RNAmap2D – calculation, visualization and analysis of contact and distance maps for RNA and protein-RNA complex structures
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Kristian Rother | Janusz M. Bujnicki | Michal J. Pietal | Natalia Szostak | J. Bujnicki | K. Rother | Natalia M Szostak | Kristian Rother
[1] Mark de Berg,et al. Computational Geometry: Algorithms and Applications, Second Edition , 2000 .
[2] Holger Gohlke,et al. Constraint counting on RNA structures: linking flexibility and function. , 2009, Methods.
[3] H. Scheraga,et al. Experimental and theoretical aspects of protein folding. , 1975, Advances in protein chemistry.
[4] Phillips Dc,et al. The development of crystallographic enzymology. , 1970 .
[5] C. Orengo,et al. Analysis and assessment of ab initio three‐dimensional prediction, secondary structure, and contacts prediction , 1999, Proteins.
[6] P. Tompa,et al. Limitations of induced folding in molecular recognition by intrinsically disordered proteins. , 2009, Chemphyschem : a European journal of chemical physics and physical chemistry.
[7] Janusz M. Bujnicki,et al. DARS-RNP and QUASI-RNP: New statistical potentials for protein-RNA docking , 2011, BMC Bioinformatics.
[8] Gergely Fördös,et al. SeqX: a tool to detect, analyze and visualize residue co-locations in protein and nucleic acid structures , 2005, BMC Bioinformatics.
[9] M. P. Cummings. PHYLIP (Phylogeny Inference Package) , 2004 .
[10] Michael Lappe,et al. CMView: Interactive contact map visualization and analysis , 2011, Bioinform..
[11] Mark de Berg,et al. Computational geometry: algorithms and applications , 1997 .
[12] BMC Bioinformatics , 2005 .
[13] Wojciech Kasprzak,et al. Solution structure of the cap-independent translational enhancer and ribosome-binding element in the 3′ UTR of turnip crinkle virus , 2010, Proceedings of the National Academy of Sciences.
[14] Janusz M. Bujnicki,et al. Template-Based and Template-Free Modeling of RNA 3D Structure: Inspirations from Protein Structure Modeling , 2012 .
[15] L. Scott,et al. RNA structure determination by NMR. , 2008, Methods in molecular biology.
[16] M Vendruscolo,et al. Recovery of protein structure from contact maps. , 1997, Folding & design.
[17] Burkhard Rost,et al. EVAcon: a protein contact prediction evaluation service , 2005, Nucleic Acids Res..
[18] D. Baker,et al. Automated de novo prediction of native-like RNA tertiary structures , 2007, Proceedings of the National Academy of Sciences.
[19] D. Phillips. The development of crystallographic enzymology. , 1970, Biochemical Society symposium.
[20] Feng Ding,et al. RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction. , 2012, RNA.
[21] Eric Westhof,et al. RNA 3D Structure Analysis and Prediction , 2012, Nucleic Acids and Molecular Biology.
[22] David E Draper,et al. A guide to ions and RNA structure. , 2004, RNA.
[23] R. Knight,et al. PyCogent: a toolkit for making sense from sequence , 2007, Genome Biology.
[24] K. Dill. Dominant forces in protein folding. , 1990, Biochemistry.
[25] Ronny Lorenz,et al. The Vienna RNA Websuite , 2008, Nucleic Acids Res..
[26] Janusz M. Bujnicki,et al. PROTMAP2D: visualization, comparison and analysis of 2D maps of protein structure , 2007, Bioinform..
[27] Kotagiri Ramamohanarao,et al. PConPy - a Python module for generating 2D protein maps , 2008, Bioinform..
[28] A. Ferré-D’Amaré,et al. RNA folds: insights from recent crystal structures. , 1999, Annual review of biophysics and biomolecular structure.
[29] Andrei N. Lupas,et al. CLANS: a Java application for visualizing protein families based on pairwise similarity , 2004, Bioinform..
[30] K Schulten,et al. VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.
[31] J. Gibrat,et al. Protein secondary structure assignment revisited: a detailed analysis of different assignment methods , 2005, BMC Structural Biology.
[32] Feng Ding,et al. iFoldRNA: three-dimensional RNA structure prediction and folding , 2008, Bioinform..
[33] E. Westhof,et al. Geometric nomenclature and classification of RNA base pairs. , 2001, RNA.
[34] J. Bujnicki,et al. ModeRNA: a tool for comparative modeling of RNA 3D structure , 2011, Nucleic acids research.
[35] T. Hermann,et al. Self-assembling RNA square , 2011, Proceedings of the National Academy of Sciences.
[36] Jeffrey Chang,et al. Biopython: Python tools for computational biology , 2000, SIGB.
[37] John D. Westbrook,et al. Tools for the automatic identification and classification of RNA base pairs , 2003, Nucleic Acids Res..