Inspired by: Howard M Salis
Software used to analyze biological sequences.
2023 Articles
17 979 articles
LinearCoFold and LinearCoPartition: linear-time algorithms for secondary structure prediction of interacting RNA molecules
- He Zhang, Sizhen Li, Ning Dai, Liang Zhang, David H Mathews, Liang Huang
- Nucleic Acids Res, 10.1093/nar/gkad664
Genome-Wide RNA Secondary Structure Prediction
- Risa Karakida Kawaguchi, Hisanori Kiryu, Risa Karakida Kawaguchi, …, Hisanori Kiryu, Risa Karakida Kawaguchi, Hisanori Kiryu
- Methods Mol Biol, 10.1007/978-1-0716-2768-6_3
Computational aided design of a halotolerant CMP kinase for enzymatic synthesis of cytidine triphosphate
- Qingshi Wen, Jie Zhang, Rongxin Miao, …, Ziyi Yan, Hanjie Ying, Junzhi Wang
- Bioprocess Biosyst Eng, 10.1007/s00449-022-02827-4
Nucleic Acid Structure Prediction Including Pseudoknots Through Direct Enumeration of States: A User’s Guide to the LandscapeFold Algorithm
- Ofer Kimchi, Michael P Brenner, Lucy J Colwell, …, Ofer Kimchi, Michael P Brenner, Lucy J Colwell
- Methods Mol Biol, 10.1007/978-1-0716-2768-6_4
Toward learning the rules that predict siRNA efficacy
- Xavier Bofill-De Ros, Xavier Bofill-De Ros
- None, 10.1016/j.omtn.2023.07.023
Ion channel chameleons: Switching ion selectivity by alternative splicing
- Allen L Hsu, Manu Ben-Johny, Allen L Hsu, …, Manu Ben-Johny, Allen L Hsu, Manu Ben-Johny
- J Biol Chem, 10.1016/j.jbc.2023.102946
GHOST-NOT and GHOST-YES: Two programs for generating high-speed biosensors with randomized oligonucleotide binding sites with NOT or YES Boolean logic functions based on experimentally validated algorithms
- Dimitrios Kaloudas, Nikolet Pavlova, Robert Penchovsky, …, Dimitrios Kaloudas, Nikolet Pavlova, Robert Penchovsky
- J Biotechnol, 10.1016/j.jbiotec.2023.07.005
REDfold: accurate RNA secondary structure prediction using residual encoder-decoder network
- Chun-Chi Chen, Yi-Ming Chan, Chun-Chi Chen, Yi-Ming Chan, Chun-Chi Chen, Yi-Ming Chan
- BMC Bioinformatics, 10.1186/s12859-023-05238-8
Investigating pioneer factor activity and its coordination with chromatin remodelers using integrated synthetic oligo assay
- Hengye Chen, Chao Yan, Archana Dhasarathy, …, Archana Dhasarathy, Michael Kladde, Lu Bai
- STAR Protoc, 10.1016/j.xpro.2023.102279
Shapify: Paths to SARS-CoV-2 frameshifting pseudoknot
- Luke Trinity, Ian Wark, Lance Lansing, …, Lance Lansing, Hosna Jabbari, Ulrike Stege
- PLoS Comput Biol, 10.1371/journal.pcbi.1010922
2022 Articles
1 816 articles
Substrate Specificity and Kinetics of RNA Hydrolysis by SARS-CoV-2 NSP10/14 Exonuclease
- Tyler L Dangerfield, Kenneth A Johnson, Tyler L Dangerfield, Kenneth A Johnson, Tyler L Dangerfield, Kenneth A Johnson
- None, 10.1021/acsbiomedchemau.2c00046
A flexible RecC surface loop required for Chi hotspot control of RecBCD enzyme
- Susan K Amundsen, Alex Richardson, Khoi Ha, …, Alex Richardson, Khoi Ha, Gerald R Smith
- Genetics, 10.1093/genetics/iyac175
Predictive modeling reveals that higher-order cooperativity drives transcriptional repression in a synthetic developmental enhancer
- Yang Joon Kim, Kaitlin Rhee, Jonathan Liu, …, Meghan A Turner, Stephen J Small, Hernan G Garcia
- Elife, 10.7554/elife.73395
Experimental and computational analysis of the ancestry of an evolutionary young enzyme from histidine biosynthesis
- Thomas Kinateder, Lukas Drexler, Kristina Straub, …, Kristina Straub, Rainer Merkl, Reinhard Sterner
- Protein Sci, 10.1002/pro.4536
Hydrophobic mismatch and sequence specificity compete when transmembrane helix-helix interactions are measured with the TOXCAT assay
- Nadja Hellmann, Dirk Schneider, Nadja Hellmann, Dirk Schneider
- None, 10.3389/fchem.2022.1049310
Substrate Recognition Properties from an Intermediate Structural State of the UreA Transporter
- Manuel Sanguinetti, Lucianna Helene Silva Santos, Juliette Dourron, …, Sotiris Amillis, Sergio Pantano, Ana Ramón
- Int J Mol Sci, 10.3390/ijms232416039
Csk αC Helix: A Computational Analysis of an Essential Region for Conformational Transitions
- Raphael Vinicius Rodrigues Dias, Carolina Tatiani Alves Ferreira, Patricia Ann Jennings, …, Patricia Ann Jennings, Paul Charles Whitford, Leandro Cristante de Oliveira
- J Phys Chem B, 10.1021/acs.jpcb.2c05408
Silent codon positions in the A-rich HIV RNA genome that do not easily become A: Restrictions imposed by the RNA sequence and structure
- Ben Berkhout, Formijn J van Hemert, Ben Berkhout, Formijn J van Hemert
- None, 10.1093/ve/veac072
New Understandings from the Biophysical Study of the Structure, Dynamics, and Function of Nucleic Acids 2.0
- Joon-Hwa Lee, Joon-Hwa Lee, Joon-Hwa Lee, Joon-Hwa Lee
- Int J Mol Sci, 10.3390/ijms232415822
Ranking Peptide Binders by Affinity with AlphaFold
- Liwei Chang, Alberto Perez, Liwei Chang, …, Alberto Perez, Liwei Chang, Alberto Perez
- Angew Chem Int Ed Engl, 10.1002/anie.202213362