Results
author = "Elofsson, Arne"
Prediction of MHC class I binding peptides, using SVMHC
Description :
Abstract
Background
T-cells are key players in regulating a specific immune response. Activation of cytotoxic T-cells requires recognition of specific peptides bound to Major Histocompatibility Complex (MHC) class I molecules. MHC-peptide complexes are potential tools for diagnosis ...
Repository :
DOAJ-Articles
Language(s) :
English
The evolution of filamin - a protein domain repeat perspective
Author(s) :
Elofsson, Arne
Description :
Particularly in higher eukaryotes, some protein domains are found in tandem repeats, performing broad functions often related to cellular organization. For instance, the eukaryotic protein filamin interacts with many proteins and is crucial for the cytoskeleton. The functional properties of long rep...
Repository :
Publikationer från Stockholms universitet
Language(s) :
English
ProfNet, a method to derive profile-profile alignment scoring functions that improves the alignments of distantly related proteins
Description :
Abstract
Background
Profile-profile methods have been used for some years now to detect and align homologous proteins. The best such methods use information from the background distribution of amino acids and substitution tables either when constructing the profiles or in the scorin...
Repository :
DOAJ-Articles
Language(s) :
English
Prediction of MHC class I binding peptides, using SVMHC
Description :
Repository :
Europe PubMed Central
Language(s) :
English
Rapid membrane protein topology prediction
Description :
Summary: State-of-the-art methods for topology of α-helical membrane proteins are based on the use of time-consuming multiple sequence alignments obtained from PSI-BLAST or other sources. Here, we examine if it is possible to use the consensus of topology prediction methods that are based on single ...
Repository :
Europe PubMed Central
Language(s) :
English
KalignP: Improved multiple sequence alignments using position specific gap penalties in Kalign2
Description :
Summary: Kalign2 is one of the fastest and most accurate methods for multiple alignments. However, in contrast to other methods Kalign2 does not allow externally supplied position specific gap penalties. Here, we present a modification to Kalign2, KalignP, so that it accepts such penalties. Further,...
Repository :
Europe PubMed Central
Language(s) :
English
Ranking models of transmembrane β-barrel proteins using Z-coordinate predictions
Description :
Motivation: Transmembrane β-barrels exist in the outer membrane of gram-negative bacteria as well as in chloroplast and mitochondria. They are often involved in transport processes and are promising antimicrobial drug targets. Structures of only a few β-barrel protein families are known. Therefore, ...
Repository :
Europe PubMed Central
Language(s) :
English
ProfNet, a method to derive profile-profile alignment scoring functions that improves the alignments of distantly related proteins
Description :
Repository :
Europe PubMed Central
Language(s) :
English
Identification of correct regions in protein models using structural, alignment, and consensus information
Description :
In this study we present two methods to predict the local quality of a protein model: ProQres and ProQprof. ProQres is based on structural features that can be calculated from a model, while ProQprof uses alignment information and can only be used if the model is created from an alignment. In additi...
Repository :
Europe PubMed Central
Language(s) :
English
All are not equal: A benchmark of different homology modeling programs
Description :
Modeling a protein structure based on a homologous structure is a standard method in structural biology today. In this process an alignment of a target protein sequence onto the structure of a template(s) is used as input to a program that constructs a 3D model. It has been shown that the most impor...
Repository :
Europe PubMed Central
Language(s) :
English