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Yeast Cytokinesis

Volume 1369 of the series Methods in Molecular Biology pp 363-377

Toolbox for Protein Structure Prediction

  • Daniel Barry RocheAffiliated withInstitut de Biologie Computationnelle, LIRMM, CNRS, Université de MontpellierCEA, DSV, IG, GenoscopeCNRS-UMR8030Université d’Évry Val d’EssonnePRES UniverSud Paris Email author 
  • , Liam James McGuffinAffiliated withSchool of Biological Sciences, University of Reading

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Abstract

Protein tertiary structure prediction algorithms aim to predict, from amino acid sequence, the tertiary structure of a protein. In silico protein structure prediction methods have become extremely important, as in vitro-based structural elucidation is unable to keep pace with the current growth of sequence databases due to high-throughput next-generation sequencing, which has exacerbated the gaps in our knowledge between sequences and structures.

Here we briefly discuss protein tertiary structure prediction, the biennial competition for the Critical Assessment of Techniques for Protein Structure Prediction (CASP) and its role in shaping the field. We also discuss, in detail, our cutting-edge web-server method IntFOLD2-TS for tertiary structure prediction. Furthermore, we provide a step-by-step guide on using the IntFOLD2-TS web server, along with some real world examples, where the IntFOLD server can and has been used to improve protein tertiary structure prediction and aid in functional elucidation.

Key words

Protein tertiary structure prediction Protein structure Fold recognition Template-based mode ling Template-free model ing Critical Assessment of Techniques for Protein Structure Prediction (CASP) Bioinformatics web server s Model quality assessment method s Continuous Automated Model EvaluatiOn (CAMEO) Protein Model Portal (PMP) Protein Structure Initiative (PSI)