Results 71 to 80 of about 542,743 (309)

Modulation of Homer1 EVH1 domain internal dynamics by putative autism‐associated mutations

FEBS Letters, EarlyView.
The putative autism‐associated M65I and S97L variants of the EVH1 domain of the postsynaptic scaffold protein Homer1 do not exhibit substantial changes in their overall structure or partner binding. Both of them, but especially the M65I variant, show altered internal dynamics relative to the wild‐type domain on the μs‐ms timescale, indicated by the ...
Fanni Farkas, Brigitta Maruzs, Zsófia E. Kálmán, Tomas Klumpler, Gyula Batta, Bálint Péterfia, Zoltán Gáspári   +6 more
wiley   +1 more source

The Pfam protein families database [PDF]

Nucleic Acids Research, 2009
Pfam is a widely used database of protein families and domains. This article describes a set of major updates that we have implemented in the latest release (version 24.0). The most important change is that we now use HMMER3, the latest version of the popular profile hidden Markov model package.
Robert D. Finn, Jaina Mistry, John G. Tate, Penny C. Coggill, Andreas Heger, Joanne E. Pollington, O. Luke Gavin, Prasad Gunasekaran, Goran Ceric, Kristoffer Forslund, Liisa Holm, Erik L. L. Sonnhammer, Sean R. Eddy, Alex Bateman   +13 more
openaire   +4 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   +1 more source

MisPred: a resource for identification of erroneous protein sequences in public databases

, 2013
Correct prediction of the structure of protein-coding genes of higher eukaryotes is still a difficult task; therefore, public databases are heavily contaminated with mispredicted sequences.
Nagy, Alinda, Patthy, László
core   +1 more source

Subtype‐specific enhancer RNAs define transcriptional regulators and prognosis in breast cancers

Molecular Oncology, EarlyView.
This study employed machine learning methodologies to perform the subtype‐specific classification of RNA‐seq data sets, which are mapped on enhancers from TCGA‐derived breast cancer patients. Their integration with gene expression (referred to as ProxCReAM eRNAs) and chromatin accessibility profiles has the potential to identify lineage‐specific and ...
Aamena Y. Patel, Peyman Zarrineh, Nathnael T. Tuffa, Jigar H. Sheth, Sumitra Mohan, Mudassar Iqbal, Sankari Nagarajan   +6 more
wiley   +1 more source

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

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   +1 more source

COMP–PMEPA1 axis promotes epithelial‐to‐mesenchymal transition in breast cancer cells

Molecular Oncology, EarlyView.
This study reveals that cartilage oligomeric matrix protein (COMP) promotes epithelial‐to‐mesenchymal transition (EMT) in breast cancer. We identify PMEPA1 (protein TMEPAI) as a novel COMP‐binding partner that mediates EMT via binding to the TSP domains of COMP, establishing the COMP–PMEPA1 axis as a key EMT driver in breast cancer.
Konstantinos S. Papadakos, Gilar Gorji‐bahri, Lejla Gradjan, Julia Zajac, Kacper Gil, Yvonne Thokozile Nduku, Anna M. Blom   +6 more
wiley   +1 more source

Algorithmic complexity of protein identification: combinatorics of weighted strings

, 2004
Cieliebak M, Erlebach T, Lipták Z, Stoye J, Welzl E. Algorithmic complexity of protein identification: combinatorics of weighted strings. Discrete Applied Mathematics.
Lipták, Zsuzsanna, Welzl, Emo, Jens Stoye, Stoye, Jens, Erlebach, Thomas, Stoye, Jens ; https://orcid.org/, Mark Cieliebak, Thomas Erlebach, Emo Welzl, Cieliebak, Mark   +9 more
core   +1 more source

Pre‐analytical optimization of cell‐free DNA and extracellular vesicle‐derived DNA for mutation detection in liquid biopsies

Molecular Oncology, EarlyView.
Pre‐analytical handling critically determines liquid biopsy performance. This study defines practical best‐practice conditions for cell‐free DNA (cfDNA) and extracellular vesicle–derived DNA (evDNA), showing how processing time, storage conditions, tube type, and plasma input volume affect DNA integrity and mutation detection.
Jonas Dohmen, Lucrezia De Santis, Bret M. Stephens, Vincent Bernard, Jörg C. Kalff, Lara Braun, Phillipp Leyendecker, Johannes Röttgen, Daniel Weissinger, Anirban Maitra, Paola A. Guerrero, Alexander Semaan   +11 more
wiley   +1 more source

Compressive genomics for protein databases [PDF]

Bioinformatics, 2013
Abstract Motivation: The exponential growth of protein sequence databases has increasingly made the fundamental question of searching for homologs a computational bottleneck. The amount of unique data, however, is not growing nearly as fast; we can exploit this fact to greatly accelerate homology search.
Noah M. Daniels, Andrew Gallant, Jian Peng 0001, Lenore J. Cowen, Michael Baym, Bonnie Berger   +5 more
openaire   +5 more sources