RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme.
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Katarzyna J Purzycka | K. Weeks | Zhichao Miao | E. Westhof | D. Patel | Katarzyna Pachulska-Wieczorek | R. Adamiak | J. SantaLucia | A. Ferré-D’Amaré | Rhiju Das | F. Major | Siqi Tian | W. Kladwang | J. Piccirilli | J. Bujnicki | F. Ding | N. Dokholyan | A. Krokhotin | K. Kappel | R. Batey | Xiaojun Xu | W. Dawson | C. Cheng | Fang-Chieh Chou | A. Ren | Marcin Biesiada | K. Purzycka | Shi-jie Chen | Caleb Geniesse | Thomas H. Mann | Alexander J Becka | M. Boniecki | M. Antczak | S. Dunin-Horkawicz | G. Łach | Marcin Magnus | M. Popenda | Greggory M Rice | J. Sarzynska | M. Szachniuk | Arpit Tandon | J. J. Trausch | Jian Wang | B. Williams | Yi Xiao | Dong Zhang | T. Zok | Michal J. Boniecki | K. J. Purzycka | Maciej Antczak | Marta Szachniuk | Benfeard Williams
[1] Statistical Mechanics Of Chain Molecules , 1970 .
[2] Michael Zuker,et al. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information , 1981, Nucleic Acids Res..
[3] T. Blundell,et al. Comparative protein modelling by satisfaction of spatial restraints. , 1993, Journal of molecular biology.
[4] H. Stanley,et al. Discrete molecular dynamics studies of the folding of a protein-like model. , 1998, Folding & design.
[5] D. Turner,et al. Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs. , 1998, Biochemistry.
[6] Michael Zuker,et al. Algorithms and Thermodynamics for RNA Secondary Structure Prediction: A Practical Guide , 1999 .
[7] Richard Bonneau,et al. Improving the performance of rosetta using multiple sequence alignment information and global measures of hydrophobic core formation , 2001, Proteins.
[8] D. Lilley,et al. Structure, folding and activity of the VS ribozyme: importance of the 2‐3‐6 helical junction , 2001, The EMBO journal.
[9] Michael Zuker,et al. Mfold web server for nucleic acid folding and hybridization prediction , 2003, Nucleic Acids Res..
[10] C. Dominguez,et al. HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. , 2003, Journal of the American Chemical Society.
[11] Janusz M. Bujnicki,et al. GeneSilico protein structure prediction meta-server , 2003, Nucleic Acids Res..
[12] E. Westhof,et al. Topology of three-way junctions in folded RNAs. , 2006, RNA.
[13] D. Baker,et al. Automated de novo prediction of native-like RNA tertiary structures , 2007, Proceedings of the National Academy of Sciences.
[14] F. Ding,et al. Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms. , 2008, RNA.
[15] Feng Ding,et al. iFoldRNA: three-dimensional RNA structure prediction and folding , 2008, Bioinform..
[16] F. Ding,et al. Ab initio folding of proteins with all-atom discrete molecular dynamics. , 2008, Structure.
[17] Marek Blazewicz,et al. RNA FRABASE version 1.0: an engine with a database to search for the three-dimensional fragments within RNA structures , 2007, Nucleic Acids Res..
[18] Eric Westhof,et al. New metrics for comparing and assessing discrepancies between RNA 3D structures and models. , 2009, RNA.
[19] Feng Ding,et al. Native-like RNA tertiary structures using a sequence-encoded cleavage agent and refinement by discrete molecular dynamics. , 2009, Journal of the American Chemical Society.
[20] D. Lilley,et al. Formation of an active site in trans by interaction of two complete Varkud Satellite ribozymes. , 2009, RNA.
[21] Robert D. Finn,et al. Rfam: updates to the RNA families database , 2008, Nucleic Acids Res..
[22] R. Montange,et al. Free state conformational sampling of the SAM-I riboswitch aptamer domain. , 2010, Structure.
[23] Vincent B. Chen,et al. Correspondence e-mail: , 2000 .
[24] Edmund K. Burke,et al. RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures , 2010, BMC Bioinformatics.
[25] R. Breaker,et al. Bacterial aptamers that selectively bind glutamine , 2011, RNA biology.
[26] D. Lilley,et al. Do the hairpin and VS ribozymes share a common catalytic mechanism based on general acid-base catalysis? A critical assessment of available experimental data. , 2011, RNA.
[27] F. Ding,et al. Discrete molecular dynamics , 2012 .
[28] Kristian Rother,et al. Bioinformatics Applications Note Structural Bioinformatics Moderna Server: an Online Tool for Modeling Rna 3d Structures , 2022 .
[29] J. Bujnicki,et al. ModeRNA: a tool for comparative modeling of RNA 3D structure , 2011, Nucleic acids research.
[30] Jacek Blazewicz,et al. Automated 3D structure composition for large RNAs , 2012, Nucleic acids research.
[31] Feng Ding,et al. Discrete molecular dynamics: an efficient and versatile simulation method for fine protein characterization. , 2012, The journal of physical chemistry. B.
[32] Julius B. Lucks,et al. An RNA Mapping DataBase for curating RNA structure mapping experiments , 2012, Bioinform..
[33] Jinwei Zhang,et al. YbxF and YlxQ are bacterial homologs of L7Ae and bind K-turns but not K-loops. , 2012, RNA.
[34] Feng Ding,et al. RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction. , 2012, RNA.
[35] Yangyu Huang,et al. Automated and fast building of three-dimensional RNA structures , 2012, Scientific Reports.
[36] Christopher A. Lavender,et al. Three-Dimensional RNA Structure Refinement by Hydroxyl Radical Probing , 2012, Nature Methods.
[37] Dominique Barth,et al. Automated prediction of three-way junction topological families in RNA secondary structures , 2012, Comput. Biol. Chem..
[38] Sean R. Eddy,et al. Rfam 11.0: 10 years of RNA families , 2012, Nucleic Acids Res..
[39] Jef D Boeke,et al. Retrotransposon Ty1 RNA contains a 5'-terminal long-range pseudoknot required for efficient reverse transcription. , 2013, RNA.
[40] R. Breaker,et al. Riboswitches in eubacteria sense the second messenger c-di-AMP , 2013, Nature chemical biology.
[41] Rhiju Das,et al. Atomic-Accuracy Prediction of Protein Loop Structures through an RNA-Inspired Ansatz , 2012, PloS one.
[42] D. Mathews,et al. Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots , 2013, Proceedings of the National Academy of Sciences.
[43] Tomasz Zok,et al. MCQ4Structures to compute similarity of molecule structures , 2013, Central European Journal of Operations Research.
[44] Rob Knight,et al. Structural basis for diversity in the SAM clan of riboswitches , 2014, Proceedings of the National Academy of Sciences.
[45] Dinshaw J. Patel,et al. c-di-AMP binds the ydaO riboswitch in two pseudo-symmetry-related pockets , 2014, Nature chemical biology.
[46] Xiaojun Xu,et al. Vfold: A Web Server for RNA Structure and Folding Thermodynamics Prediction , 2014, PloS one.
[47] Yang Zhang,et al. The I-TASSER Suite: protein structure and function prediction , 2014, Nature Methods.
[48] Rhiju Das,et al. The mutate-and-map protocol for inferring base pairs in structured RNA. , 2013, Methods in molecular biology.
[49] A. Ferré-D’Amaré,et al. Crystal structure of a c‐di‐AMP riboswitch reveals an internally pseudo‐dimeric RNA , 2014, The EMBO journal.
[50] Steven Busan,et al. RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP) , 2014, Nature Methods.
[51] Jacek Blazewicz,et al. RNApdbee—a webserver to derive secondary structures from pdb files of knotted and unknotted RNAs , 2014, Nucleic Acids Res..
[52] Rhiju Das,et al. Standardization of RNA Chemical Mapping Experiments , 2014, Biochemistry.
[53] A. Serganov,et al. Structural insights into recognition of c-di-AMP by the ydaO riboswitch. , 2014, Nature chemical biology.
[54] R. Batey,et al. Metal Ion-Mediated Nucleobase Recognition by the ZTP Riboswitch. , 2015, Chemistry & biology.
[55] Jian Wang,et al. 3 dRNAscore : a distance and torsion angle dependent evaluation function of 3 D RNA structures , 2015 .
[56] Janusz M. Bujnicki,et al. NPDock: a web server for protein–nucleic acid docking , 2015, Nucleic Acids Res..
[57] Rhiju Das,et al. Consistent global structures of complex RNA states through multidimensional chemical mapping , 2015, eLife.
[58] R. Breaker,et al. An ancient riboswitch class in bacteria regulates purine biosynthesis and one-carbon metabolism. , 2015, Molecular cell.
[59] Rhiju Das,et al. Modeling complex RNA tertiary folds with Rosetta. , 2015, Methods in enzymology.
[60] Yi Xue,et al. Structural and Dynamic Basis for Low-Affinity, High-Selectivity Binding of L-Glutamine by the Glutamine Riboswitch. , 2015, Cell reports.
[61] Xiaojun Xu,et al. A Method to Predict the 3D Structure of an RNA Scaffold. , 2015, Methods in molecular biology.
[62] Nikolay V. Dokholyan,et al. iFoldRNA v2: folding RNA with constraints , 2015, Bioinform..
[63] Jian Wang,et al. 3dRNAscore: a distance and torsion angle dependent evaluation function of 3D RNA structures , 2015, Nucleic acids research.
[64] Sarah W Burge,et al. Rfam: annotating families of non-coding RNA sequences. , 2015, Methods in molecular biology.
[65] Katarzyna J Purzycka,et al. Automated 3D RNA structure prediction using the RNAComposer method for riboswitches. , 2015, Methods in enzymology.
[66] Feng Ding,et al. RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures , 2015, RNA.
[67] A. Tramontano,et al. Critical assessment of methods of protein structure prediction: Progress and new directions in round XI , 2016, Proteins.
[68] Janusz M Bujnicki,et al. Computational modeling of RNA 3D structures and interactions. , 2016, Current opinion in structural biology.
[69] Janusz M Bujnicki,et al. RNA 3D Structure Modeling by Combination of Template-Based Method ModeRNA, Template-Free Folding with SimRNA, and Refinement with QRNAS. , 2016, Methods in molecular biology.
[70] Rhiju Das,et al. Blind tests of RNA nearest-neighbor energy prediction , 2016, Proceedings of the National Academy of Sciences.
[71] Susanne Hertz,et al. Statistical Mechanics Of Chain Molecules , 2016 .
[72] Tomasz Zok,et al. New functionality of RNAComposer: an application to shape the axis of miR160 precursor structure. , 2016, Acta biochimica Polonica.
[73] Siqi Tian,et al. RNA structure through multidimensional chemical mapping , 2016, bioRxiv.
[74] David E. Kim,et al. Simultaneous Optimization of Biomolecular Energy Functions on Features from Small Molecules and Macromolecules. , 2016, Journal of chemical theory and computation.
[75] Janusz M. Bujnicki,et al. SimRNAweb: a web server for RNA 3D structure modeling with optional restraints , 2016, Nucleic Acids Res..
[76] J. Bujnicki,et al. SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction , 2015, Nucleic acids research.