title: CASP6 assessment of contact prediction.
abstract: Here we present the evaluation results of the Critical Assessment of Protein Structure Prediction (CASP6) contact prediction category. Contact prediction was assessed with standard measures well known in the field and the performance of specialist groups was evaluated alongside groups that submitted models with 3D coordinates. The evaluation was mainly focused on long range contact predictions for the set of new fold targets, although we analyzed predictions for all targets. Three groups with similar levels of accuracy and coverage performed a little better than the others. Comparisons of the predictions of the three best methods with those of CASP5/CAFASP3 suggested some improvement, although there were not enough targets in the comparisons to make this statistically significant.
authors.affiliation: Protein Design Group, Centro Nacional de Biotecnologia (CNB-CSIC), C/Darwin 3, Cantoblanco, Madrid, Spain.
authors.forename: Osvaldo
authors.initials: O
authors.lastname: Graña
authors.affiliation: University of Washington, Department of Biochemistry, Seattle, Washington.
authors.forename: David
authors.initials: D
authors.lastname: Baker
authors.affiliation: Stockholm Bioinformatics Center, Stockholm University, Stockholm, Sweden.
authors.forename: Robert M
authors.initials: RM
authors.lastname: MacCallum
authors.affiliation: Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, Tennessee.
authors.forename: Jens
authors.initials: J
authors.lastname: Meiler
authors.affiliation: CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York.
authors.forename: Marco
authors.initials: M
authors.lastname: Punta
authors.affiliation: CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York.
authors.forename: Burkhard
authors.initials: B
authors.lastname: Rost
authors.affiliation: Protein Design Group, Centro Nacional de Biotecnologia (CNB-CSIC), C/Darwin 3, Cantoblanco, Madrid, Spain.
authors.forename: Michael L
authors.initials: ML
authors.lastname: Tress
authors.affiliation: Protein Design Group, Centro Nacional de Biotecnologia (CNB-CSIC), C/Darwin 3, Cantoblanco, Madrid, Spain.
authors.forename: Alfonso
authors.initials: A
authors.lastname: Valencia
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D003201:Computers; D003627:Data Interpretation, Statistical; D030562:Databases, Protein; D008958:Models, Molecular; D011487:Protein Conformation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D040901:Proteomics / Q000379:methods*; D015203:Reproducibility of Results; D016415:Sequence Alignment; D012984:Software