ClusPro-DC: Dimer Classification by the Cluspro Server for Protein–Protein Docking
نویسندگان
چکیده
منابع مشابه
New additions to the ClusPro server motivated by CAPRI.
The heavily used protein-protein docking server ClusPro performs three computational steps as follows: (1) rigid body docking, (2) RMSD based clustering of the 1000 lowest energy structures, and (3) the removal of steric clashes by energy minimization. In response to challenges encountered in recent CAPRI targets, we added three new options to ClusPro. These are (1) accounting for small angle X...
متن کاملAccounting for observed small angle X-ray scattering profile in the protein-protein docking server cluspro
The protein-protein docking server ClusPro is used by thousands of laboratories, and models built by the server have been reported in over 300 publications. Although the structures generated by the docking include near-native ones for many proteins, selecting the best model is difficult due to the uncertainty in scoring. Small angle X-ray scattering (SAXS) is an experimental technique for obtai...
متن کاملClusPro: a fully automated algorithm for protein-protein docking
ClusPro (http://nrc.bu.edu/cluster) represents the first fully automated, web-based program for the computational docking of protein structures. Users may upload the coordinate files of two protein structures through ClusPro's web interface, or enter the PDB codes of the respective structures, which ClusPro will then download from the PDB server (http://www.rcsb.org/pdb/). The docking algorithm...
متن کاملPerformance of the first protein docking server ClusPro in CAPRI rounds 3-5.
To evaluate the current status of the protein-protein docking field, the CAPRI experiment came to life. Researchers are given the receptor and ligand 3-dimensional (3D) coordinates before the cocrystallized complex is published. Human predictions of the complex structure are supposed to be submitted within 3 weeks, whereas the server ClusPro has only 24 h and does not make use of any biochemica...
متن کاملClusPro: an automated docking and discrimination method for the prediction of protein complexes
MOTIVATION Predicting protein interactions is one of the most challenging problems in functional genomics. Given two proteins known to interact, current docking methods evaluate billions of docked conformations by simple scoring functions, and in addition to near-native structures yield many false positives, i.e. structures with good surface complementarity but far from the native. RESULTS We...
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ژورنال
عنوان ژورنال: Journal of Molecular Biology
سال: 2017
ISSN: 0022-2836
DOI: 10.1016/j.jmb.2016.10.019