Softwares

CRISPR related tools

1. ProTiler: An integrative pipeline for the de novo identification of essential protein domains from CRISPR/Cas9 tiling-sgRNA screens.

2. GuidePro: A two-layer ensemble predictor that enables the integration of multiple factors for the prioritization of sgRNAs in protein knockouts.

3. A GuidePro-based web application for prioritizing sgRNAs that target protein-coding genes in human, monkey and mouse genomes is also available. 

4. MoPAC: A shiny-driven application for the analysis and visualization of CRISPR/Cas9 screens on multiple samples.

5. MaGeCK: A model based analysis tool for identifying important genes from CRISPR/Cas9 screens.

6. SSC: An online tool for predicting sgRNA activity in CRISPR applications.

7. CRISPR-DO: A web application for the genome-wide design and optimization of sgRNA sequences in five genomes (human, mouse, fly, worm and zebrafish)

3D protein structure analysis

1. mFASD: structure-based method for predicting certein type of metal binding sites including ZN, FE CU, MN, CA, MG, etc. for any given protein region with known 3D structure.

2. AFTME: an alignment-free method for the automatic mapping of 3D motifs to different FGs of a specific ligand through two-dimensional clustering and built 481 FG-binding motifs that are highly conserved across different ligand-binding pockets