International Journal of Computational Biology and Bioinformatics vol 2 issue 1 by JournalsPub

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International Journal of Computational Biology and Bioinformatics

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International Journal of Computational Biology and Bioinformatics International Journal of Computational Biology and Bioinformatics is a concerning recent advancement and emerging technology in computational biology and bioinformatics. Journal also covers a wide range of topics including synthetic biology and structural genomics. Journal publishes both experimental and theoretical papers.

Focus and Scope of the Journal !

Computer simulation

! Mathematical biology ! Molecular modeling ! Network biology ! Structural genomics ! Synthetic biology ! Systems biology ! Bioinformatics ! Computational genomics and proteomics ! Biomedical image processing, modelling and simulation ! Sequence assembly, search, and alignment ! Computational biomedical data engineering

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PUBLICATION MANAGEMENT TEAM

Chairman Mr. Puneet Mehrotra Managing Director, JournalsPub, New Delhi

INTERNAL MEMBERS

Associate Manager Hidam Renubala

Commissioning Editors Ankita Singh

Priyanka Garg

Akanksha Marwah

Chhavi Goel

Deepika Bhadauria

Shrawani Verma

EDITORIAL BOARD MEMBERS Dr. P Mary Anupama Department of Biotechnology, ANITS, Sangivalasa, Visakhapatnam (A.P.), India

Dr. Ir. Sreenivas Reddy Bathula Department of Biotechnology, Bapuji Institute of Engineering & Technology, Karnataka, India

Dr. Xiaojun Chen Institute of Biomedical Manufacturing and Life Quality Engineering, Shanghai Jiao Tong University (SJTU), China

Dr. Nayira College of Medicine, Imam University, Saudi Arabia

Dr Rahul Raghavan Department of Biotechnology, University of Calicut, Kerala, India

Dr. Abid Qureshi Institute of Microbial Technology, Bioinformatics Center, Chandigarh, India

Dr. Divya Verma Department of Botany Kalindi College, University of Delhi New Delhi, India.

Dr. Aumreetam Dinabandhu ICAR - NRC on Plant Biotechnology, Pusa Campus, New Delhi, India

Dr. Sanjay Mahendrakumar Dave Department of Biotechnology, Hemchandracharya North Gujarat University, Gujarat, India

Ashish Runthala Department of Biological Sciences, Birla Institute of Technology & Science Rajasthan, India

From the Editor's Desk Dear Readers, We would like to present, with great pleasure, the inaugural volume of a new scholarly journal, International Journal of Computational Biology and Bioinformatics. This journal is part of the Applied Sciences, and is devoted to the scope of present Computational Biology and Bioinformatics issues, from theoretical aspects to application-dependent studies and the validation of emerging technologies. This new journal was planned and established to represent the growing needs of Computational Biology and Bioinformatics as an emerging and increasingly vital field, now widely recognized as an integral part of scientific and technical investigations. Its mission is to become a voice of Computational Biology and Bioinformatics, addressing researchers and practitioners in this area. The core vision of International Journal of Computational Biology and Bioinformatics in JournalsPub is to propagate novel awareness and know-how for the profit of mankind ranging from the academic and professional research societies to industry practitioners in a range of topics in Computational Biology and Bioinformatics in general. JournalsPub acts as a pathfinder for the scientific community to publish their papers at excellently, well-timed & successfully. International Journal of Computational Biology and Bioinformatics focuses on original high-quality research in the realm of Computer simulation, Mathematical biology, Molecular modeling, Network biology, Structural genomics, Synthetic biology, Systems biology, Bioinformatics, Computational genomics and proteomics, Biomedical image processing, Modelling and simulation, Sequence assembly, search, and alignment, Computational biomedical data engineering etc. The Journal is intended as a forum for practitioners and researchers to share the techniques of Computational Biology and Bioinformatics and solutions in the area. Many scientists and researchers have contributed to the creation and the success of Computational Biology and Bioinformatics. We are very thankful to everybody within that community who supported the idea of creating an innovative platform. We are certain that this issue will be followed by many others, reporting new developments in the field of Computational Biology and Bioinformatics. This issue would not have been possible without the great support of the Editorial Board members, and we would like to express our sincere thanks to all of them. We would also like to express our gratitude to the editorial staff of JournalsPub, who supported us at every stage of the project. It is our hope that this fine collection of articles will be a valuable resource for Computational Biology and Bioinformatics readers and will stimulate further research into the vibrant area of Computational Biology and Bioinformatics. Puneet Mehrotra Managing Director

Contents 1. Editorial Letter B.D. Bulchandani

2. Molecular Docking of Antipain Inhibitor Using Hex Software Shridhar Shrimant Bagali, Bychapur Siddaiah Gowrishankar

3. Network Biology: Short Article Neha Purohit

4. Molecular Model Rashmi Malhotra

5. Monte Carlo Method Manish Jain

International Journal of Computational Biology & Bioinformatics Vol. 2: Issue 1

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Editorial Letter Dr. B.D. Bulchandani Associate Professor Department of Biotechnology, Sobhasaria Group of Institutions, Sikar Rajasthan Technical University, Kota, India

What Biology has to do with Computation?Thisis one question that flashes the mind of every beginner in the field of Computational Biology. The answer for the question lies in multifarious facts and developments that have made a bridge for biologists to follow computation. Thanks to modern versions and miniaturization of computers, which has made them a house hold term and a sophisticated automation tool for present day researchers.Computers have long been known for their ability to perform billions of simple calculations per second and for being able to store billions of bits of information to be used at random. This all has been made possible by developing and using the appropriate and specific computer programs to face and cater to the wide range of problems, ever perceived by modern man in general and scientifically trained skilled individual in particular, that would otherwise have remained out of reach and any solution. Impending possibilities of computation have spawned several interdisciplinary activities where the objective is to utilize the capacities of computers to gain knowledge from ever expanding huge amounts of data and intervene the functional aspects for the sake of betterment. This very union of computation and biology, which has been unexpected in many senses, is attributed toand propelled by the recently unveiled fact, that life itself is an amazing array of information technology.Whereall the information to make and execute all life processes lies in the quadruplet of nitrogen bases (A, G, C and T) present in the DNA

of any organism, that make the genes and overall genetic constitution. The physiology of any organism right from bacteria through plants to complex animals including human beings is determined by their constituent genes, these in turn at its most basic outlay can be viewed as digital information. According to a recent report by Anthony Kervalage of Celera, an average loaded sequencing laboratory can produce over 100 gigabytes, some even more, of these genomic data per day with ease and precision. This incredible pace of processing has been matched by the drastic fall in the price of data mining from wide sources and developments in computer hard ware as well as sophisticated software technology, the most important areas worth mentioning have been disk storage and speeded internet allowing faster computation and methods for accessing and exchange. This fascinating field of computational biology started with developing all these required tools to organize data in an advanced and wellstructured way, analyse and interpret them on several fronts including homology search, gene annotation and gene prediction, has made several leaps with the development of algorithms that include neural networks, rule based system, dynamic programming and hidden Markov models to facilitate machine based learning and large scale data management.In other words, computation

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International Journal of Computational Biology and Bioinformatics Vol. 2: Issue 1

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Molecular Docking of Antipain Inhibitor Using Hex Software Shridhar Shrimant Bagali1*, Bychapur Siddaiah Gowrishankar2 1

Department of Petrochemical Engineering, KBNCE, Kalaburagi, Karnataka, India Department of Biotechnology, Siddaganga Institute of Technology, Tumkur, Karnataka, India

Abstract cellular functions through protein-ligand interaction, which leads to significant conformational

Keywords: protein–ligand interactions, Docking, Harmonic Surface and Fourier transform.

INTRODUCTION Bioinformatics is multidisciplinary science dealing the connection of molecular biology and computer science as well as programming. Recent days, molecular biology data based software development is challenging and fascinating in the field of bioinformatics. Bioinformatics is a new tool in the growing area of science in the computational approach to biological solutions for design of new drug. Design of drug includes blowing up in molecular sequence and structural information may increase in demanding position in study of fundamental biomedical solution. Bioinformatics mainly deals gene discovery, design of molecular modeling, site-directed mutagenesis and experiments of many other prospective research had been correlated with respect to the structure and function of genes and proteins.[1] Proteins are complex molecules made up of amino acids joined with peptide bonds. Proteins play a vital role in structural and functional activities in all living cells. Many proteins are enzymes or subunits of enzymes, catalyzing chemical reactions. In biology, a ligand is an extracellular substance that binds to receptors called protein. In chemistry, a ligand is an atom, ion or functional group that donates its electrons through a coordinate covalent bond to one or more central atoms or ions, usually metals. An array of such ligands IJCBB (2016) 3–8 © JournalsPub 2016. All Rights Reserved

around a center is termed a complex. The importance of protein ligand binding in biological systems should not be underestimated. Any organism must have a mechanism of interacting with its environment. Individual cells must be able to interact with a complex variety of different molecules, derived from not only the outside environment but also generated within the cell itself. Protein-ligand interaction has an important function in living organisms and which will be used in wide verities of molecules. The goal is to build a complete computer-aided drug design system. There is tool need to development, such as Docking. The act of coupling two or more orbiting objects; the operation of mechanically connecting together, or in same manner being together, orbital payloads are called docking. Docking is process of fitting together two molecules in 3d space. Docking allows the scientists to virtually screen a database of compounds and predict the strongest binders based on various scoring functions. Macromolecular interactions are essential for biological life's existence, as each biological process involves protein protein interactions; the area of molecular docking encompasses protein protein interactions and protein ligand interactions.[2–6]

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International Journal of Computational Biology and Bioinformatics Vol. 2: Issue 1

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Network Biology: Short Article Neha Purohit* Department of Biotechnology, Amity University, Uttar Pradesh, India

Abstract Network representation of intracellular biological systems regularly considers molecular segments inside a cell as hubs and their immediate or circuitous communications as connections or links. Distinctive sorts of intracellular molecular biological systems can be spoken to by various sorts of numerical structures called graph. Rapid advances in network biology indicate that cellular networks are governed by universal laws and offer a new conceptual framework that could potentially revolutionize our view of biology and disease pathologies in the twenty-first century. Keywords: biological systems, network biology

INTRODUCTION A biological system is any system that applies to biological frameworks. A system is any framework with sub-units that are connected into an entire, for example, animal types units connected into an entire sustenance web. Biological systems give a numerical investigation of associations found in environmental, transformative, and physiological concentrates, for example, neural [1] networks. The examination of biological systems concerning human ailments has prompted the field of system prescription. Complex biological networks might be spoken to and broke down as processable systems. For instance, biological systems or ecosystems can be displayed as systems of collaborating species or a protein can be demonstrated as a system of amino acids. Separating a protein more distant, amino acids can be spoken to as a system of associated molecules, for example, carbon, nitrogen, and oxygen. Nodes and edges are the fundamental segments of a system. Nodes speak to

units in the system, while edges speak to the collaborations between the units. Nodes can speak to a wide-exhibit of natural units, from individual life forms to individual neurons in the mind. Two essential properties of a system are degree and centrality. Degree (or availability, an unmistakable use from that utilized as a part of chart hypothesis) is the quantity of edges that interface a hub, while betweenness is a measure of how focal a hub is in a network.[2] Nodes with high betweenness basically serve as extensions between various segments of the system (i.e. communications must go through this hub to achieve different bits of the system). In informal communities, hubs with high degree or high betweenness may assume essential parts in the general structure of a system. Bioinformatics has increasingly shifted its focus from individual genes, proteins, and search algorithms to large-scale networks often denoted as -omes such as biome, interactome, genome and proteome. Such theoretical studies have revealed that

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International Journal of Computational Biology and Bioinformatics Vol. 2: Issue 1

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Molecular Model Rashmi Malhotra* Department of Computational Biology, Sharda University, Uttar Pradesh, India

Abstract Molecular modeling is an accumulation of (PC based) methods for inferring, representing and controlling the structures and responses of particles, and those properties that are subject to these three dimensional structures. This is a standard tool used for searching for, rationalizing and predicting structure and reactivity of organic, bio-organic and organometallic molecules. Keywords: molecular graphics, molecular modeling

INTRODUCTION Molecular modelling includes every single hypothetical strategy and computational procedures used to model or copy the conduct of particles. The procedures are utilized as a part of the fields of computational science, drug design, computational science and materials science for contemplating sub-atomic frameworks going from little substance frameworks to expansive organic particles and material gatherings.[1] The most Molecular mechanics is one aspect of molecular modelling, as it refers to the use of classical mechanics/Newtonian mechanics to describe the physical basis behind the models. Molecular models typically describe atoms (nucleus and electrons collectively) as point charges with an associated mass. The interactions between neighbouring atoms are described by spring-like interactions (representing chemical bonds) and van der Waals forces. The Lennard-Jones potential is commonly used to describe van der Waals forces.[3] The electrostatic interactions are computed based on Coulomb's law. Atoms are assigned coordinates in Cartesian space or in internal coordinates, and can

straightforward counts can be performed by hand, however definitely PCs are required to perform sub-atomic demonstrating of any sensibly estimated framework. The normal element of submolecular displaying strategies is the molecular level portrayal of the subatomic frameworks. This may incorporate regarding particles as the littlest individual unit (the Molecular mechanics approach), or expressly displaying electrons of every iota (the quantum science approach).[2] also be assigned velocities in dynamical simulations. The atomic velocities are related to the temperature of the system, a macroscopic quantity. The collective mathematical expression is known as a potential function and is related to the system internal energy (U), a thermodynamic quantity equal to the sum of potential and kinetic energies. Methods which minimize the potential energy are known as energy minimization techniques (e.g., steepest descent and conjugate gradient), while methods that model the behaviour of the system with propagation of time are known as molecular dynamics.

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International Journal of Computational Biology and Bioinformatics Vol. 2: Issue 1

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Monte Carlo Method Manish Jain* Department of Bioinformatics, SRM University, Chennai, India

Abstract Monte Carlo simulations are utilized to display the likelihood of various results in a procedure that cannot without much of a stretch be anticipated because of the mediation of arbitrary variables. Monte Carlo simulation outfits the leader with a scope of conceivable results and the probabilities they will happen for any decision of activity. It demonstrates the compelling conceivable outcomes—the results of pulling out all the stops and for the most traditionalist choice—alongside every single conceivable outcome for widely appealing choices. Keywords: computational algorithm, Monte Carlo, simulation

INTRODUCTION Monte Carlo methods (or Monte Carlo trials) are a wide class of computational calculations that depend on rehashed arbitrary testing to get numerical results. Their crucial thought is utilizing haphazardness to take care of issues that may be deterministic on a basic level. They are regularly utilized as a part of physical and numerical issues and are most helpful when it is troublesome or difficult to utilize different methodologies. Monte Carlo techniques are mostly utilized as a part of three particular issue classes:[1] improvement, numerical combination, and producing draws from a probability circulation. In physical science related issues, Monte Carlo methods are entirely helpful for reproducing frameworks with numerous coupled degrees of flexibility, for example, liquids, cluttered materials, emphatically coupled solids, and cell structures (see cell Potts model, communicating molecule frameworks, McKean-Vlasov forms, active models of

gasses). Different cases incorporate demonstrating marvels with critical instability in inputs, for example, the computation of danger in business and, in math, assessment of multidimensional positive integrals with confused limit conditions.[2,3] In application to space and oil investigation issues, Monte Carlo– based expectations of disappointment, cost invades and plan overwhelms are routinely superior to anything human instinct or option "delicate" strategies. On a basic level, Monte Carlo strategies can be utilized to take care of any issue having a probabilistic elucidation. By the law of vast numbers, integrals portrayed by the normal estimation of some irregular variable can be approximated by taking the experimental mean (a.k.a. the specimen mean) of autonomous examples of the variable.[4] At the point when the likelihood circulation of the variable is parametrized, mathematicians frequently utilize a Markov Chain Monte Carlo (MCMC) sampler. The focal thought is to outline a reasonable Markov chain model

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« « « «

¬ ¬ International Journal of Industrial Engineering

Manufacturing International Journal of Mechanical Dynamics and Analysis International Journal of Fracture and damage Mechanics International Journal of Structural Mechanics and Finite Elements

and Design ¬ International Journal of Manufacturing and

Materials Processing ¬ International Journal of Mechanical Handling and

Automation 5 more...

Electronics and Telecommunication « International Journal of Radio Frequency Design « International Journal of VLSI Design and Technology « International Journal of Embedded Systems and Emerging

Technologies « International Journal of Digital Electronics « International Journal of Digital Communication and Analog

Chemical Engineering « International Journal of Renewable Energy and its

Commercialization « International Journal of Environmental Chemistry « International Journal of Agrochemistry « International Journal of Prevention and Control of Industrial

Pollution

5 more...

Signals

1 more...

Civil Engineering

Architecture « International Journal of Housing and Human Settlement

Planning « International Journal of Architecture and Infrastructure

Planning « International Journal of Rural and Regional Planning

« « « «

Development

« International Journal of Town Planning and Management

2 more...

Electrical Engineering

Computer Science and Engineering « « « « «

Nursing « « « « «

International Journal of Computational Biology & Bioinformatics IJCBB

Material Sciences and Engineering

« « « «

5 more...

Biotechnology « International Journal of Industrial Biotechnology and « « « «

Jan – Jun 2016

Nanotechnology « International Journal of Applied Nanotechnology « International Journal of Nanomaterials and Nanostructures « International Journals of Nanobiotechnology

Chemistry

Physics « International Journal of Solid State Materials « International Journal of Optical Sciences