Results 1 to 10 of about 1,646,583 (118)

findMySequence: a neural-network-based approach for identification of unknown proteins in X-ray crystallography and cryo-EM

IUCrJ, 2022
Although experimental protein-structure determination usually targets known proteins, chains of unknown sequence are often encountered. They can be purified from natural sources, appear as an unexpected fragment of a well characterized protein or appear ...
Grzegorz Chojnowski, Adam J. Simpkin, Diego A. Leonardo, Wolfram Seifert-Davila, Dan E. Vivas-Ruiz, Ronan M. Keegan, Daniel J. Rigden   +6 more
doaj   +1 more source

Using AnnoTree to Get More Assignments, Faster, in DIAMOND+MEGAN Microbiome Analysis

mSystems, 2022
In microbiome analysis, one main approach is to align metagenomic sequencing reads against a protein reference database, such as NCBI-nr, and then to perform taxonomic and functional binning based on the alignments. This approach is embodied, for example,
Anupam Gautam, Hendrik Felderhoff, Caner Bağci, Daniel H. Huson   +3 more
doaj   +1 more source

Identification and Expression Analysis of Calcium-Dependent Protein Kinases Gene Family in Potato Under Drought Stress

Frontiers in Genetics, 2022
Calcium-dependent protein kinases (CDPKs) are a class of serine/threonine protein kinases encoded by several gene families that play key roles in stress response and plant growth and development.
Simon Dontoro Dekomah, Simon Dontoro Dekomah, Yihao Wang, Yihao Wang, Tianyuan Qin, Tianyuan Qin, Derong Xu, Derong Xu, Chao Sun, Chao Sun, Panfeng Yao, Yuhui Liu, Zhenzhen Bi, Zhenzhen Bi, Jiangping Bai, Jiangping Bai   +15 more
doaj   +1 more source

New alignment method for remote protein sequences by the direct use of pairwise sequence correlations and substitutions

Frontiers in Bioinformatics, 2023
Understanding protein sequences and how they relate to the functions of proteins is extremely important. One of the most basic operations in bioinformatics is sequence alignment and usually the first things learned from these are which positions are the ...
Kejue Jia, Mesih Kilinc, Mesih Kilinc, Robert L. Jernigan, Robert L. Jernigan   +4 more
doaj   +1 more source

Entropy Analysis of Protein Sequences Reveals a Hierarchical Organization

Entropy, 2021
Background: Analyzing the local sequence content in proteins, earlier we found that amino acid residue frequencies differ on various distances between amino acid positions in the sequence, assuming the existence of structural units.
Anastasia A. Anashkina, Irina Yu. Petrushanko, Rustam H. Ziganshin, Yuriy L. Orlov, Alexei N. Nekrasov   +4 more
doaj   +1 more source

AlphaFold2 Update and Perspectives

BioMedInformatics, 2023
Access to the three-dimensional (3D) structural information of macromolecules is of major interest in both fundamental and applied research. Obtaining this experimental data can be complex, time consuming, and costly.
Sébastien Tourlet, Ragousandirane Radjasandirane, Julien Diharce, Alexandre G. de Brevern   +3 more
doaj   +1 more source

Generative power of a protein language model trained on multiple sequence alignments

eLife, 2023
Computational models starting from large ensembles of evolutionarily related protein sequences capture a representation of protein families and learn constraints associated to protein structure and function.
Damiano Sgarbossa, Umberto Lupo, Anne-Florence Bitbol   +2 more
doaj   +1 more source

Protein-protein interaction hotspots carved into sequences. [PDF]

PLoS Computational Biology, 2007
Protein-protein interactions, a key to almost any biological process, are mediated by molecular mechanisms that are not entirely clear. The study of these mechanisms often focuses on all residues at protein-protein interfaces.
Yanay Ofran, Burkhard Rost
doaj   +1 more source

Learning meaningful representations of protein sequences

Nature Communications, 2022
"Representation learning plays an increasing role in protein sequence analysis. This paper seeks to clarify how to ensure that such representations are meaningful, proposing best practices both for the choice of methods and the subsequence ...
Nicki Skafte Detlefsen, Søren Hauberg, Wouter Boomsma   +2 more
doaj   +1 more source

A novel sequence-based prediction method for ATP-binding sites using fusion of SMOTE algorithm and random forests classifier

Biotechnology & Biotechnological Equipment, 2020
Correctly identifying the protein-ATP binding site is valuable for both protein function annotation and new drug discovery. However, the number of non-ATP-binding residues is much more than the number of ATP-binding residues, which makes the prediction a
Jiazhi Song, Guixia Liu, Chuyi Song, Jingqing Jiang   +3 more
doaj   +1 more source