List of Software#

1. CEA
2. CKSAAP-Palm
3. CNetA
4. CNetQ
5. Corbi
6. DGPsubNet
7. DeterminePPI
8. EllipsoidFN
9. GNTInfer
10. GRNInfer
11. HMC
12. InferPPI
13. LOHCRP
14. MCDGPA
15. MDCInfer
16. MILP_k
17. MNAligner
18. MarkRank
19. Mimic
20. NCCAUC
21. NRWRH
22. NetGen
23. NetPredATC
24. PECA
25. PRNA
26. PSN
27. PTG
28. PTMPred
29. PreDR
30. PrePPItar
31. QMC
32. SABIC
33. SANA
34. Samo
35. VPECA

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 (3)#

• 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