and Multiple Base Pairings. Journal of Chemical Theory and Computation 11:7, pages 3510-3522.
Crossref
Ping Ge & Shaojie Zhang. (2015) Computational analysis of RNA structures with chemical probing data. Methods 79-80, pages 60-66.
Crossref
Jian Wang, Yunjie Zhao, Chunyan Zhu & Yi Xiao. (2015) 3dRNAscore: a distance and torsion angle dependent evaluation function of 3D RNA structures. Nucleic Acids Research 43:10, pages e63-e63.
Crossref
Kirill A. Afonin, Mathias Viard, Ioannis Kagiampakis, Christopher L. Case, Marina A. Dobrovolskaia, Jen Hofmann, Ashlee Vrzak, Maria Kireeva, Wojciech K. Kasprzak, Vineet N. KewalRamani & Bruce A. Shapiro. (2014) Triggering of RNA Interference with RNA–RNA, RNA–DNA, and DNA–RNA Nanoparticles. ACS Nano 9:1, pages 251-259.
Crossref
K.J. Purzycka, M. Popenda, M. Szachniuk, M. Antczak, P. Lukasiak, J. Blazewicz & R.W. Adamiak. 2015. Computational Methods for Understanding Riboswitches. Computational Methods for Understanding Riboswitches 3 34 .
Zhijie Tan, Wenbing Zhang, Yazhou Shi & Fenghua Wang. 2015. Advance in Structural Bioinformatics. Advance in Structural Bioinformatics 143 183 .
Farzin Haque & Peixuan Guo. 2015. RNA Nanotechnology and Therapeutics. RNA Nanotechnology and Therapeutics 1 19 .
Jérôme Waldispühl & Vladimir Reinharz. 2015. RNA Bioinformatics. RNA Bioinformatics 101 121 .
Camilla Faoro & Sandro F. Ataide. (2014) Ribonomic approaches to study the RNA‐binding proteome. FEBS Letters 588:20, pages 3649-3664.
Crossref
Feng Gao, Wojciech K. Kasprzak, Christine Szarko, Bruce A. Shapiro & Anne E. Simon. (2014) The 3′ Untranslated Region of Pea Enation Mosaic Virus Contains Two T-Shaped, Ribosome-Binding, Cap-Independent Translation Enhancers. Journal of Virology 88:20, pages 11696-11712.
Crossref
Kirill A. Afonin, Mathias Viard, Alexey Y. Koyfman, Angelica N. Martins, Wojciech K. Kasprzak, Martin Panigaj, Ravi Desai, Arti Santhanam, Wade W. Grabow, Luc Jaeger, Eliahu Heldman, Jakob Reiser, Wah Chiu, Eric O. Freed & Bruce A. Shapiro. (2014) Multifunctional RNA Nanoparticles. Nano Letters 14:10, pages 5662-5671.
Crossref
Ya-Zhou Shi, Feng-Hua Wang, Yuan-Yan Wu & Zhi-Jie Tan. (2014) A coarse-grained model with implicit salt for RNAs: Predicting 3D structure, stability and salt effect. The Journal of Chemical Physics 141:10.
Crossref
Ashton Trey Belew, Arturas Meskauskas, Sharmishtha Musalgaonkar, Vivek M. Advani, Sergey O. Sulima, Wojciech K. Kasprzak, Bruce A. Shapiro & Jonathan D. Dinman. (2014) Ribosomal frameshifting in the CCR5 mRNA is regulated by miRNAs and the NMD pathway. Nature 512:7514, pages 265-269.
Crossref
Emma S. E. Eriksson, Lokesh Joshi, Martin Billeter & Leif A. Eriksson. (2014) De novo tertiary structure prediction using RNA123—benchmarking and application to Macugen. Journal of Molecular Modeling 20:8.
Crossref
Maciej Antczak, Tomasz Zok, Mariusz Popenda, Piotr Lukasiak, Ryszard W. Adamiak, Jacek Blazewicz & Marta Szachniuk. (2014) RNApdbee—a webserver to derive secondary structures from pdb files of knotted and unknotted RNAs. Nucleic Acids Research 42:W1, pages W368-W372.
Crossref
Ya-Zhou Shi, Yuan-Yan Wu, Feng-Hua Wang & Zhi-Jie Tan. (2014) RNA structure prediction: Progress and perspective. Chinese Physics B 23:7, pages 078701.
Crossref
Kirill A. Afonin, Wojciech K. Kasprzak, Eckart Bindewald, Maria Kireeva, Mathias Viard, Mikhail Kashlev & Bruce A. Shapiro. (2014) In Silico Design and Enzymatic Synthesis of Functional RNA Nanoparticles . Accounts of Chemical Research 47:6, pages 1731-1741.
Crossref
. 2014. RNA Nanotechnology. RNA Nanotechnology 1 4 .
Oscar Taxilaga-Zetina, Patricia Pliego-Pastrana & Mauricio D. Carbajal-Tinoco. (2014) RNA pseudo-knots simulated with a one-bead coarse-grained model. The Journal of Chemical Physics 140:11.
Crossref
Satoshi Yamasaki, Takatsugu Hirokawa, Kiyoshi Asai & Kazuhiko Fukui. (2014) Tertiary Structure Prediction of RNA–RNA Complexes Using a Secondary Structure and Fragment-Based Method. Journal of Chemical Information and Modeling 54:2, pages 672-682.
Crossref
Irina Tuszynska, Dorota Matelska, Marcin Magnus, Grzegorz Chojnowski, Joanna M. Kasprzak, Lukasz P. Kozlowski, Stanislaw Dunin-Horkawicz & Janusz M. Bujnicki. (2014) Computational modeling of protein–RNA complex structures. Methods 65:3, pages 310-319.
Crossref
Chad R. Bernier, Anton S. Petrov, Chris C. Waterbury, James Jett, Fengbo Li, Larry E. Freil, Xiao Xiong, Lan Wang, Blacki L. R. Migliozzi, Eli Hershkovits, Yuzhen Xue, Chiaolong Hsiao, Jessica C. Bowman, Stephen C. Harvey, Martha A. Grover, Zachary J. Wartell & Loren Dean Williams. (2014) RiboVision suite for visualization and analysis of ribosomes. Faraday Discuss. 169, pages 195-207.
Crossref
David Porciani, Giovanni Signore, Laura Marchetti, Paolo Mereghetti, Riccardo Nifosì & Fabio Beltram. (2014) Two Interconvertible Folds Modulate the Activity of a DNA Aptamer Against Transferrin Receptor. Molecular Therapy - Nucleic Acids 3, pages e144.
Crossref
Baiju G. Nair & Yoshihiro Ito. 2021. Encyclopedia of Polymeric Nanomaterials. Encyclopedia of Polymeric Nanomaterials 1 11 .
Feng Gao, Suna P. Gulay, Wojciech Kasprzak, Jonathan D. Dinman, Bruce A. Shapiro & Anne E. Simon. (2013) The Kissing-Loop T-Shaped Structure Translational Enhancer of Pea Enation Mosaic Virus Can Bind Simultaneously to Ribosomes and a 5′ Proximal Hairpin. Journal of Virology 87:22, pages 11987-12002.
Crossref
Aaron T. Frank, Sung-Hun Bae & Andrew C. Stelzer. (2013) Prediction of RNA 1 H and 13 C Chemical Shifts: A Structure Based Approach . The Journal of Physical Chemistry B 117:43, pages 13497-13506.
Crossref
Meikang Qiu, Emil Khisamutdinov, Zhengyi Zhao, Cheryl Pan, Jeong-Woo Choi, Neocles B. Leontis & Peixuan Guo. (2013) RNA nanotechnology for computer design and in vivo computation . Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 371:2000, pages 20120310.
Crossref
Yi Zhao, Jian Wang, XiaoWei Chen, HaiTao Luo, YunJie Zhao, Yi Xiao & RenSheng Chen. (2013) Large-scale study of long non-coding RNA functions based on structure and expression features. Science China Life Sciences 56:10, pages 953-959.
Crossref
Christian Laing, Segun Jung, Namhee Kim, Shereef Elmetwaly, Mai Zahran & Tamar Schlick. (2013) Predicting Helical Topologies in RNA Junctions as Tree Graphs. PLoS ONE 8:8, pages e71947.
Crossref
Piotr Lukasiak, Maciej Antczak, Tomasz Ratajczak, Janusz M. Bujnicki, Marta Szachniuk, Ryszard W. Adamiak, Mariusz Popenda & Jacek Blazewicz. (2013) RNAlyzer—novel approach for quality analysis of RNA structural models. Nucleic Acids Research 41:12, pages 5978-5990.
Crossref
James D. Stephenson, Haitao Li, Julia C. Kenyon, Martyn Symmons, Dave Klenerman & Andrew M.L. Lever. (2013) Three-Dimensional RNA Structure of the Major HIV-1 Packaging Signal Region. Structure 21:6, pages 951-962.
Crossref
Namhee Kim, Katherine Niccole Fuhr & Tamar Schlick. 2013. Biophysics of RNA Folding. Biophysics of RNA Folding 23 51 .
Yunjie Zhao, Yangyu Huang, Zhou Gong, Yanjie Wang, Jianfen Man & Yi Xiao. (2012) Automated and fast building of three-dimensional RNA structures. Scientific Reports 2:1.
Crossref
Feng Gao, Wojciech Kasprzak, Vera A. Stupina, Bruce A. Shapiro & Anne E. Simon. (2012) A Ribosome-Binding, 3′ Translational Enhancer Has a T-Shaped Structure and Engages in a Long-Distance RNA-RNA Interaction. Journal of Virology 86:18, pages 9828-9842.
Crossref
Marc Parisien & François Major. (2012) Determining RNA three-dimensional structures using low-resolution data. Journal of Structural Biology 179:3, pages 252-260.
Crossref
Mariusz Popenda, Marta Szachniuk, Maciej Antczak, Katarzyna J. Purzycka, Piotr Lukasiak, Natalia Bartol, Jacek Blazewicz & Ryszard W. Adamiak. (2012) Automated 3D structure composition for large RNAs. Nucleic Acids Research 40:14, pages e112-e112.
Crossref
Vladimir Reinharz, François Major & Jérôme Waldispühl. (2012) Towards 3D structure prediction of large RNA molecules: an integer programming framework to insert local 3D motifs in RNA secondary structure. Bioinformatics 28:12, pages i207-i214.
Crossref
José Almeida Cruz, Marc-Frédérick Blanchet, Michal Boniecki, Janusz M. Bujnicki, Shi-Jie Chen, Song Cao, Rhiju Das, Feng Ding, Nikolay V. Dokholyan, Samuel Coulbourn Flores, Lili Huang, Christopher A. Lavender, Véronique Lisi, François Major, Katarzyna Mikolajczak, Dinshaw J. Patel, Anna Philips, Tomasz Puton, John Santalucia, Fredrick Sijenyi, Thomas Hermann, Kristian Rother, Magdalena Rother, Alexander Serganov, Marcin Skorupski, Tomasz Soltysinski, Parin Sripakdeevong, Irina Tuszynska, Kevin M. Weeks, Christina Waldsich, Michael Wildauer, Neocles B. Leontis & Eric Westhof. (2012) RNA-Puzzles : A CASP-like evaluation of RNA three-dimensional structure prediction . RNA 18:4, pages 610-625.
Crossref
John Paul Bida & L. James MaherIIIIII. (2012) Improved prediction of RNA tertiary structure with insights into native state dynamics. RNA 18:3, pages 385-393.
Crossref
Christian Laing, Dongrong Wen, Jason T. L. Wang & Tamar Schlick. (2012) Predicting coaxial helical stacking in RNA junctions. Nucleic Acids Research 40:2, pages 487-498.
Crossref
Wojciech K. Kasprzak & Bruce A. Shapiro. 2012. RNA 3D Structure Analysis and Prediction. RNA 3D Structure Analysis and Prediction 119 142 .
Kristian Rother, Magdalena Rother, Michał Boniecki, Tomasz Puton, Konrad Tomala, Paweł Łukasz & Janusz M. Bujnicki. 2012. RNA 3D Structure Analysis and Prediction. RNA 3D Structure Analysis and Prediction 67 90 .
Parin Sripakdeevong, Kyle Beauchamp & Rhiju Das. 2012. RNA 3D Structure Analysis and Prediction. RNA 3D Structure Analysis and Prediction 43 65 .
Neocles Leontis & Eric Westhof. 2012. RNA 3D Structure Analysis and Prediction. RNA 3D Structure Analysis and Prediction 5 17 .
Yun-Xing Wang, Jinbu Wang & Xiaobing Zuo. 2012. RNA 3D Structure Analysis and Prediction. RNA 3D Structure Analysis and Prediction 335 359 .
Hyun-Ju Park & So-Jung Park. 2013. Biophysical approaches to translational control of gene expression. Biophysical approaches to translational control of gene expression 235 252 .
Kirill A Afonin, Wade W Grabow, Faye M Walker, Eckart Bindewald, Marina A Dobrovolskaia, Bruce A Shapiro & Luc Jaeger. (2011) Design and self-assembly of siRNA-functionalized RNA nanoparticles for use in automated nanomedicine. Nature Protocols 6:12, pages 2022-2034.
Crossref
Rong Guo, Arturas Meskauskas, Jonathan D. Dinman & Anne E. Simon. (2011) Evolution of a helper virus-derived, ribosome binding translational enhancer in an untranslated satellite RNA of Turnip crinkle virus. Virology 419:1, pages 10-16.
Crossref
Yelena V. Lerman, Scott D. Kennedy, Neelaabh Shankar, Marc Parisien, Francois Major & Douglas H. Turner. (2011) NMR structure of a 4 × 4 nucleotide RNA internal loop from an R2 retrotransposon: Identification of a three purine–purine sheared pair motif and comparison to MC-SYM predictions. RNA 17:9, pages 1664-1677.
Crossref
Kristian Rother, Magdalena Rother, Michał Boniecki, Tomasz Puton & Janusz M. Bujnicki. (2011) RNA and protein 3D structure modeling: similarities and differences. Journal of Molecular Modeling 17:9, pages 2325-2336.
Crossref
Matthew G. Seetin & David H. Mathews. (2011) Automated RNA tertiary structure prediction from secondary structure and low-resolution restraints. Journal of Computational Chemistry 32:10, pages 2232-2244.
Crossref
Wojciech Kasprzak, Eckart Bindewald, Tae-Jin Kim, Luc Jaeger & Bruce A. Shapiro. (2011) Use of RNA structure flexibility data in nanostructure modeling. Methods 54:2, pages 239-250.
Crossref
Christian Laing & Tamar Schlick. (2011) Computational approaches to RNA structure prediction, analysis, and design. Current Opinion in Structural Biology 21:3, pages 306-318.
Crossref
Girish C. Shukla, Farzin Haque, Yitzhak Tor, L. Marcus Wilhelmsson, Jean-Jacques Toulmé, Hervé Isambert, Peixuan Guo, John J. Rossi, Scott A. Tenenbaum & Bruce A. Shapiro. (2011) A Boost for the Emerging Field of RNA Nanotechnology. ACS Nano 5:5, pages 3405-3418.
Crossref
Magdalena Rother, Kristian Rother, Tomasz Puton & Janusz M. Bujnicki. (2011) ModeRNA: a tool for comparative modeling of RNA 3D structure. Nucleic Acids Research 39:10, pages 4007-4022.
Crossref
Amber R. Davis, Charles C. Kirkpatrick & Brent M. Znosko. (2011) Structural characterization of naturally occurring RNA single mismatches. Nucleic Acids Research 39:3, pages 1081-1094.
Crossref
Sichun Yang, Marc Parisien, François Major & Benoît Roux. (2010) RNA Structure Determination Using SAXS Data. The Journal of Physical Chemistry B 114:31, pages 10039-10048.
Crossref
Christian Laing & Tamar Schlick. (2010) Computational approaches to 3D modeling of RNA. Journal of Physics: Condensed Matter 22:28, pages 283101.
Crossref
Alexander Keller, Matthias Wolf & Thomas Dandekar. (2010) Ribosomal RNA phylogenetics: the third dimension. Biologia 65:3, pages 388-391.
Crossref
Song Cao, David P. Giedroc & Shi-Jie Chen. (2010) Predicting loop–helix tertiary structural contacts in RNA pseudoknots. RNA 16:3, pages 538-552.
Crossref
Magdalena A. Jonikas, Randall J. Radmer & Russ B. Altman. (2009) Knowledge-based instantiation of full atomic detail into coarse-grain RNA 3D structural models. Bioinformatics 25:24, pages 3259-3266.
Crossref
Marc Parisien, José Almeida Cruz, Éric Westhof & François Major. (2009) New metrics for comparing and assessing discrepancies between RNA 3D structures and models. RNA 15:10, pages 1875-1885.
Crossref
Jinbu Wang, Xiaobing Zuo, Ping Yu, Huan Xu, Mary R. Starich, David M. Tiede, Bruce A. Shapiro, Charles D. Schwieters & Yun-Xing Wang. (2009) A Method for Helical RNA Global Structure Determination in Solution Using Small-Angle X-Ray Scattering and NMR Measurements. Journal of Molecular Biology 393:3, pages 717-734.
Crossref
J. R. Thompson & M. Tepfer. (2009) The 3' untranslated region of cucumber mosaic virus (CMV) subgroup II RNA3 arose by interspecific recombination between CMV and tomato aspermy virus. Journal of General Virology 90:9, pages 2293-2298.
Crossref
Yurong Xin, Christian Laing, Neocles B. Leontis & Tamar Schlick. (2008) Annotation of tertiary interactions in RNA structures reveals variations and correlations. RNA 14:12, pages 2465-2477.
Crossref
Vera A. Stupina, Arturas Meskauskas, John C. McCormack, Yaroslava G. Yingling, Bruce A. Shapiro, Jonathan D. Dinman & Anne E. Simon. (2008) The 3′ proximal translational enhancer of Turnip crinkle virus binds to 60S ribosomal subunits. RNA 14:11, pages 2379-2393.
Crossref
Eckart Bindewald, Calvin Grunewald, Brett Boyle, Mary O’Connor & Bruce A. Shapiro. (2008) Computational strategies for the automated design of RNA nanoscale structures from building blocks using NanoTiler. Journal of Molecular Graphics and Modelling 27:3, pages 299-308.
Crossref
John C. McCormack, Xuefeng Yuan, Yaroslava G. Yingling, Wojciech Kasprzak, Rodolfo E. Zamora, Bruce A. Shapiro & Anne E. Simon. (2008) Structural Domains within the 3′ Untranslated Region of Turnip Crinkle Virus. Journal of Virology 82:17, pages 8706-8720.
Crossref