title: Toolbox for Protein Structure Prediction.
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.
authors.affiliation: Institut de Biologie Computationnelle, LIRMM, CNRS, Université de Montpellier, Montpellier, France. daniel.roche@lirmm.fr.|CEA, DSV, IG, Genoscope, Évry, France. daniel.roche@lirmm.fr.|CNRS-UMR8030, Évry, France. daniel.roche@lirmm.fr.|Université d'Évry Val d'Essonne, Évry, France. daniel.roche@lirmm.fr.|PRES UniverSud Paris, Saint-Aubin, France. daniel.roche@lirmm.fr.
authors.forename: Daniel Barry
authors.initials: DB
authors.lastname: Roche
authors.affiliation: School of Biological Sciences, University of Reading, Reading, UK.
authors.forename: Liam James
authors.initials: LJ
authors.lastname: McGuffin
mesh_terms: D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D008958:Models, Molecular; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012984:Software; D064878:Web Browser
chemical_list: D011506:Proteins
keywords: Bioinformatics web server s; Continuous Automated Model EvaluatiOn (CAMEO); Critical Assessment of Techniques for Protein Structure Prediction (CASP); Fold recognition; Model quality assessment method s; Protein Model Portal (PMP); Protein Structure Initiative (PSI); Protein structure; Protein tertiary structure prediction; Template-based mode ling; Template-free model ing