Amber 10 DA Case, TA Darden, TE Cheatham, CL Simmerling, J Wang, RE Duke, ... University of California, 2008 | 12103* | 2008 |
Amber 2021 DA Case, HM Aktulga, K Belfon, I Ben-Shalom, SR Brozell, DS Cerutti, ... University of California, San Francisco, 2021 | 5441 | 2021 |
Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure DH Mathews, J Sabina, M Zuker, DH Turner Journal of molecular biology 288 (5), 911-940, 1999 | 4843 | 1999 |
RNAstructure: software for RNA secondary structure prediction and analysis JS Reuter, DH Mathews BMC bioinformatics 11, 1-9, 2010 | 1960 | 2010 |
Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure DH Mathews, MD Disney, JL Childs, SJ Schroeder, M Zuker, DH Turner Proceedings of the National Academy of Sciences 101 (19), 7287-7292, 2004 | 1859 | 2004 |
Algorithms and thermodynamics for RNA secondary structure prediction: a practical guide M Zuker, DH Mathews, DH Turner RNA biochemistry and biotechnology, 11-43, 1999 | 1452 | 1999 |
Accurate SHAPE-directed RNA structure determination KE Deigan, TW Li, DH Mathews, KM Weeks Proceedings of the National Academy of Sciences 106 (1), 97-102, 2009 | 779 | 2009 |
Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding. AE Walter, DH Turner, J Kim, MH Lyttle, P Müller, DH Mathews, M Zuker Proceedings of the National Academy of Sciences 91 (20), 9218-9222, 1994 | 638 | 1994 |
NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure DH Turner, DH Mathews Nucleic acids research 38 (suppl_1), D280-D282, 2010 | 635 | 2010 |
Dynalign: an algorithm for finding the secondary structure common to two RNA sequences DH Mathews, DH Turner Journal of molecular biology 317 (2), 191-203, 2002 | 526 | 2002 |
Prediction of RNA secondary structure by free energy minimization DH Mathews, DH Turner Current opinion in structural biology 16 (3), 270-278, 2006 | 523 | 2006 |
AMBER 10; University of California: San Francisco, 2008 DA Case, TA Darden, TE Cheatham III, CL Simmerling, J Wang, RE Duke, ... Google Scholar There is no corresponding record for this reference, 2008 | 508 | 2008 |
High-throughput SHAPE analysis reveals structures in HIV-1 genomic RNA strongly conserved across distinct biological states KA Wilkinson, RJ Gorelick, SM Vasa, N Guex, A Rein, DH Mathews, ... PLoS biology 6 (4), e96, 2008 | 469 | 2008 |
Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization DH Mathews Rna 10 (8), 1178-1190, 2004 | 451 | 2004 |
RNAstructure: web servers for RNA secondary structure prediction and analysis S Bellaousov, JS Reuter, MG Seetin, DH Mathews Nucleic acids research 41 (W1), W471-W474, 2013 | 418 | 2013 |
FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing JG Underwood, AV Uzilov, S Katzman, CS Onodera, JE Mainzer, ... Nature methods 7 (12), 995-1001, 2010 | 385 | 2010 |
Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots CE Hajdin, S Bellaousov, W Huggins, CW Leonard, DH Mathews, ... Proceedings of the National Academy of Sciences 110 (14), 5498-5503, 2013 | 349 | 2013 |
Predicting oligonucleotide affinity to nucleic acid targets DH Mathews, ME Burkard, SM Freier, JR Wyatt, DH Turner Rna 5 (11), 1458-1469, 1999 | 312 | 1999 |
Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change AV Uzilov, JM Keegan, DH Mathews BMC bioinformatics 7, 1-30, 2006 | 275 | 2006 |
Revolutions in RNA secondary structure prediction DH Mathews Journal of molecular biology 359 (3), 526-532, 2006 | 271 | 2006 |