List of Software#

1. ADR
2. CKSAAP-Palm
3. DeterminePPI
4. GNTInfer
5. GRNInfer
6. HMC
7. InferPPI
8. LOHCRP
9. MCDGPA
10. MDCInfer
11. MNAligner
12. ModularityOptimization
13. NRWRH
14. PPICPM
15. PPINA
16. PRNA
17. PSN
18. PTG
19. PTMPred
20. SABIC
21. Samo
22. SANA
23. StruComp

Genome Analysis (6)#

• HMC: Haplotype inference tool based on Markov Chain model
• PTG: Pasimonious tree-grow method for haplotype inference
• LOHCRP: LOH inference and segmentation tool based on conditional random field model
• CKSAAP-Palm: A tool for predicting palmitoylation sites from protein sequences
• PTMPred: A tool for predicting post-transcriptional modification sites from protein sequences
• PRNA: Prediction of protein-RNA binding sites by a random forest method with combined features

Molecular Networks (9)#

Gene Regulatory Networks Inference (2)#

• GNTInfer: Gene network reconstruction tool with compound targets by integrating multiple microarray datasets and prior information
• GRNInfer: Gene regulatory network inference tool from multiple microarray datasets

PPI Networks Inference (3)#

• MDCInfer: PPI prediction tool based on multiple domain cooperation analysis
• DeterminePPI: Inferring protein-protein interactions by parsimony principle
• InferPPI: Predicting protein interactions based on parsimony tendency of domain interactions

Network Module Analysis (2)#

• PPICPM: Identification of functional modules in PPI network by clique percolation clustering
• ModularityOptimization: Modularity optimization in community identification of complex networks

Network Alignment (2)#

• MNAligner: Alignment of molecular networks by quadratic programming
• PPINA: Alignment of protein interaction networks by integer quadratic programming

Structure Biology (5)#

• Samo: Protein structure alignment tool based on multiple objective optimization
• SANA: Protein Structure Alignment by Neighborhood Alignment
• SABIC: protein Structure Alignment Based on Internal Coordinates
• StruComp: Evaluating protein similarity from coarse structures
• PSN: Protein pocket similarity networks

Systems Biology (2)#

• ADR: Detecting and analyzing differentially activated pathways in brain regions of Alzheimer's disease patients
• MCDGPA: Modularized Candidate Disease Genes Prioritization Algorithm
• NRWRH: Network-based Random Walk with Restart on the Heterogeneous network