Meet the editors

Dr. Payam Behzadi was born in 1973, in Tehran, Iran. He began his collaboration with the Department of Microbiology, College of Basic Sciences, Shahr-e-Qods Branch, Islamic Azad University as a faculty member (with an MSc degree in Microbiology) in 2004. He finally got his Ph.D. degree in Molecular biology in 2016 (BSc and MSc in Microbiology; Ph.D. in Molecular Biology) and now continues his scientific activities in the position of

Assistant Professor at the same university. He has several students from different academic levels including BSc, MSc, and Ph.D. Dr. Payam Behzadi has authored and edited more than 20 chapters and academic books and more than 70 original and review articles. His scientific research interests are: urinary tract infections, antibiotics, bioinformatics, genetics, gene profiling, molecular biology and cellular and molecular immunology. Dr. Payam Behzadi trains as an ice skater in his free time.

Prof. Nicola Bernabò is an Associate Professor of Veterinary Physiology at the Faculty of Veterinary Medicine, University of Teramo, Italy. He received his degree in veterinary medicine from the University of Pisa (1999), his Master's degree in biotechnology of reproduction from the University of Teramo (2002), and Ph.D. degree in endocrinology of domestic animals from the University of Bologna (2004). His research interests include en-

docrinology of reproduction, the biochemistry of sperm capacitation, and systems biology. In particular, his work is focused on the development of computational models representing the complex biochemical events that occur during the acquisition of fertilizing ability by male gametes either in domestic animals or humans. Prof. Bernabò is the author of more than sixty works published in international peer-reviewed journals, conference proceedings, as well as book chapters, and he has been awarded national and international prizes for his research activity.

Contents

**Section 1**

**Section 2**

*by Payam Behzadi*

in Human Testis

**Section 3**

of Proteins

**Section 4**

Ibuprofenate

**Preface XI**

Introduction **1**

**Chapter 1 3**

Wet Labs and Dry Labs: From In Vitro to In Silico Studies **9**

**Chapter 2 11**

Bioinformatics and the Related Software Tools and Databases **35**

**Chapter 3 37**

**Chapter 4 65**

Computational Biology and Chemical Monitoring **81**

**Chapter 5 83**

Biological Evaluation and Molecular Docking Studies of Benzalkonium

*by Kodakkat Parambil Safna Hussan, Mohamed Shahin Thayyil, Thaikadan Shameera Ahamed and Karuvanthodi Muraleedharan*

Search for Human-Specific Proteins Based on Availability Scores of Short Constituent Sequences: Identification of a WRWSH Protein

*by Shiho Endo, Kenta Motomura, Masakazu Tsuhako, Yuki Kakazu,* 

Bioinformatics as a Tool for the Structural and Evolutionary Analysis

*by Edna María Hernández-Domínguez, Laura Sofía Castillo-Ortega,* 

*Yarely García-Esquivel, Virginia Mandujano-González, Gerardo Díaz-Godínez and Jorge Álvarez-Cervantes*

Scaffolding Contigs Using Multiple Reference Genomes *by Yi-Kung Shieh, Shu-Cheng Liu and Chin Lung Lu*

Introductory Chapter: From Hard to Soft Biology

*Morikazu Nakamura and Joji M. Otaki*

## Contents



Preface

The employment of computers, software tools, and internet services in basic sciences and medicine has led to changes in investigation methodologies. This occurrence resulted in the establishment of multidisciplinary sciences involving bioinformatics and systems biology. The computational multidisciplinary sciences represented new types of studies and laboratories. In silico investigations and dry laboratories have been the invaluable products of these sciences. The serious and continuous activities in this regard led to the accumulation of a huge amount of digital data (bioinformatic data) in the form of databases. These progressions and facilities resulted in invaluable outcomes such as computational biology and chemistry. I call them soft biology and chemistry.

The reason for the success and progression in soft biology and chemistry is the appearance of effective and precise bioinformatic software tools and databases such as the National Center for Biotechnology Information (NCBI) (https://www.ncbi.nlm. nih.gov/), Kyoto Encyclopedia of Genes and Genomes (KEGG) (https://www.genome. jp/kegg/), and Research Collaboratory for Structural Bioinformatics PDB (RCSBPDB)

Visualization and 3-dimentionization of different biomolecules, structures, and complexes are the most fantastic facilities that are provided and represented by bioinformatics, systems biology, computational biology, and chemistry.

The results of traditional investigations within wet labs by molecular biologists, biologists, biochemists, and chemists produced only raw data including nucleotides

With the appearance of bioinformatics and the use of computational technologies, we are able to visualize these data to have their putative spatial configurations and conformations. Today, we are able to 3-dimensionalize the discovered raw data to have a limited imaging capability of their natural structure to understand the related

Moreover, the use of computational biology and chemistry has had effective consequences in pharmaceutics. As we know, the traditional procedure of preparation and provision of a drug or antibiotic includes several control and check processes in different levels of assays. These procedures and processes cost a lot of money and takes a long

Recruitment of computational biology and chemistry represents a great opportunity for pharmaceutics. Drug designing is a brilliant bonus to pharmaceutics to shorten technical

procedures and duration of time to reduce the costs of drugs and antibiotics.

All in all, we are at the beginning point of the soft biology and chemistry pathway. The progressions of these scientific disciplines support us to have incredible imaging, illustration, and interpretation of the obtained raw data in traditional wet labs. In the future we can have a precise image of the reason of spatial architecture of different biomolecules and their interactions with other structures and complexes. The dry labs

(https://www.rcsb.org/).

and amino acid sequences.

duration of time.

characteristics, practicalities, and functionalities.

determine the future of biology and chemistry!
