Molecular modeling is a tool encompasses computational techniques used to mimic Deoxyribonucleic Acid(DNA) and protein. Docking is a study in the field of Molecular modeling which predicts the preferred orientation of Protein DNA Binding. In this book Molecular modeling of Nucleoside Diphosphate Kinase (NDP kinase-cancer metastatic suppressor protein) and its interaction with pBR322 DNA and matrix metalloproteases (MMP-2) enhancer responsible element (RE-1) is discussed. This book also includes NDP kinase Topoisomersae interaction and Topoisomerase interaction with pBR322 DNA. The readers of the present book will be benefited to understand the basics of Molecular Modeling, Protein-DNA and Protein-Protein interactions.