Results 1 to 10 of about 537,357 (107)

TOPAZ: asymmetric suffix array neighbourhood search for massive protein databases [PDF]

BMC Bioinformatics, 2018
Background Protein homology search is an important, yet time-consuming, step in everything from protein annotation to metagenomics. Its application, however, has become increasingly challenging, due to the exponential growth of protein databases.
Alan Medlar, Liisa Holm
doaj   +2 more sources

Large protein databases reveal structural complementarity and functional locality [PDF]

Nature Communications
Recent breakthroughs in protein structure prediction have led to a surge in high-quality 3D models, highlighting the need for efficient computational solutions. In our work, we examine the structural clusters from the AlphaFold Protein Structure Database
Paweł Szczerbiak, Lukasz M. Szydlowski, Witold Wydmański, P. Douglas Renfrew, Julia Koehler Leman, Tomasz Kosciolek   +5 more
doaj   +2 more sources

mPies: a novel metaproteomics tool for the creation of relevant protein databases and automatized protein annotation [PDF]

Biology Direct, 2019
Metaproteomics allows to decipher the structure and functionality of microbial communities. Despite its rapid development, crucial steps such as the creation of standardized protein search databases and reliable protein annotation remain challenging.
Johannes Werner, Augustin Géron, Jules Kerssemakers, Sabine Matallana-Surget   +3 more
doaj   +2 more sources

An analysis of proteogenomics and how and when transcriptome-informed reduction of protein databases can enhance eukaryotic proteomics [PDF]

Genome Biology, 2022
Background Proteogenomics aims to identify variant or unknown proteins in bottom-up proteomics, by searching transcriptome- or genome-derived custom protein databases.
Laura Fancello, Thomas Burger
doaj   +2 more sources

Databases of ligand-binding pockets and protein-ligand interactions

Computational and Structural Biotechnology Journal
Many research groups and institutions have created a variety of databases curating experimental and predicted data related to protein-ligand binding. The landscape of available databases is dynamic, with new databases emerging and established databases ...
Kristy A. Carpenter, Russ B. Altman
doaj   +3 more sources

Protein Databases Related to Liquid-Liquid Phase Separation. [PDF]

Int J Mol Sci, 2020
Li Q, Wang X, Dou Z, Yang W, Huang B, Lou J, Zhang Z.   +6 more
europepmc   +2 more sources

Deciphering protein-protein interactions. Part I. Experimental techniques and databases. [PDF]

PLoS Computational Biology, 2007
Benjamin A Shoemaker, Anna R Panchenko
doaj   +3 more sources

Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases. [PDF]

Nucleic Acids Res, 2019
Tørresen OK, Star B, Mier P, Andrade-Navarro MA, Bateman A, Jarnot P, Gruca A, Grynberg M, Kajava AV, Promponas VJ, Anisimova M, Jakobsen KS, Linke D.   +12 more
europepmc   +2 more sources

Optimizing metaproteomics database construction: lessons from a study of the vaginal microbiome

mSystems, 2023
Metaproteomics, a method for untargeted, high-throughput identification of proteins in complex samples, provides functional information about microbial communities and can tie functions to specific taxa.
Elliot M. Lee, Sujatha Srinivasan, Samuel O. Purvine, Tina L. Fiedler, Owen P. Leiser, Sean C. Proll, Samuel S. Minot, Brooke L. Deatherage Kaiser, David N. Fredricks   +8 more
doaj   +1 more source

PROTEIN IDENTIFICATION USING SEQUENCE DATABASES

Scientific Journal of Astana IT University, 2020
The bottom-up proteomics approach (also known as the shotgun approach), based on the digestion of proteins in peptides and their sequencing using tandem mass spectrometry (MS/MS), has become widespread.
Ye. Golenko, A. Ismailova, Ye. Rais
doaj   +3 more sources