Limitations of Ab Initio Predictions of Peptide Binding to MHC Class II Molecules
نویسندگان
چکیده
منابع مشابه
Limitations of Ab Initio Predictions of Peptide Binding to MHC Class II Molecules
Successful predictions of peptide MHC binding typically require a large set of binding data for the specific MHC molecule that is examined. Structure based prediction methods promise to circumvent this requirement by evaluating the physical contacts a peptide can make with an MHC molecule based on the highly conserved 3D structure of peptide:MHC complexes. While several such methods have been d...
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Since determining the crystallographic structure of all peptide-MHC complexes is infeasible, an accurate prediction of the conformation is a critical computational problem. These models can be useful for determining binding energetics, predicting the structures of specific ternary complexes with T-cell receptors, and designing new molecules interacting with these complexes. The main difficultie...
متن کاملClass II-associated invariant chain peptide-independent binding of invariant chain to class II MHC molecules.
The class II-associated invariant chain peptide (CLIP) region of invariant chain (Ii) is believed to play a critical role in the assembly and transport of MHC class II alphabetaIi complexes through its interaction with the class II peptide-binding site. The role of the CLIP sequence was investigated by using mutant Ii molecules with altered affinity for the DR1 peptide-binding site. Both high- ...
متن کاملAutomated benchmarking of peptide-MHC class I binding predictions
MOTIVATION Numerous in silico methods predicting peptide binding to major histocompatibility complex (MHC) class I molecules have been developed over the last decades. However, the multitude of available prediction tools makes it non-trivial for the end-user to select which tool to use for a given task. To provide a solid basis on which to compare different prediction tools, we here describe a ...
متن کاملPeptide length-based prediction of peptide-MHC class II binding
MOTIVATION Algorithms for predicting peptide-MHC class II binding are typically similar, if not identical, to methods for predicting peptide-MHC class I binding despite known differences between the two scenarios. We investigate whether representing one of these differences, the greater range of peptide lengths binding MHC class II, improves the performance of these algorithms. RESULTS A non-...
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ژورنال
عنوان ژورنال: PLoS ONE
سال: 2010
ISSN: 1932-6203
DOI: 10.1371/journal.pone.0009272