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Purification and preparation of Marchantia polymorpha Auxin Response Factor 2 for phase separation studies

FEBS Open Bio, EarlyView.
We describe detailed protocols for the purification and preparation of Marchantia polymorpha Auxin Response Factor 2 (MpARF2). This protein is fused to an MBP solubility tag and an mNG fluorescent tag and is purified from Escherichia coli. The presented procedures make it possible to study MpARF2 assemblies, which could arise from phase separation ...
Bas Janssen, Robin Romein, Willy A. M. van den Berg, Simon Lindhoud, Jan Willem Borst, Carlo P. M. van Mierlo   +5 more
wiley   +1 more source

Language models can identify enzymatic binding sites in protein sequences. [PDF]

Comput Struct Biotechnol J
Nana Teukam YG, Kwate Dassi L, Manica M, Probst D, Schwaller P, Laino T.   +5 more
europepmc   +1 more source

Improving protein function prediction by learning and integrating representations of protein sequences and function labels. [PDF]

Bioinform Adv
Boadu F, Cheng J.
europepmc   +1 more source

iDLB-Pred: identification of disordered lipid binding residues in protein sequences using convolutional neural network. [PDF]

Sci Rep
Malebary SJ, Alromema N.
europepmc   +1 more source

Co-evolution of alpha-helical transmembrane protein residues: large-scale variant profiling and complete mutational landscape of 2277 known PDB entries representing 504 unique human protein sequences. [PDF]

J Mol Evol
Karagöl T, Karagöl A, Zhang S.
europepmc   +1 more source

Protein complex structure modeling by cross-modal alignment between cryo-EM maps and protein sequences. [PDF]

Nat Commun
Chen S, Zhang S, Fang X, Lin L, Zhao H, Yang Y.   +5 more
europepmc   +1 more source

New avian protein sequences improve resolution of palaeoproteomic approaches to taxonomic identification & reveal widespread intraspecies variability

Codlin M, Yeomans L, Stiller J, Demarchi B.   +3 more
europepmc   +1 more source

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Aligning a DNA sequence with a protein sequence

Proceedings of the first annual international conference on Computational molecular biology - RECOMB '97, 1997
We develop several algorithms for the problem of aligning DNA sequence with a protein sequence. Our methods account for frameshift errors, but not for introns in the DNA sequence. Thus, they are particularly appropriate for comparing a cDNA sequence that suffers from sequencing errors with an amino acid sequence or a protein sequence database.
Zheng Zhang 0004, William R. Pearson, Webb Miller   +2 more
openaire   +2 more sources

Protein Sequence Modules

Journal of Biomolecular Structure and Dynamics, 2005
Conserved protein sequence segments are commonly believed to correspond to functional sites in the protein sequence. A novel approach is proposed to profile the changing degree of conservation along the protein sequence, by evaluating the occurrence frequencies of all short oligopeptides of the given sequence in a large proteome database.
E, Aharonovsky, E N, Trifonov
openaire   +2 more sources