1) EPAD: a context-specific distance-dependent statistical potential for protein study. See our paper http://www.cell.com/structure/abstract/S0969-2126(12)00145-1 for the technical details. The whole package is available at EPAD.tar.gz, which also includes some APIs (Application Programming Interface) so that you can easily integrate EPAD into your own projects. A simple user guide is available at EPAD_guide.html and the documentation for the EPAD APIs is available at EPAD_API_ref.pdf. To use EPAD, please also download the NR protein sequence database at NR.part1, NR.part2, and NR.part3.
2) DeepAlign: a program for pairwise protein structure alignment. Different from many other tools, DeepAlign aligns two protein structures using evolutionary information and beta strand orientation in addition to geometric similarity. Therefore, DeepAlign favors the alignment of evolutionarily-related residues and also aligns beta sheets more correctly than the others. The DeepAlign alignments are also much more consistent with manual alignments than the others. See our paper http://www.nature.com/srep/2013/130314/srep01448/full/srep01448.html for technical details. The whole package is available at DeepAlign_V1.00. Below see the ROC curves of DeepAlign, DALI, Matt and TMalign on (A) SABmark-sup and (B) SABmakr-twi.
4) RaptorX: a server and a standalone program for protein sequence-structure alignment and structure prediction by threading, available at http://raptorx.uchicago.edu. RaptorX excels at the alignment of hard targets, which have less than 30% sequence identity with solved structures in PDB. As shown in the below figure, blindly tested on the 50 hardest CASP9 template-based modeling targets, RaptorX outperforms all the CASP9 participating servers including those using consensus and refinement methods.
Figure 1. Performance of top 25 groups on the 50 hardest CASP9 TBM targets. X: group numbers. Y: the number of top 25 groups outperformed by a given group. The figure is taken from the CASP9 assessor’s presentation at http://predictioncenter.org/casp9/doc/presentations/CASP9_TBM.pdf.
5) RaptorX-SS8: a program for protein 3-class and 8-class secondary structure prediction. Please download the code raptorx-ss8.tgz and readme file. RaptorX-SS8 is also integrated into the RaptorX server.
7) CNF: a program for conditional neural fields, a variant of conditional random fields.
8) TreePack: a program for protein side-chain packing. It is available at TreePack.