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Protein loop modeling by using fragment assembly and analytical loop closure
Protein loop modeling by using fragment assembly and analytical loop closure
- Source :
- Proteins. 78(16)
- Publication Year :
- 2010
-
Abstract
- Protein loops are often involved in important biological functions such as molecular recognition, signal transduction, or enzymatic action. The three dimensional structures of loops can provide essential information for understanding molecular mechanisms behind protein functions. In this article, we develop a novel method for protein loop modeling, where the loop conformations are generated by fragment assembly and analytical loop closure. The fragment assembly method reduces the conformational space drastically, and the analytical loop closure method finds the geometrically consistent loop conformations efficiently. We also derive an analytic formula for the gradient of any analytical function of dihedral angles in the space of closed loops. The gradient can be used to optimize various restraints derived from experiments or databases, for example restraints for preferential interactions between specific residues or for preferred backbone angles. We demonstrate that the current loop modeling method outperforms previous methods that employ residue-based torsion angle maps or different loop closure strategies when tested on two sets of loop targets of lengths ranging from 4 to 12.
- Subjects :
- Physics
Models, Molecular
Quantitative Biology::Biomolecules
Computational Biology
Proteins
Protein structure prediction
Dihedral angle
Topology
Biochemistry
Protein Structure, Secondary
Article
Loop (topology)
Protein structure
Fragment (logic)
Structural Biology
Computational chemistry
Thermodynamics
Loop modeling
Molecular Biology
Current loop
Algorithms
Analytic function
Subjects
Details
- ISSN :
- 10970134
- Volume :
- 78
- Issue :
- 16
- Database :
- OpenAIRE
- Journal :
- Proteins
- Accession number :
- edsair.doi.dedup.....d918498c8c754d631522fc4a4a1a3753