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| ZincBinder: Svm based approach for predicting zinc metal binding sites in protein sequences |
| Developed By: Abhishikha Srivastava, Manish Kumar |
| Department of Biophysics, University of Delhi South Campus New Delhi, India |
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| About ZincBinder |
| ============= |
| Zinc metal ions play structural, signaling and regulatory roles in many biological systems that includes stablization of membranes and various transcription factors and also the catalytic activity of various enzymes. We have developed a method "Zincbinder" for predicting zinc metal binding site from their amino acid sequence. We have developed SVM models using PSSM and achieved maximum accuracy 86.2% respectively. Its webversion is available from http://proteininformatics.org/mkumar/zincbinder |
| Availability and requirement |
| ====================== |
ZincBinder is written in PERL language, in order to run Zincbinder one need to have or install PERL (http://www.perl.com/). It is a SVM based program where models have been developed using SVM_light.Thus user should have or install svm_classify of SVM_light from http://www.cs.cornell.edu/People/tj/svm_light/.
Operating system(s): Plateform Independent Programming language :perl Other requirements: gcc++ compiler License: GNU GPL Any restrictions to use by non-academics: none |
| Downloand and Installation |
| ========================== |
1. Download znbinder_standalone.tar.gz 2. Unzip using command: gunzip znbinder_standalone.tar.gz 3. Extract files: tar -xvzf znbinder_standalone.tar 4. Change directory: cd standlone 5. Run program : perl znbinder.pl |
| How to Use |
| ========== |
1. Run using "znbinder.pl" or "./znbinder.pl" or "perl znbinder.pl" 2. Usage: znbinder.pl -i [input_file] -t [threshold] |
Options: -i Input_file containing sequence(s) in the FASTA format. -t SVM threshold (from -1.00 to 1.00; default 0.1) |
| Files and Directory |
| ================== |
README description file helps to understand and use all the related program in zincbinder directory having SVM models with main program zincbinder.pl . |
| Example Usage |
| perl zincbinder.pl -i seq.fasta -t 0.0 |
ZincBinder is maintained by Dr. Manish Kumar's Lab at Department of Biophysics, University of Delhi South Campus. We acknowledge your comments or contribution to this resource. Please send your sugestions to Email: manish at south dot du dot ac dot in