Contents

#### **Preface** XI


X Contents

**Section 4 Molecular Modeling 157**  Chapter 7 **Incorporating Molecular Dynamics Simulations into Rational Drug Design: A Case Study on Influenza a Neuraminidases 159**  Ly Le Chapter 8 **Using Molecular Modelling to Study Interactions Between Molecules with Biological Activity 185**  María J. R. Yunta **Section 5 Structural Bioinformatics 213**  Chapter 9 **On the Assessment of Structural Protein Models with ROSETTA-Design and HMMer: Value, Potential and Limitations 215**  León P. Martínez-Castilla and Rogelio Rodríguez-Sotres **Section 6 Intelligent Data Analysis 239**  Chapter 10 **Bacterial Promoter Features Description and Their Application on** *E. coli in silico* **Prediction and Recognition Approaches 241**  Scheila de Avila e Silva and Sergio Echeverrigaray Chapter 11 **Computational Approaches for Designing Efficient and Specific siRNAs 261**  Suman Ghosal, Shaoli Das and Jayprokas Chakrabarti Chapter 12 **Novel microRNA Cloning Using Bioinformatics 277**  Yoshiaki Mizuguchi, Takuya Mishima, Eiji Uchida and Toshihiro Takizawa Chapter 13 **Ensemble Clustering for Biological Datasets 287**  Harun Pirim and Şadi Evren Şeker Chapter 14 **Research on Pattern Matching with Wildcards and Length Constraints: Methods and Completeness 299**  Haiping Wang, Taining Xiang and Xuegang Hu
