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Current Protocols|July 24, 2023
RNA Secondary Structure Analysis Using RNAstructureSara E Ali, Abhinav Mittal, David H MathewsNucleic Acids Research|May 12, 2009
Stochastic sampling of the RNA structural alignment spaceArif Ozgun Harmanci, Gaurav Sharma, David H MathewsBioinformatics (Oxford, England)|November 22, 2015
AccessFold: predicting RNA-RNA interactions with consideration for competing self-structureLaura DiChiacchio, Michael F Sloma, David H MathewsJournal of Chemical Theory and Computation|January 22, 2010
Effects of Restrained Sampling Space and Nonplanar Amino Groups on Free-Energy Predictions for RNA with Imino and Sheared Tandem GA Base Pairs Flanked by GC, CG, iGiC or iCiG Base PairsIlyas Yildirim, Harry A Stern, Jiri Sponer, et al.Journal of Chemical Information and Modeling|May 13, 2009
Evaluating docking methods for prediction of binding affinities of small molecules to the G protein betagamma subunitsMin-Sun Park, Axel L Dessal, Alan V Smrcka, et al.Systematic Biology|November 18, 2010
Quantifying the impact of dependent evolution among sites in phylogenetic inferenceChris A Nasrallah, David H Mathews, John P HuelsenbeckBioinformatics (Oxford, England)|July 14, 2020
LinearPartition: linear-time approximation of RNA folding partition function and base-pairing probabilitiesHe Zhang, Liang Zhang, David H Mathews, et al.BMC Bioinformatics|March 29, 2006
Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy changeAndrew V Uzilov, Joshua M Keegan, David H MathewsNucleic Acids Research|September 20, 2006
A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formationZhi John Lu, Douglas H Turner, David H MathewsJournal of Molecular Biology|October 20, 2024
memerna: Sparse RNA folding including coaxial stackingEliot Courtney, Amitava Datta, David H Mathews, et al.Pageof 20