CASP6 assessment of contact prediction.
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.
Graña
Osvaldo
O
Protein Design Group, Centro Nacional de Biotecnologia (CNB-CSIC), C/Darwin 3, Cantoblanco, Madrid, Spain.
Baker
David
D
University of Washington, Department of Biochemistry, Seattle, Washington.
MacCallum
Robert M
RM
Stockholm Bioinformatics Center, Stockholm University, Stockholm, Sweden.
Meiler
Jens
J
Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, Tennessee.
Punta
Marco
M
CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York.
Rost
Burkhard
B
CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York.
Tress
Michael L
ML
Protein Design Group, Centro Nacional de Biotecnologia (CNB-CSIC), C/Darwin 3, Cantoblanco, Madrid, Spain.
Valencia
Alfonso
A
Protein Design Group, Centro Nacional de Biotecnologia (CNB-CSIC), C/Darwin 3, Cantoblanco, Madrid, Spain.
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