RaptorX / RaptorX-SS8
RaptorX is a protein structure prediction server developed by Xu group, excelling at predicting 3D structures for protein sequences without close homologs in the Protein Data Bank (PDB). Given an input sequence, RaptorX predicts its secondary and tertiary structures as well as solvent accessibility and disordered regions. RaptorX also assigns the following confidence scores to indicate the quality of a predicted 3D model: P-value for the relative global quality, GDT (global distance test) and uGDT (un-normalized GDT) for the absolute global quality, and RMSD for the absolute local quality of each residue in the model. RaptorX-Binding is a web server that predicts the binding sites of a protein sequence, based upon the predicted 3D model by RaptorX.
RaptorX-SS8 is a software package that predicts both 3-class and 8-class protein secondary structure using a probabilistic graphical model Conditional Neural Fields (CNFs).
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Morten Källberg, Haipeng Wang, Sheng Wang, Jian Peng, Zhiyong Wang, Hui Lu & Jinbo Xu.
Template-based protein structure modeling using the RaptorX web server.
Nature Protocols 7, 1511–1522, 2012.
Proteomics. 2011 Oct;11(19):3786-92. doi: 10.1002/pmic.201100196.
Protein 8-class secondary structure prediction using conditional neural fields.
Wang Z, Zhao F, Peng J, Xu J.