Using DNN, we can not only raise the accuracy of contact prediction: we also have an opportunity to weight sequences in an MSA in an end-to-end manner. Recently, we have become able to access an increasing numbe
Clinical characteristics and therapeutic sequences of KRAS G12C advanced Non-Small Cell Lung Cancer (aNSCLC) patients (pts) treated by sotorasib in the French post-marketing authorization early access (post-MA EA)Abstract #1307P, Poster, September 14 Bemarituzumab Fibroblast ...
et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol. Syst. Biol. 7, 539 (2011). Article Google Scholar Thompson, J. D., Gibson, T. J. & Higgins, D. G. Multiple sequence alignment using ClustalW and ClustalX In Current ...
a protein’s biological function often depends on multiple conformational substates2, and disease-causing point mutations often cause population changes within these substates3,4. We demonstrate that clustering a multiple-sequence alignment by sequence similarity enables AlphaFold...
default 5 to 10: this increases the specificity (-htand-tt) despite decreasing the sensitivity. RepeatModeler consensus sequences were classified based on RepBase (v. 20181026) and Dfam (v. 3.1) databases, whereas MITEs were not further classified and considered only as non-autonomous DNA ...
A novel randomized iterative strategy for aligning multiple protein sequences. Comput Appl Biosci. 1991;7:479–84. 44. Gotoh O. Optimal alignment between groups of sequences and its application to multiple sequence alignment. Comput Appl Biosci. 1993;9: 361–70. 45. Braun EL, Kimball RT. ...
The full-length coding sequences of three AChEs were cloned into pFASTBac-HTa vector (Invitrogen) with the ClonExpress Ⅱ One Step Cloning Kit (Vazyme, China). The vector with an enhanced green fluorescent protein (eGFP, GenBank accession number: AAK15492) was used as a control. The ...
et al. SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res. 46, W296–W303 (2018). Article CAS PubMed PubMed Central Google Scholar Varadi, M. et al. AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space...
hydrophilic amino acids, and spontaneously self-assemble into 3D hydrogel scaffolds woven from nanofibers once exposed to physiological media or salt solutions [123, 124], and hydrogel scaffolds presenting different properties can be designed by varying the length, pattern, and sequence of amino acid...
CMKLR1 protein sequences are used in screening of candidate compounds (including antibodies, peptides, lipids, small organic molecules, etc.) for the ability to bind to and modulate CMKLR1 activity. Agents that inhibit or reduce CMKLR1 activity are of interest as therapeutic agents for decreasing...