Computational StrategiesTowards Improved Protein Function Prophecy of Xylanases from Thermomyces lanuginosus; Contents; Abstract; 1 Introduction; 1.1 ... Introduction; References; 2 Background; 2.1 ... Protein Structure; 2.1.1 Classification of Protein Structure; 2.1.2 Protein Surface; 2.2 ... Protein -- Protein Interaction; 2.3 ... Protein Binding Site Prediction; 2.3.1 Identification of Protein -- Ligand Binding Site; 2.3.2 Protein -- Protein Binding Site Prediction; 2.3.2.1 Surface Patch-Based Prediction Methods; 2.3.2.2 Machine Learning Prediction Approaches; 2.4 ... Protein -- Protein Docking
2.4.1 Rigid-Body Docking2.4.2 Fast Fourier Transform; 2.4.3 Benchmark for Testing the Docking Algorithms; 2.4.4 Critical Assessment of Predicted Interactions; 2.4.5 Protein Interface Prediction and Protein Docking; 2.5 ... Flexible Docking; 2.5.1 Side-Chain Flexibility; 2.5.2 Backbone Flexibility; 2.5.3 Soft Docking; References; 3 Materials and Methods; 3.1 ... Selection of Sequences, 3D Structures and Multiple Sequence Alignment; 3.2 ... Mutant Generation; 3.3 ... Energy Minimization; 3.4 ... Stereo-Chemical Quality Check and Analysis of Non-Bonded Interactions; 3.5 ... Protein -- Protein Docking; 3.6 ... InterProScan
3.7 ... Identification of Functionally Important Regions of Wild Type viz. Endo-1, 4-beta xylanases3.8 ... 3d2GO Server: From Protein 3D Structure to Gene Ontology Term; References; 4 Results and Discussions; 5 Conclusion; References
Summary
Annotation This Brief reports on the interplay of an amino-acid mutation towards substrate which could lead to enhanced effects on mutant. These effects need to be given consideration in the engineering processes of protein stability and further exploration of such learning are required to provide novel indication for selection of an enzymes. There are very few reports showing such stable, energy efficient model towards improved protein function prediction screening in-silico structure based mutagenesis of xylanases from Thermomyces lanuginosus
