In Silico Meet @ Department of Pharmacoinformatics (Dated: 19-September-2013)

About In Silico Meet

In Silico meet is a weekly (Every Thursday) gathering of students and faculty of Department of Pharmacoinformatics to discuss, to learn and to make other learn from there knowledge.  Each week, two speakers give presentation on topic related to latest happenings and advancements in research and technology related to interest of speaker and that matches with the departmental research interests.

Speakers of the Week

Invitation for In Silico Meet  at Dept. of Pharmacoinformatics, NIPER S.A.S. Nagar

Presentations:

Speaker #1: K. Guru Prasad

In Silico Models of Cancer

Cancers can develop from many mechanisms by individually or collective of group of mechanisms, to better understand and to intervene in mechanisms therapeutically we need In Silico models of cancer. In my talk I will briefly explain different types of network models, model development and validation followed by a case study.

{Presentation Will be Updated Soon}

Speaker#2:  Abdul Wahid Khan

Cluster computing: An Introduction

Many computations in bio-medical research such as simulations, bootstrapping, database searches (such as BLAST), and many Monte Carlo algorithms are embarrassingly parallel. This means that the computation can be split up into smaller computations; each of those calculations can be performed in parallel threads that do not need to interact with each other. Computations with this feature can be easily cluster, with a gain in speed that is approximately proportional to the number of processors. In this presentation  i introduce some of the concepts behind cluster computing, examples where they have been used, and lay out scenarios where they may be useful for bio-medical researchers in the future.

{Presentation Will be Updated Soon}

*Important*: Ask your questions below….

If you have any question or doubt about these presentations., feel free to ask questions in the comment box below.

In Silico Meet @ Department of Pharmacoinformatics (Dated: 29-Aug-2013)

About In Silico Meet

In Silico meet is a weekly (Every Thursday) gathering of students and faculty of Department of Pharmacoinformatics to discuss, to learn and to make other learn from there knowledge.  Each week, two speakers give presentation on topic related to latest happenings and advancements in research and technology related to interest of speaker and that matches with the departmental research interests.

Speakers of the Week

in silico meet invitation

Presentations

Speaker #1: Vivek Neekhra

Wireless technology in medicine

The combination of cheap wearable sensors and mobile-enabled doctor consultation could soon benefit even relatively remote communities in the developing world.  The very first thing anyone wants is healthcare for their family, but there’s shortage of physicians and even the basic needs are not being fulfilled.  Since mobile telephone signals are present everywhere and today almost everyone has access to it so we can use this wireless technology in health care system
I am going to explain Wireless technologies available, ongoing clinical trials, wireless solutions for diseases like Diabetes, Alzheimer’s and many more including FDA guidelines for approval of health aaps and above all the opportunities it brings to Informatics students.

Speaker#2: Siama Colney

ClusPro: A tool for protein-protein docking

Prediction of protein-protein interactions is one of the most challenging problems in functional genomics. Most docking methods evaluate billions of docked conformations by simple scoring functions adding to near-native structures yielding many false positive structures, with good surface complementarity but far from the native.
ClusPro, the first fully automated and a fast algorithm for filtering docked conformations with good surface complementarity was developed. The ranking is based on the clustering properties of the proteins. Basic needs are protein structures from PDB files and a valid institutional email account.

 

*Important*: Ask your questions below….

If you have any question or doubt about these presentations., feel free to ask questions in the comment box below.

 

In Silico Meet @ Department of Pharmacoinformatics (Dated: 4-Apr-2013)

About In Silico Meet

In Silico meet is a weekly (Every Thursday) gathering of students and faculty of Department of Pharmacoinformatics to discuss, to learn and to make other learn from there knowledge.  Each week, two speakers give presentation on topic related to latest happenings and advancements in research and technology related to interest of speaker and that matches with the departmental research interests.

Speakers of the Week

Presentations

Speaker #1: Abhay Mori

An Assessment and Evaluation of Scoring function for Protein Ligand Interactions

Molecular docking is a tool most widely used in the structure based drug discovery. It is used to identify or search possible best conformers of compound/s that usually bind with receptor (target protein). Many types of software are available for molecular docking; they use different scoring functions for final ranking of poses/compounds. To assess efficiency of these software, it is required to understand differences between scoring functions. A basic comparison is explained in my presentation with help of a case study.

Speaker#2: Pankaj Kumar

Druggability Propensity of protein surface to form pockets

Druggability assessment of a target protein that can bind with high affinity and specificity to small, drug-like compounds based solely on its 3D structure has been a longstanding goal of structural biologists and computational scientists. Here we discuss some of the approaches involved in pocket analysis to identify druggable pockets of targets which can play a key role in in silico drug design, which is a fundamental step in structure-based drug design.

Tips & Tricks: SCImago Journal & Country Rank: A must visit site for every researchers

SJR-Logo

The SCImago Journal & Country Rank is a portal that includes the journals and country scientific indicators developed from the information contained in the Scopus® database.

Overall as well as for specific area of research. It is with filters like Subject Area:, Subject Category:, Country: etc.

  • Journal Search:

Returns everything about journal with very nice information like Subject Category, Scope, Citation vs. Self-Citation  (for last 13 Yrs), Cites per Document (for last 13 Yrs) and etc. etc. [Example for: JACS]

  • Country Rankings: [Example: India]
  • And the best thing to do is Compare:

You can compare four  journals/Country’s at a time for parameters like:

[Example: JACS + NAR + Nature Chem. + JCIM]

ReSite: A Tool for Molecular Docking Analysis

ReSite: A Tool for Molecular Docking Analysishttps://i1.wp.com/www.niper.gov.in/pi_dev_tools/ReSite/images/resitelogo1_01.png

The image below, generated by a molecular visualizer, shows us how tedious it is to visualize and analyze the interactions of a particular ligand with its surrounding residues in a specific docked pose. Thus, ReSite focuses on reporting all the amino acid residues present in the active site, for every docked pose, that are presumed to be involved in the ligand interactions, based on a  parameter of distance constraint.

ReSite

A image showing results from Molecular Docking procedure.

Most of the interactions occur within a distance of 3-10 angstroms between the docked ligand and the respective amino acid residues of the active site. ReSite utilises this above stated range while stating the distance constraint parameter as a user input to define the surrounding residues.

Details:

Molecular Docking is a computer algorithm which predicts the preferred orientation of a rigid or flexible ligand into the binding site of the receptor and predicts the binding affinity of the complex based on scoring functions. For understanding  the structural principles that determines the strength of a protein-ligand complex, the ability to acknowledge the  residues involved in binding are required. As it is often tedious to visualize the surrounding active site residues of the various docking poses of each and every ligand, there is a need for a quick , textual presentation of these residues.

Here we present ReSite-a tool developed at Department of Pharmacoinformatics, NIPER (S.A.S. Nagar) that focuses on reporting all the residues present within a distance constraint in the active site playing a key role in protein-ligand interactions.

Download:

You can download ReSite just filling an small user registration form here.

How To Use:

Before using this Tool the user is expected to have performed molecular docking from any of the available docking software and the .exe file of this tool has been downloaded.

INPUT FILES

1. Receptor Input File (.pdb file)

The receptor .pdb file is utilized as a protein input file. The input files must be present in the same folder where the .exe file is kept.

2. Ligand Input File (.sdf file)

The ligand .sdf file generated after molecular docking has to be submitted as input.

DISTANCE CONSTRAINT

The user will be asked to enter the distance constraint value within which they would like to list the active site residues. (The range of 3-10 angstroms is where most ligand interactions take place)

OUTPUT FILE

The readable Excel Sheet Format (.csv) file will be saved in the same destination folder where the input files and .exe file is located.

Students from Department of Pharmacoinformatics (NIPER S.A.S. Nagar) develops online server “CPMD IFGen Server”: The CPMD input file generator.

The CPMD IFGen Server developed at Department of Pharmacoinformatics, NIPER (S.A.S. Nagar) helps to automate the process of extracting the coordinates of atoms from the submitted *.mol2/*.pdb file and to generate an input file (*.inp format) for CPMD calculations. The user can also edit the default parameters set by the server and add special sections required for the calculations.

Link: http://www.databases.niper.ac.in/IFGen/

Home page of CPMD IFGen web-server

Home page of CPMD IFGen web-server