CRIP: Computational Resources for predicting protein-macromolecular interactions

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Biomolecular Interactions
 Brief Introduction
 Diseases prediction
 Personal Drugs
 Vaccines
 Biomarkers

Protein-Protein
 Databases
 Prediction Servers
 Slides/Links
 Datasets/References

Protein-DNA
 Databases
 Prediction Servers
 Slides/Links
 Datasets/References

Protein-RNA
 Databases
 Prediction Servers
 Slides/Links
 Datasets/References

Protein-Metabolite
 Databases
 Prediction Servers
 Slides/Links
 Datasets/References

Protein-Lipid
 Databases
 Prediction Servers
 Slides/Links
 Datasets/References

Protein-Carbohydrate
 Databases
 Prediction Servers
 Slides/Links
 Datasets/References

 Protein molecules also play critical role in regulation and control of various cellular processes. Transcription factors are DNA binding proteins (mostly) which regulate expression of genes inside the cell. Following are the databases of protein-DNA interactions-
S.No Database Link Comment
1. DnaProt http://kronos.biol.uoa.gr/~mariak/DB-dna/overview.html DnaProt, this resource, has been designed as an attempt to classify protein sequences from completely sequenced genomes and more specifically those that characteristically recognize specific DNA chains.
2. JASPAR http://mordor.cgb.ki.se/cgi-bin/jaspar2005/jaspar_db.pl The high-quality transcription factor binding profile database
3. Protein-DNA Recognition http://gibk26.bse.kyutech.ac.jp/jouhou/3dinsight/recognition.html A comprehensive collection of protein-nucleic acid information/tools
4. ProNIT http://gibk26.bse.kyutech.ac.jp/jouhou/pronit/pronit.html ProNIT database provides experimentally determined thermodynamic interaction data between proteins and nucleic acids.
5. DPInteract http://arep.med.harvard.edu/dpinteract/ For 55 E. coli DNA-binding proteins with known binding sites, we have compiled DNA-binding site matrices and performed searches over the complete E. coli K12 genome. The search matrices and results are located at: http://arep.med.harvard.edu/ecoli_matrices
6. DB-PABP http://pabp.bcf.ku.edu/DB_PABP/index.jsp The interactions between polyanions (PAs) and polyanion binding proteins (PABPs) have been found to play significant roles in many essential biological processes including intracellular organization, transport and protein folding.
7. TRANSFAC http://www.biobase-international.com/pages/index.php?id=transfac TRANSFAC is a database about eukaryotic transcription regulating DNA sequence elements and the transcription factors binding to and acting through them.
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