From Protein Structure to Function with Bioinformatics.pdf

xivContents9.4.2 Elastic Network Models .................................................. 2389.4.3 CONCOORD .................................................................. 2399.5 Summary and Outlook .................................................................. 24210 Integrated Servers for Structure-InformedFunction Prediction ............................................................................... 251Roman A. Laskowski10.1 Introduction ................................................................................... 25110.1.1 The Problem of Predicting Functionfrom Structure ................................................................. 25210.1.2 Structure-Function PredictionMethods .......................................................................... 25310.2 ProKnow ....................................................................................... 25410.2.1 Fold Matching ................................................................. 25410.2.2 3D Motifs ........................................................................ 25610.2.3 Sequence Homology ....................................................... 25710.2.4 Sequence Motifs ............................................................. 25710.2.5 Protein Interactions ......................................................... 25810.2.6 Combining the Predictions .............................................. 25810.2.7 Prediction Success .......................................................... 25810.3 ProFunc ......................................................................................... 25910.3.1 ProFunc’s Structure-Based Methods .............................. 25910.3.2 Assessment of the Structural Methods ............................ 26710.4 Conclusion .................................................................................... 26911 Case Studies: Function Predictions of StructuralGenomics Results ................................................................................... 273James D. Watson and Janet M. Thornton11.1 Introduction ................................................................................... 27311.2 Large Scale Function PredictionCase Studies .................................................................................. 27511.3 Some Specific Examples ............................................................... 28111.4 Community Annotation ................................................................ 28711.5 Conclusions ................................................................................... 28812 Prediction of Protein Function fromTheoretical Models ................................................................................. 293Iwona A. Cymerman, Daniel J. Rigden,and Janusz M. Bujnicki12.1 Background ................................................................................... 29312.2 Protein Models as a Community Resource ................................... 29512.2.1 Model Quality ................................................................. 29612.2.2 Databases of Models ....................................................... 297