Results 61 to 70 of about 25,474 (119)

Protein Inference and Protein Quantification: Two Sides of the Same Coin [PDF]

arXiv, 2012
Motivation: In mass spectrometry-based shotgun proteomics, protein quantification and protein identification are two major computational problems. To quantify the protein abundance, a list of proteins must be firstly inferred from the sample. Then the relative or absolute protein abundance is estimated with quantification methods, such as spectral ...
arxiv  

Knowledge-based energy functions for computational studies of proteins [PDF]

, 2006
This chapter discusses theoretical framework and methods for developing knowledge-based potential functions essential for protein structure prediction, protein-protein interaction, and protein sequence design. We discuss in some details about the Miyazawa-Jernigan contact statistical potential, distance-dependent statistical potentials, as well as ...
arxiv   +1 more source

Is the intrinsic disorder of proteins the cause of the scale-free architecture of protein-protein interaction networks? [PDF]

arXiv, 2006
In protein-protein interaction networks certain topological properties appear to be recurrent: networks maps are considered scale-free. It is possible that this topology is reflected in the protein structure. In this paper we investigate the role of protein disorder in the network topology.
arxiv  

Refining the Protein-Protein Interactome using Gene Expression Data [PDF]

arXiv, 2010
Proteins interact with other proteins within biological pathways, forming connected subgraphs in the protein-protein interactome (PPI). Proteins are often involved in multiple biological pathways which complicates interpretation of interactions between proteins.
arxiv  

Protein token: a dynamic unit in protein interactions [PDF]

arXiv, 2018
In this study, we introduced a new unit, named "protein token", as a dynamic protein structural unit for protein-protein interactions. Unlike the conventional structural units, protein token is not based on the sequential or spatial arrangement of residues, but comprises remote residues involved in cooperative conformational changes during protein ...
arxiv  

Global protein function prediction in protein-protein interaction networks [PDF]

Nature Biotech. 21, 697-700 (2003), 2003
The determination of protein functions is one of the most challenging problems of the post-genomic era. The sequencing of entire genomes and the possibility to access gene's co-expression patterns has moved the attention from the study of single proteins or small complexes to that of the entire proteome. In this context, the search for reliable methods
arxiv  

Develop machine learning based predictive models for engineering protein solubility [PDF]

arXiv, 2018
Protein activity is a significant characteristic for recombinant proteins which can be used as biocatalysts. High activity of proteins reduces the cost of biocatalysts. A model that can predict protein activity from amino acid sequence is highly desired, as it aids experimental improvement of proteins.
arxiv  

Editorial: Rho family GTPases and their effectors in neuronal survival and neurodegeneration

Frontiers in Cellular Neuroscience, 2023
Daniel A. Linseman, Qun Lu
doaj   +1 more source

Accurate and efficient protein embedding using multi-teacher distillation learning [PDF]

arXiv
Motivation: Protein embedding, which represents proteins as numerical vectors, is a crucial step in various learning-based protein annotation/classification problems, including gene ontology prediction, protein-protein interaction prediction, and protein structure prediction.
arxiv  

PI(3,4,5)P3-mediated Cdc42 activation regulates macrophage podosome assembly. [PDF]

Cell Mol Life Sci
Qi Y, Yu CH.
europepmc   +1 more source