bioinfoProject

Validation of Time Series Technique for Prediction of Conformational States of Amino Acids

a project for fulfillment of M.Sc (Master of Science) in Bioinformatics.

Concepts

• Time series
• Protein's secondary structure
• Ramachandran Plot
• Feynman Problem Solving Algorithm

Description

• entries in PDBSelect (proteins) downloaded from PDB & curated.
• amino acid (AA) residue sequence used as Time Series by assigning Potential (normalized probability of occurrence of single amino acid residue in allowed conformational regions of Ramachandran plot).
• done :
  • development of novel clustering methods by evaluating various time series models (AR, ARMA, ARIMA)
  • forecasting of conformational states of AA & AA residues.
  • prediction of missing residues in proteins from PDB

Peoples

• Sagar Nikam (Student) BIM-2010-20
• Dr. Sangeet Sawant (Guide) Bioinformatics Center, University of Pune, Pune
• Dr. Mohan Kale (Co-guide) Dept. of Statistics, University of Pune, Pune

Links

• Wiki
• Project Report
• Presentation
• Videos
  • Downloading PDB files in batch
  • Downloading PDB files from internet-funny
  • ARMA checking
  • Checking chain breaks of Protein Structure
  • Protein phi-psi angle validation using PDB goodies

Resources

• Programming

  • R
  • RStudio, Tinn-R
  • packages: bio3d, itsmr, forecast, tseries,timsac, wordcloud

• other softwares

  • ITSM 2000
  • Phylowidget

• Forums

  • R Nabble
  • BioStars
  • Cross Validated

• Research Paper

  • Prediction of conformational states of amino acids using a Ramachandran plot link

• Computing

  • last corner Windows(Vista) desktop, near window, in practical Lab No.1 at Bioinformatics Center, University of Pune, Pune
  • PC of ManojkumarBhosale & Laptop of Kiran Bankar, in University's Boys Hotel No.8, Room No. 512 & 128.

License

Apache 2.0 & MIT

Like

Built With

• r