Results 11 to 20 of about 5,258,715 (348)

Coevolutionary Analysis of Protein Subfamilies by Sequence Reweighting [PDF]

Entropy, 2019
Extracting structural information from sequence co-variation has become a common computational biology practice in the recent years, mainly due to the availability of large sequence alignments of protein families.
Duccio Malinverni, Alessandro Barducci
doaj   +5 more sources

Integrative visual analysis of protein sequence mutations [PDF]

BMC Proceedings, 2014
BACKGROUND: An important aspect of studying the relationship between protein sequence, structure and function is the molecular characterization of the effect of protein mutations.
Albrecht, Mario, Domingues, Francisco, Doncheva, Nadezhda, Klein, Karsten, Morris, John, Wybrow, Michael   +5 more
core   +9 more sources

Sequence composition and environment effects on residue fluctuations in protein structures [PDF]

, 2009
The spectrum and scale of fluctuations in protein structures affect the range of cell phenomena, including stability of protein structures or their fragments, allosteric transitions and energy transfer. The study presents a statistical-thermodynamic analysis of relationship between the sequence composition and the distribution of residue fluctuations ...
Anatoly M. Ruvinsky, Hubbard S. J., Ilya A. Vakser   +2 more
arxiv   +6 more sources

Analysis of protein chameleon sequence characteristics [PDF]

Bioinformation, 2009
Conversion of local structural state of a protein from an alpha-helix to a beta-strand is usually associated with a major change in the tertiary structure. Similar changes were observed during the self assembly of amyloidogenic proteins to form fibrils, which are implicated in severe diseases conditions, e.g., Alzheimer disease. Studies have emphasized
Ghozlane, Amine, Joseph, Agnel, Bornot, Aurélie, de Brevern, Alexandre   +3 more
openaire   +4 more sources

ProteinBERT: a universal deep-learning model of protein sequence and function

bioRxiv, 2021
Self-supervised deep language modeling has shown unprecedented success across natural language tasks, and has recently been repurposed to biological sequences. However, existing models and pretraining methods are designed and optimized for text analysis.
N. Brandes, Dan Ofer, Yam Peleg, Nadav Rappoport, M. Linial   +4 more
semanticscholar   +1 more source

A clustered set of three Sp-family genes is ancestral in the Metazoa: evidence from sequence analysis, protein domain structure, developmental expression patterns and chromosomal location

BMC Evolutionary Biology, 2010
BackgroundThe Sp-family of transcription factors are evolutionarily conserved zinc finger proteins present in many animal species. The orthology of the Sp genes in different animals is unclear and their evolutionary history is therefore controversially ...
Nina D. Schaeper, Nikola-Michael Prpic, E. Wimmer   +2 more
semanticscholar   +1 more source

Sequence of a putative human housekeeping gene (HK33) localized on chromosome 1 [PDF]

, 1994
A gene (X33) localized on human chromosome 1 has been detected by crossreaction of its fusion protein with a monospecific antiserum directed against human vitamin-D-binding protein (hDBP; group-specific component).
Chirgwin, Church, Estaller, Feinberg, Hoffmann, Johnson, Kozak, Manley, McLeod, Meissner, Proudfood, Proudfood, Prunier, Sambrook, Sanger, Sheets, Smith, Tabor, Yanisch-Perron   +18 more
core   +1 more source

Designing hardware for protein sequence analysis [PDF]

Bioinformatics, 2003
Abstract We present the architecture of PROSIDIS, a special purpose co-processor designed to search for the occurrence of substrings similar to a given ‘template string’ within a proteome. Actual tests show speed up figures ranging from 5 to 50 with respect to conventional general-purpose processors.
Marongiu, Alessandro, Palazzari, Paolo, Rosato, Vittorio   +2 more
openaire   +4 more sources

Density Peak clustering of protein sequences associated to a Pfam clan reveals clear similarities and interesting differences with respect to manual family annotation

BMC Bioinformatics, 2021
Background The identification of protein families is of outstanding practical importance for in silico protein annotation and is at the basis of several bioinformatic resources.
Elena Tea Russo, Alessandro Laio, Marco Punta   +2 more
doaj   +1 more source

MGnify: the microbiome sequence data analysis resource in 2023

Nucleic Acids Res., 2022
The MGnify platform (https://www.ebi.ac.uk/metagenomics) facilitates the assembly, analysis and archiving of microbiome-derived nucleic acid sequences.
Lorna J. Richardson, B. Allen, Germana Baldi, Martin Beracochea, Maxwell L. Bileschi, Tony Burdett, Josephine Burgin, Juan Caballero, G. Cochrane, Lucy J. Colwell, Tom Curtis, Alejandra Escobar-Zepeda, Tatiana A. Gurbich, Varsha Kale, A. Korobeynikov, Shriya Raj, Alexander B. Rogers, Ekaterina A. Sakharova, Santiago Sanchez, D. Wilkinson, R. Finn   +20 more
semanticscholar   +1 more source