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 web-servers for the prediction of binding sites/residues in DNA-binding proteins-
S.No Web-servers Link Comment
1. DNA Binding Protein prediction http://www.enzim.hu/~szia/dnabind.html This server predicts whether a protein is DNA-binding from its structure and/or sequence.
2. DNAbinder http://www.imtech.res.in/raghava/dnabinder/help.html A web server for predicting DNA-binding proteins
3. DBS-PRED http://www.netasa.org/dbs-pred/ This program predicts the DNA-binding in a protein from their sequence information.
4. DP-Bind http://lcg.rit.albany.edu/dp-bind/ This web-server takes a user-supplied sequence of a DNA-binding protein and predicts residue positions involved in interactions with DNA.
5. PreDs http://pre-s.protein.osaka-u.ac.jp/preds/ PreDs is a server making the prediction of dsDNA-binding site on protein surfaces, according to our prediction method developed by focusing our attention on the shape of the molecular surface and the electrostatic potential on the surface.
6. DISPLAR http://pipe.scs.fsu.edu/displar.html DISPLAR is a neural network method. Given the structure of a protein known to bind DNA, the method predicts residues that contact DNA.
7. ZIFIBI http://bioinfo.hanyang.ac.kr/ZIFIBI/frameset.php Prediction of DNA binding sites for zinc finger proteins
8. DISIS http://cubic.bioc.columbia.edu/services/disis/ Prediction of DNA-binding residues from sequence
9. ProteDNA http://serv.csbb.ntu.edu.tw/ProteDNA/ Predictor of sequence-specific DNA-binding residues in transcription factors