Protein structure prediction: challenging targets for CASP10

Abstract

Functional characterization of proteins being one of the major issues in molecular biology is still unsolved due to several resource and technical limitations of experimental structure determination methods. A suitable methodology for accurate prediction of protein confirmations simply from sequence is therefore emerging as the primary modeling goal of researchers today. Global blind protein structure prediction summit, entitled Critical Assessment of Structure Prediction (CASP), critically assesses the modeling methodologies, to track our algorithmic path development. But our success is still impeded by incompetent modeling methodologies and several key technical lacunas. There is still a great need to focus some key issues for bridging the major though considered trivial gaps, in the upcoming CASP to pave and demarcate our correct way of developing a consistently accurate prediction methodology in the near future. Major problems resulting in divergence of our predicted models from their actual native states are thus highlighted with suggested more stringent and reliable assessment considerations in the CASP test.

Keywords:

• CASP
• PDB
• BLAST
• template
• refinement
• alignment
• assessment

Acknowledgments

I am very grateful to Dr. Shibasish Chowdhury for his continuous support in the algorithmic development, offering path fixing comments and editing of this manuscript. I really praise his guidance methodology for nurturing my talent and making me capable enough to learn these concepts inside-out and publish this manuscript single-handedly.