COPYRIGHTED PROJECTS

Dear Readers/Followers,

I am pleased to inform you that the following projects submitted in the Bioinformatics Laboratory, Applied Botany Center, Gujarat University, Ahmedadbad is a part of the progressive projects developed in this Center with our research group. If you found any contents or disclosure of such titles for endorsement in public domain, it should be considered as 'Copyright Infringement' and no part can be reproduced in any means without the consent from the department and from me. Modifying the titles is also not allowed.
Any guide/co-guide are not involved in this projects.

KINDLY UNDERSTAND THAT THE PROJECTS MENTIONED BELOW ARE NOT DISTRIBUTED UNDER CREATIVE COMMON RIGHTS. Thank You.

1. Plant Bioactive Driven Fragment-based Drug Designing and Epitope-based Immunoinformatics Study of EspC protein of Mycobacterium tuberculosis  (Techniques : Fragment-based Drug Designing, Immunoinformatics)

2.2D-QSAR Analysis of Dihydrofolate reductase (DHFR) inhibitors with activity in Toxoplasma gondii and Lactobacillus casei  (Techniques : 2D-QSAR)

3. Pharmacophore-assisted Molecular Optimization of Calcineurin Inhibitors for Human Prion      Disease (Techniques : Molecular Docking, Pharmacophore Mapping, Manual Interpretation [Copyrighted protocol])

4. Biocomputational Analysis of Citrullinated Filaggrin Repeats for Rheumatoid Arthritis  (Techniques : Electrostatic Potential, Antigencity)

Concepts in Bioinformatics- All together in PPTS

Here, I am making it very easy to navigate and understand the key concepts of the hot spots topics.

Bioinformatics Practicals- A Complete Illustrated Guide to Beginners	http://www.slideshare.net/prasanthperceptron/bioinfo-practicals-prasanth-kumar
Epitope Prediction and its Algorithms	http://www.slideshare.net/prasanthperceptron/epitope-prediction-and-its-algorithms-7368259
Gene Order/Synteny	http://www.slideshare.net/prasanthperceptron/gene-order-7368257
Virtual Library Screening (VLS)	http://www.slideshare.net/prasanthperceptron/vls-7368188
The Mechanism of Protein Folding	http://www.slideshare.net/prasanthperceptron/the-mechanism-of-protein-folding
Sequence Alignment and its Algorithms	http://www.slideshare.net/prasanthperceptron/sequence-alignments-complete-coverage
SAGE technology	http://www.slideshare.net/prasanthperceptron/sage-technology
Proteome Databases	http://www.slideshare.net/prasanthperceptron/proteome-databases
Protein-Protein Interactions	http://www.slideshare.net/prasanthperceptron/protein-protein-interactions
Protein-DNA Interactions	http://www.slideshare.net/prasanthperceptron/protein-dna-interaction
Protein-DNA Interactions –An Illustrated Example	http://www.slideshare.net/prasanthperceptron/protein-dna-interaction-practical
Primary Databases-NCBI	http://www.slideshare.net/prasanthperceptron/primary-databases-ncbi
Pharmacophore Identification	http://www.slideshare.net/prasanthperceptron/pharmacophore-identification
Bibliographical Databases- MEDLINE	http://www.slideshare.net/prasanthperceptron/medline-7368165
In silico drug design an intro	http://www.slideshare.net/prasanthperceptron/in-silico-drug-design-an-intro
Identification of disease genes	http://www.slideshare.net/prasanthperceptron/identification-of-disease-genes
Genomics Application using GRAMENE	http://www.slideshare.net/prasanthperceptron/genomics-application-using-gramene
Gene Expression Profiling – Part I	http://www.slideshare.net/prasanthperceptron/gene-expression-profiling-i
Gene Expression Profiling – Part II	http://www.slideshare.net/prasanthperceptron/gene-expression-profiling-ii
Fragment Based Drug Designing (FBDD)	http://www.slideshare.net/prasanthperceptron/fbdd
De novo Drug Design	http://www.slideshare.net/prasanthperceptron/de-novo-drug-design
Biological Databases	http://www.slideshare.net/prasanthperceptron/biological-databases
Secondary Structural Elements with special attention to Ramachandran Plot	http://www.slideshare.net/prasanthperceptron/secondary-structural-elements-ramachandran-plot
Potential Energy Surface (PES) and Molecular Graphics	http://www.slideshare.net/prasanthperceptron/potential-energy-surface-molecular-graphics
Diagnosis of Genetic Diseases and Infectious Diseases	http://www.slideshare.net/prasanthperceptron/diagnosis-of-genetic-disorders-infectious-diseases-2188671
Softwares for Phylogenetic Analysis- What we expect?	http://www.slideshare.net/prasanthperceptron/softwares-for-phylogentic-analysis

ORganic VIrtual Library (ORVIL) – A combinatorial library construction based on organic constituents and without scaffold hopping

You can access the abstract and full text article at http://indianjournals.com/ijor.aspx?target=ijor:ijaritac&volume=2&issue=2&article=006

ABSTRACT                                                                                                                                

Rapid construction of virtual combinatorial library is a prerequisite for in silico library enumeration and design. ORganic VIrtual Library (ORVIL) is a perl program to generate a combinatorial library using most frequently observed 200 organic substituents. It is designed to explore the organic chemical space in the given query structure without affecting the entire backbone of the molecule enabling minimum molecular complexities. Its particular features are its simplicity to use, portable SMILES format and high speed of library construction. Benchmarking of Tamoxifen (drug for breast cancer) was performed which revealed a compound having similar architecture of known drug analogue, Toremifene.

Keywords: virtual combinatorial library, organic substituents, molecular complexities, SMILES format

THE BLESSINGS OF MANAKULA VINAYAGAR

The blessings of Manakula Vinayagar is always showered on me and I pray my god to bless me forever for success and prosperity in my life and the people around me. Shown image is of Shri Manakula Vinayagar, Pondicherry.

COMPUTATIONAL STUDIES ON THE INTERACTION OF CORE HISTONE TAIL DOMAINS WITH CpG ISLAND

S. PRASANTH KUMAR 1, RAVI G. KAPOPARA 1,YOGESH T. JASRAI 1 AND RAKESH M. RAWAL 2.

1. Bioinformatics Laboratory, Department of Botany, University School of Sciences,
Ahmedabad- 380 009. 2. Division of Medicinal Chemistry and Pharmacogenomics, Department of Cancer Biology, Cancer & Research Institute (GCRI), Ahmedabad- 380 016.


Download the accepted galley proof here:
http://www.ijpbs.net/vol-3/issue-1/bio/B%20-%2068.pdf
Copyrights Reserved- International Journal of Pharma and Bio Sciences.

ABSTRACT:

It has been elucidated through in vitro studies that core histone tail domains preferentially interact with linker DNA. In the present study, we studied these interaction computationally using molecular docking and isocontour-based electrostatic map approach in order to identify the domains and regions of H3 and H4 tails and DNA contributing for the physical associativeness. We also explored the interaction made by the linker DNA containing methylated CpG dinucleotides (CpG island) with the normal and post-translational modified histone tails. We report that these interactions are electrostatically unfavored if one of the biomolecular partners is methylated thereby negatively charged zones of DNA and histone tails are required to be absent nearby.

KEYWORDS: Core histone tail domain, linker DNA, CpG island, Molecular docking, Isocontour-based

electrostatic potential map.

Here is the snapshot of a study undergone:

MY RESEARCH PROFILE

Dear Followers/Readers/Bloggers,

Wanna know more about me. Here is my CV
http://www.slideshare.net/prasanthperceptron/prasanth-kumar-cv-8494674

UPLOADING SEQUENCES TO THE DATABASES/SEQUENCE SUBMISSIONS

Sequence can be submitted in NCBI GenBank using:

1. Sequin
2. BankIt

Sequin

Sequin is a stand-alone software tool developed by the National Center for Biotechnology Information (NCBI) for submitting and updating sequences to the GenBank, EMBL, and DDBJ databases. Sequin has the capacity to handle long sequences and sets of sequences (segmented entries, as well as population, phylogenetic, and mutation studies). It also allows sequence editing and updating, and provides complex annotation capabilities. In addition, Sequin contains a number of built-in validation functions for enhanced quality assurance.

File Formats Accepted

Sequin normally expects to read sequence files in FASTA format. Note that most sequence analysis software packages include FASTA or "raw" as one of the available output formats. Population studies, phylogenetic studies, mutation studies, and environmental samples may be entered in either FASTA format, or in PHYLIP, NEXUS, MACAW, or FASTA+GAP formats if you are submitting an alignment.

Creating a Submission

Sequin is organized into a series of forms for entering submitting authors, entering organism and sequences, entering information such as strain, gene, and protein names, viewing the complete submission, and editing and annotating the submission. The goal is to go quickly from raw sequence data to an assembled record that can be viewed, edited, and submitted to your database of choice.

Submitting Authors Form: The pages in the Submitting Authors form ask you to provide the release date, a working title, names and contact information of submitting authors, and affiliation information.

Submission page: This page asks for a tentative title for a manuscript describing the sequence and will initially mark the manuscript as being unpublished. When the article is published, the database staff will update the sequence record with the new citation. This page also lets you indicate that a record should be held confidential by the database until a specified date, although the preferred policy is to release the record immediately into the public databases. It also contains pages of contact, author and author’s affiliation.

Sequence Format Form: Submission Type: Single Sequence if you have a single contiguous mRNA or genomic DNA sequence.  Segmented Sequence if you have a single collection of non-overlapping, non-contiguous sequences that cover a specified genetic region from a single source. A standard example is a set of genomic DNA sequences that encode exons from a gene along with fragments of their flanking introns. Gapped Sequence if you have a single non-contiguous mRNA or genomic DNA sequence. A gapped sequence contains specified gaps of known or unknown length where the exact nucleotide sequence has not been determined. Sequence Format: FASTA, FASTA+GAP, NEXUS, PHYLIP,etc. Then we have to fill Organism page and Annotation page (this is optional) before final submission. Now, the program will supply an automatic identifier which will be used for deposition in database and for future correspondence.

BankIt

BankIt is a web based tool developed by the National Center for Biotechnology Information (NCBI) for submitting and updating sequences to the GenBank,

Creating a Submission

Contact Information: Name, address, phone number, fax number and email address of the submitter must be entered when registering and submitting for the first time

Release date information: Immediately after it is processed at NCBI or on a date the submitter specifies

Reference information: Sequence authors: names of the researchers who are credited with the sequence Publication information: Unpublished, In-Press, or Published; and applicable citation information (paper's title, authors, journal title, volume, issue, year, pages)

Submission Category and Type: Original sequencing or Third Party Annotation

Single sequence, sequence set (phylogenetic, population, environmental, etc), or batch

Nucleotide sequence(s): Input (cut-and-paste) single or multiple sequences or Upload them as a FASTA file; FASTA files should include organisms in their definition lines

Sequences must be at least 200 nucleotides long (unless they are complete exons, non-coding RNAs (ncRNAs), microsatellites or ancient DNA)

Molecule type: what was sequenced? (genomic DNA, mRNA, genomic RNA, cRNA, etc)

Topology: linear or circular (circular must be complete, such as a complete plasmid)

Organism name, applicable source modifiers, location : Genus and species names (if not previously provided in FASTA file) If name is new or unrecognized, provide best known taxonomic lineage If genus and/or species names are not known, provide most specific name known (for example:Bacillus sp., Uncultured bacterium, Uncultured archaeon) Most complete name for any synthetic vector (for example: Cloning vector pAB234, Transfer vector p789Abc) Source modifiers include: strain, clone, isolate, specimen-voucher, isolation-source, country Location: organelle (mitochondrion, chloroplast, etc); map and/or chromosome

Features of the sequence: Upload files or use input forms to add all applicable features (for example: CDS, gene, rRNA, tRNA, microsatellite, exon, intron)