Use of Bioperl in Bioinformatics

Bioperl is a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. As such, it does not include ready to use programs in the sense that many commercial packages and free web-based interfaces do (e.g. Entrez, SRS). On the other hand, Bioperl does provide reusable Perl modules that facilitate writing Perl scripts for sequence manipulation, accessing of databases using a range of data formats and execution and parsing of the results of various molecular biology programs including Blast, clustalw, TCoffee, genscan, ESTscan and HMMER. Consequently, bioperl enables developing scripts that can analyze large quantities of sequence data in ways that are typically difficult or impossible with web based syste...

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Molecular Dynamics on Stapled Peptide - Computational Drug Design

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What is Drug Design ?

endeavor. Drug discovery is mostly portrayed as a linear, consecutive process that starts with target and lead discovery, followed by lead optimization and pre-clinical in vitro and in vivo studies to determine if such compounds satisfy a number of pre-set criteria for initiating clinical development. For the pharmaceutical industry, the number of years to bring a drug from discovery to market is approximately 12-14 years and costing upto $1.2 - $1.4 billion dollars. Traditionally, drugs were discovered by synthesizing compounds in a time-consuming multi-step processes against a battery of in vivo biological screens and further investigating...

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Drug Lead Optimization.

Drug Lead Optimization. When a promising lead candidate has been found in a drug discovery program, the next step (a very long and expensive step!) is to optimize the structure and properties of the potential drug. This usually involves a series of modifications to the primary structure (scaffold) and secondary structure (moieties) of the compound. This process can be enhanced using software tools that explore related compounds (bioisosteres) to the lead candidate. OpenEye’s WABE is one such tool. Lead optimization tools such as WABE offer a rational approach to drug design that can reduce the time and expense of searching for related compoun...

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Similarity Searches.

Similarity Searches. A common activity in biopharmaceutical companies is the search for drug analogues. Starting with a promising drug molecule, one can search for chemical compounds with similar structure or properties to a known compound. There are a variety of methods used in these searches, including sequence similarity, 2D and 3D shape similarity, substructure similarity, electrostatic similarity and others. A variety of bioinformatic tools and search engines are available for this wo...

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Homology Modeling

Homology Modeling. Another common challenge in CADD research is determining the 3-D structure of proteins. Most drug targets are proteins, so it’s important to know their 3-D structure in detail. It’s estimated that the human body has 500,000 to 1 million proteins. However, the 3-D structure is known for only a small fraction of these. Homology modeling is one method used to predict 3-D structure. In homology modeling, the amino acid sequence of a specific protein (target) is known, and the 3-D structures of proteins related to the target (templates) are known. Bioinformatics software tools are then used to predict the 3-D structure of the target based on the known 3-D structures of the templates. MODELLER is a well-known tool in homology modeling, and the SWISS-MODEL Repository is a database...

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Sequence Analysis

Sequence Analysis. In CADD research, one often knows the genetic sequence of multiple organisms or the amino acid sequence of proteins from several species. It is very useful to determine how similar or dissimilar the organisms are based on gene or protein sequences. With this information one can infer the evolutionary relationships of the organisms, search for similar sequences in bioinformatic databases and find related species to those under investigation. There are many bioinformatic sequence analysis tools that can be used to determine the level of sequence similari...

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Virtual High-Throughput Screening (vHTS)

Virtual High-Throughput Screening (vHTS). Pharmaceutical companies are always searching for new leads to develop into drug compounds. One search method is virtual high-throughput screening. In vHTS, protein targets are screened against databases of small-molecule compounds to see which molecules bind strongly to the target. If there is a “hit” with a particular compound, it can be extracted from the database for further testing. With today’s computational resources, several million compounds can be screened in a few days on sufficiently large clustered computers. Pursuing a handful of promising leads for further development can save researchers considerable time and expense. ZINC is a good example of a vHTS compound libra...

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Computer Aided Drug Design

On the support side of the hub, Information Technology, Information Management, software applications, databases and computational resources all provide the infrastructure for bioinformatics. On the scientific side of the hub, bioinformatic methods are used extensively in molecular biology, genomics, proteomics, other emerging areas (i.e. metabolomics, transcriptomics) and in CADD research. here are several key areas where bioinformatics supports CADD research. Virtual High-Throughput Screening (vHTS). Sequence Analysis. Homology Modeling. Similarity Searches Drug Lead Optimization. Physicochemical Modeling. Drug Bioavailability and Bioactivity&nb...

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Bioinformatics in Computer-Aided Drug Design

Computer-Aided Drug Design (CADD) is a specialized discipline that uses computational methods to simulate drug-receptor interactions. CADD methods are heavily dependent on bioinformatics tools, applications and databases. As such, there is considerable overlap in CADD research and bioinformatics.Bioinformatics can be thought of as a central hub that unites several disciplines and methodologi...

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Computer Aided Drug Design

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Computer aided drug design and bioinformatics:

Drug design is an integrated developing discipline. It involves the study of effects of biologically active compound on the basis of molecular interaction in terms of molecular structure or its physiochemical properties involved. The development of new methods in the field of molecular biology and computer science, has improved the tools for drug design significantly. More and more new drugs are developed with the help of computer technique. The field of bioinformatics has become a major part of the drug design that plays a key role for validation drug targets. Bioinformatics can help in understanding of complex biological processes and help improve in understanding of complex biological processes and help improve drug discovery. Drug design is an iterative process that begins when a...

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Bioinformatics Tutorials Using ClustalW to do a multiple sequence alignment

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Bioinformatics Web Practical

It is an online practical for the prediction of the structure and function of the unknown protein by using primary and secondary biological databases First go http://umber.embnet.org/dbbrowser/bioactivity/ press "ready to go" and then "go" now you are at the page http://umber.embnet.org/dbbrowser/bioactivity/nucleicfrm.html at the top of the you have Sequence translation & identification select "materials" which contain the unknown nucleotide sequences you can also use your own sequence of interest click materials and select any fragment it is the dna sequence click the fragment and get its sequence copy this sequence and paste it in translator to get the translated sequence and also find the orf(open reading frame) of the sequence . Copy the orf and paste in OWL which is actually...

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Overview of the UniProt Bioinformatics Website

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How to predict the function of unknown or known protein using Swissprot?

First go http://expasy.org/sprot/ search uniprotkb for protein name (opsin 1) then go at this page it will give this protein in many different organism http://www.uniprot.org/uniprot/?query=opsin%201 so narrow down your search click the fields>> and select any option instead of All like organism [OS] so select in next bar human [9606] and click Add&Search the result of protein family present in humans is appeared as a result click any one of the ID so you can get the information about any protein like its domains and function etc http://www.uniprot.org/uniprot/P08100 I hope you will like it regards "Quratt ul ain Siddiq...

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Bioinformatics Tutorials (Lesson 2):Using BLAST to search for similarities

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Bioinformatics Tutorials (Lesson 1):Using SwissProt database to search for a specific protein

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Adeno-Associated Virus 9 SWISS-MODEL Structure

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How are the opsin genes related to each other?

Answering this question requires making a multiple sequence alignment and then using it to make a phylogenetic tree. For these tasks, we move to another database where it's a little easier to gather a bunch of sequences into a single FASTA file. Point your browser to http://us.expasy.org. PASY is mirrored at several locations including the following: http://www.expasy.org/  http://ca.expasy.org/ If one does not work or responds slow, try a different one. You see the home page of ExPASy, the Expert Protein Analysis System. As I said earlier, ExPASy is a complete protein tool box. With ExPASy, you can do almost any imaginable analysis or comparison of protein sequences and structures. Click Swiss-Prot and TrEMBL under Databases. Read the introduction to these databases. They are...

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How to predict the 3D Structure of known or unknown Protein ?

If you have a nucleotide or amino acid sequence of unknown or known protein and you want to predict its structure then follow the following steps given as : 1.Apply blast to your sequence and get the name of your protein which you are using as a query. eg your protein name is opsin 1 then go to http://www.ncbi.nlm.nih.gov/ and select structure from search drop down menu and enter the protein name as opsin 1. Then structure of this protein and slight function will be available at this page http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=77531 click the option of download cn3D then download this software for your own system it is a...

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Bacteriorhodopsin

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Rhodopsin interaction with transducin

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Tutorial: Examining the 3D Structure of Rhodopsin at NCBI

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What proteins in humans are similar to the red opsin?

Now return to the NCBI Map Viewer http://www.ncbi.nlm.nih.gov/mapview/. We're going to search the human genome for sequences similar to that of the red opsin. Click the B next to Homo sapiens (human). This is the NCBI's BLAST search tool. BLAST is a widely used program for finding sequences similar to a "query" sequence that you're interest in. Pick these options from the various menus: Database: Protein (Search the database of proteins sequences.) Program: blastp (Use the version of BLAST that compares protein sequences, unlike blastn, which compares nucleotide sequences.) Other Parameters, Expect: 10 (The higher the number, the less stringent that matching, and the more hits you'll get) Next, copy the FASTA data from your file protred.txt to your clipboard, and paste it into the BLAST...

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The amino-acid sequence of this OPN1LW

Things look a lot like before, but this is a protein entry, containing the amino-acid sequence in one-letter abbreviations. Just as with the mRNA entry, turn this into a FASTA display, and copy it into a new word-processor document. Save it in text format as protred.txt. Return to LocusLink. you can translate the FASTA format of the nucleotide sequence of the gene otherwise its amino acid sequence is also present in the genbank page you can access it here FASTA of the amino acid sequence is at this page http://www.ncbi.nlm.nih.gov/protein/9910...

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What is the nucleotide sequence of this gene?

Remember that we are looking at the gene for the red-sensitive opsin in humna vision, and it's located near the bottom tip of the X chromosome. Scroll down to NCBI Reference Sequences (RefSeq). You see that mRNA (messenger RNA) and protein sequences are available, along with a GenBank sequence. Click the entry number beside mRNA. This is a typical GenBank nucleotide file, and a lot of it is hard to read, but a few things are clear. First note, under references, a citations to the publication of this sequence in the scientific literature. To see an abstract of the article in which this gene was described, click the PubMed link below the reference. As you see, you've been here before. There are many ways to move from one database to another, which is both a blessing and a curse. You have to...

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Find and Characterize the gene using Bioinformatics and its tools and databases

By using Bioinformatics we have to find the specific gene in genome where it is present in the genome. Here we go: Our gene of interest is Opsin: Where are the opsin genes in the human genome?  First go to this site http://www.ncbi.nlm.nih.gov/mapview/.  Read the instructions. Note that you can look at a genome by clicking on the NAME of the species, not the B beside it. The species name takes you to a viewer for the genome of that organism. The B takes you to a BLAST search tool (later). Click Homo sapiens (human). You see a diagram of the human chromosomes, and a search box at the top. Enter "opsin" in the box next to Search for. Click Find.  You see the diagram again, with red marks at your "hits", the locations of genes whose entries contain "opsin" as a whole or partial...

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The Tools used in Bioinformatics

NCBI Map Viewer For finding genes and gene products (RNAs and proteins) that interest you BLAST For finding genes or proteins with sequences similar to yours ClustalW For comparing your sequence with others, and lots of sequences with each other Phylip For making phylogenetic trees, which show how sequences are related to each other. Treeprint For printing phylogenetic trees PSIPRED For predicting the location of helices, pleated sheets, and transmembrane elements of proteins of unknown structure Swiss-Model For automated building theoretical structural models of your sequence based on known structures (homology modeling) Deep View (also knows as Swiss-PdbViewer) For seeing and exploring macromolecular models in three dimensions, and for manual and semiautomated homology modeling PubMed For...

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Databases used in Bioinformatics

The Databases (and their acronyms!):   Genbank, operated by NCBI (National Center for Biotechnology Information) Contains all publicly available sequences of DNA, with annotations Same DNA sequence content as EMBL (European Molecular Biology Laboratory) and DDBJ (DNA Data Bank of Japan) Swiss-Prot and TrEMBL, operated by SIB (Swiss Institute of Bioinformatics) and EBI (European Bioinformatics Institute) Contains most of the publicly available sequences of proteins, with annotations Protein Data Bank Contains all publicly availalble experimentally determined structural models of proteins and nucleic acids (determined by x-ray crystallography and NMR) Swiss-Model Repository Contains many theoretical structural models of proteins (determined by automated homology modeling) Online Mendelian...

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How to use Genbank Database

The Genbank Sequence Database is an open access,annotated collection of all publically available sequences and their protein translations. This database is produced at NCBI as the part of INSDC . For making use of Genbank follow this tutorial: Making sense of the Genbank entry of the Prokaryotic Gene. Go to: www.ncbi.nlm.nih.gov/entrez/. Select Nucleotide from search drop down menu and enter your query's accession number from Genbank. eg accession number is X01714 .The output page will be displayed which will tell you E.coli dut gene for dUTPase. Then click the test button on the text bar to generate a true flat file format of the entry and you can save your entry by choosing file save from your browser's main menu. click on the hyperlink for further details of the entry. the Genbank file...

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What is Genbank Database

GenBank is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences. GenBank (at NCBI), together with the DNA DataBank of Japan (DDBJ) and the European Molecular Biology Laboratory (EMBL) comprise the International Nucleotide Sequence Database Collaboration. These three organizations exchange data on a daily basis. GenBank grows at an exponential rate, with the number of nucleotide bases doubling approximately every 14 months. Currently, GenBank contains more than 13 billion bases from over 100,000 speci...

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Biological Databases

What Is a Biological Database? A biological database is a large, organized body of persistent data, usually associated with computerized software designed to update, query, and retrieve components of the data stored within the system. A simple database might be a single file containing many records, each of which includes the same set of information. For example, a record associated with a nucleotide sequence database typically contains information such as contact name, the input sequence with a description of the type of molecule, the scientific name of the source organism from which it was isolated, and often, literature citations associated with the sequence. For researchers to benefit from the data stored in a database, two additional requirements must be met: easy access to the information a...

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Importance of Bioinformatics

Why Is Bioinformatics So Important? Although a human disease may not be found in exactly the same form in animals, there may be sufficient data for an animal model that allow researchers to make inferences about the process in humans. The rationale for applying computational approaches to facilitate the understanding of various biological processes includes: a more global perspective in experimental design the ability to capitalize on the emerging technology of database-mining - the process by which testable hypotheses are generated regarding the function or structure of a gene or protein of interest by identifying similar sequences in better characterized organi...

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Introduction to Bioinforamtics

What Is Bioinformatics Biology in the 21st century is being transformed from a purely lab-based science to an information science as well. Bioinformatics is the field of science in which biology, computer science, and information technology merge to form a single discipline. The ultimate goal of the field is to enable the discovery of new biological insights as well as to create a global perspective from which unifying principles in biology can be discerned. At the beginning of the "genomic revolution", a bioinformatics concern was the creation and maintenance of a database to store biological information, such as nucleotide and amino acid...

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