Top Canadian Universities 2015

Total govt run universities in canada=80. 

This year’s QS World University Rankings  features a total of 26 Canadian universities within the top 800 universities worldwide. Of these, three top universities in Canada are ranked within the global top 50, and a further 10 in the top 300. Read on to find out more about the top universities in Canada this year, starting with the top 10.

1. McGill University
2. University of Toronto 
3. University of British Columbia
4. University of Alberta
5. Université de Montréal
6. McMaster University
7. University of Waterloo 
8. Western University 
9. University of Calgary
10. Queen’s University
11. Simon Fraser University – ranked 225th in the world.
12. Dalhousie University – ranked joint 277th in the world.
13. University of Ottawa – ranked joint 284th in the world.
14. University of Victoria – ranked joint 319th in the world.
15. Laval University – ranked joint 324th in the world.
16. Concordia University – ranked 411-420 in the world.
17. Université du Québec – ranked 431-440 in the world 
18. York University – ranked 441-450 in the world.
19. University of Saskatchewan – ranked 451-460 in the world.
20. University of Guelph – ranked 471-480 in the world.
21. Carleton University – ranked 501-550 in the world.
22. University of Manitoba – ranked 551-600 in the world.
23. Memorial University Of Newfoundland – ranked 601-650 in the world.
24. Université de Sherbrooke – ranked 601-650 in the world.
25. University of Windsor – ranked 651-700 in the world.

26. Ryerson University – ranked 701+ in the world.

The rest of the university that did not make it to the list are:

Athabasca University

Acadia University

Algoma University

Bishop's University

Brandon University

Brock University

Cape Breton University

Capilano University

Dominican University College

École de technologie supérieure

École nationale d'administration publique

École Polytechnique de Montréal

Emily Carr University of Art and Design

First Nations University of Canada

Grant MacEwan University

HEC Montréal

Institut national de la recherche scientifique

Kwantlen Polytechnic University

Lakehead University

Laurentian University

Mount Allison University

Mount Royal University

Mount Saint Vincent University

Nipissing University

NSCAD University

Queen's University

Royal Military College of Canada

Royal Roads University

Saint Francis Xavier University

Saint Mary's University

Saint Paul University

St. Thomas University

Thompson Rivers University

Trent University

Université de Moncton

Université de Saint-Boniface

Université du Québec à Chicoutimi

Université du Québec à Rimouski

Université du Québec à Trois-Rivières

Université du Québec en Abitibi-Témiscamingue

Université du Québec en Outaouais

Université Sainte-Anne

University College of the North

University of King's College

University of Lethbridge

University of New Brunswick

University of Northern British Columbia

University of Ontario Institute of Technology

University of Prince Edward Island

University of Regina

University of the Fraser Valley

University of Winnipeg

Vancouver Island University

Wilfrid Laurier University

Pokcet finding alogorithms (incomplete list)

• SplitPocket

• A web server to identify functional surfaces of protein from structure coordinates.

• LIGSITEcsc

• A web server for the automatic identification of pockets on protein surface using the Connolly...

• KVFinder

• A highly versatile and easy-to-use tool for cavity prospection and spatial characterization....

• pocketZebra

• Web-server for selection and classification of subfamily-specific binding sites by bioinformatic...

• PocketPicker

• An automated grid-based technique for the prediction of protein binding pockets that specifies...

• metaPocket

• A meta server to identify ligand binding sites on protein surface.

• fpocket

• An open source protein pocket (cavity) detection algorithm based on Voronoi tessellation.

• PLB_SAVE

• Predicts protein-ligand binding region by computing features of solid angle, volume and depth.

• CCCPP

• Computes the void parts of the proteins, i.e. cavities, channels and pockets. The present...

• SURFNET

• Generates molecular surfaces and gaps between surfaces from 3D coordinates supplied in a...

• PocketAnalyzer(PCA)

• An automated approach to diverse pocket selection. PocketAnalyzer(PCA) combines a geometric...

• CASTp

• An online tool that locates and measures pockets and voids on 3D protein structures. CASTp...

• LISE

• A web server for a novel method for predicting small molecule binding sites on proteins.

• PocketFEATURE

• Focuses on pockets using the FEATURE system for characterizing microenvironments. The method is...

• ConCavity

• A small molecule binding site prediction algorithm that integrates evolutionary sequence...

• ghecom

• A program for finding multi-scale pockets on protein surfaces using mathematical morphology.

• POCASA

• An automatic program that implements the algorithm named Roll which can predict binding sites by...

• Methods for the prediction of protein-ligand binding sites for structure-based drug design and virtual ligand screening

• Authors: Laurie, A.T., and Jackson, R.M. Abstract: Structure Based Drug Design (SBDD) is a...

• Epock

• An efficient command-line tool that calculates pocket volumes from Molecular Dynamics (MD)...

• PockDrug

• Predicts pocket druggability, efficient on both; estimated pockets guided by the ligand proximity...

Running Antechamber for a new modified Amino Acid

S-benzylated-Cysteine  parameter generation

Using Amber 12 /AmberTools13/ Gaussian-09

Take the non-std residue attached to two adjacent amino acids (AA)
and create tripeptide.pdb from the original crystal structure containing the modified AA.

Steps to follow:-

Open xleap and do the following
Note: if having problem in Menu bars in Xleap, make sure the NUM LOCK key is OFF before starting Xleap

> source leaprc.ff12SB
> AA = loadmol2 BCS_final.mol2
> edit AA to remove the ajacent AA's.
Now added hydrogen to BCS . two H-atoms gets added. one for  NH and one for CO atoms.

Saved pdb in xleap
> savepdb AA BCS_AA.pdb
> quit

Used it as input to Antechamber to generate a DAT file.

user@localuser$ antechamber -i BCS_AA.pdb -fi pdb -o  BCS_AA_char.dat -fo gcrt -gv 1 -ge BCS_AA.gesp

Run GAUSSIAN-09 on the DAT file
user@localuser$  g09 BCS_AA_char.dat > BCS_AA_char.out

Use the OUT file to generate ESP file using espgen
user@localuser$ espgen -i BCS_AA_char.out -o BCS_AA_char.esp

Use ESP file to generate PREPIN file using Antechamber
user@localuser$ antechamber -i BCS_AA_char.out -fi gout -o BCS_AA_char.prepin -fo prepi -c resp -s 2 -rn BCS -at amber -nc 0

Note: above " i used "0" for flag -nc since the AA is neutral charge.
For negative charge modified AA in the likes of GLU/ASP -nc -1; Similarly for ARG/LYS like AA use "+1"

Use parmchk to test if all the parameters we require are available.
parmchk -i BCS_AA_char.prepin -f prepi -o BCS_AA_char.frcmod

Open xleap
>Loadoff BCS_AA_char.prepin

Enter "list" to see if BCS is added
>list
Edit BCS and delete the extra H atoms added.
>edit BCS

#check for charge after deleting atoms.
>charge BCS
Since my molecules net charge should be "0"
I had to add +0.3XXX to "N" to make the net charge "0"
This is done by selecting the atoms in Xleap.-> Edit-> Selected Atoms
which displays a table. Both 1st and 2nd column can be appropriately changed to suit ur needs.


Also change N-terminal N TYPE from "NT" to "N"
Save table by  "Save and Quit
-------------------------------------------------
Check if all is well by loading the tripeptide with BCS in middle(PRO_BCS_VAL.pdb) in tleap
using the following xleap script

xleap -s -f tleap.in

---------tleap.in------------
verbosity 2
logFile logsteps.x
source /usr/soft/amber12/dat/leap/cmd/leaprc.ff12SB
loadamberparams BCS_AA_char.frcmod
loadoff BCS_AA_char.lib
res = loadpdb ../tripep.pdb
saveAmberParm res res.prmtop res.inpcrd
--------------
No error should be displayed, Ur ready now

Happy Simulation  of your protein with a non-standard residue.

International Conference on Biomolecular Forms and Functions 2013

International Conference on Biomolecular Forms and Functions is being organised at the instittute founded by G.N Ramachandran to mark "50 years of Ramachandran Map".
For more details http://icbff2013.com/

Hero FIH Road to London Olympic Hockey Qualifiers

 The schedule for qualifier matches

for more details refer 

http://www.bharatiyahockey.org/calendar/calbulletins.asp?year=2012&mon=feb&bkmark=Hyderabad

Date	Time (IST)	Women's	Time (IST)	Men's
Feb 18	5:50 pm	India vs. Ukraine	7:50 pm	India vs. Singapore
Feb 19	5:50 pm	India vs. Canada	7:50 pm	India vs. Italy
Feb 21	5:50 pm	India vs. Poland	7:50 pm	India vs. France
Feb 22	5:50 pm	India vs. South Africa	7:50 pm	India vs. Canada
Feb 24	5:50 pm	India vs. Italy	7:50 pm	India vs. Poland
Feb 25	2:50 pm, 5:20 pm, 7:50 pm (W)		5th vs. 6th, 3rd vs. 4th, 1st vs. 2nd
Feb 26	2:50 pm, 5:20 pm, 7:50 pm (M)		5th vs. 6th, 3rd vs. 4th, 1st vs. 2nd

XX IRT - 20th International Roundtable on Nucleosides, Nucleotides and Nucleic Acids

Event    XX IRT - 20th International Roundtable on Nucleosides, Nucleotides and Nucleic Acids

Dates   Sunday to  Thursday, 5th to 9th August 2012

Place    Centre Mont-Royal, Montréal, Québec, Canada

Organisers

Masad J. Damha (McGill University)
Christopher J. Wilds (Concordia University)
Robert H.E. Hudson (University of Western Ontario)

Synopsis

The previous 19 international roundtables in this series have proved popular with academia and industry alike, and have attracted in excess of 400 attendees in recent years. This independent Roundtable is organised under the auspices of the IS3NA (International Society of Nucleosides Nucleotides and Nucleic Acids).    

The second circular is attached.  We will have a strong and varied program of plenary sessions  (see below) and contributed lectures.  Plenary lectures will be delivered by internationally-recognized scientists, including the Montgomery and Imbach-Townsend Awardees.  We will have a dynamic and engaging programme with varied cutting-edge research in medicinal chemistry, biochemistry, and molecular biology, as well as synthetic and therapeutic applications of nucleosides and oligonucleotides.
  

Dates to Note

1st February    - Conference registration opens
30th April        - Deadline for abstract submission
14th May         - Deadline for early registration
15th July          - Online registration closes
5th-9th August - XX IRT Conference, downtown Montréal, Canada 

Calh for Papers  

The call  for abstracts for both for standard talks and for posters is now open.  Please refer to the website to download a template.  Submission closes on 30th April.

  

Themes and Programme

Themes of the Roundtable are: 

Nucleos(t)ides (medicinal chemistry/mechanisms)
Oligonucleotides (medicinal chemistry/mechanisms)
Structure/Macromolecular Recognition
Biochemistry/Chemical and System Biology/Evolution
Supramolecular/Functional Nucleic Acids
Probes, Methods and Nucleoside/Nucleotide Reagents

Confirmed principal speakers are: 

Serge Beaucage, US Food and Drugs Administration, USA
C Frank Bennett, Isis Pharmaceuticals, USA
Tom Brown, University of Southampton, UK
Cynthia Burrows, University of Utah, USA
David Corey, UT Southwestern Medical Center, USA
Martin Egli, Vanderbilt University, USA
Carlos González, Instituto de Quimica-Fisica Rocasolano. CSIC, Spain
Matthias Götte, McGill University, Canada
Michal Hocek, Academy of Sciences of the Czech Republic, Czech Republic
Eric T Kool, Stanford University, USA
Emily Leproust, Agilent, USA
Muthiah Manoharan, Alnylam Pharmaceuticals, USA
Chris McGuigan, Welsh School of Pharmacy, UK
Dinshaw J Patel, Memorial Sloan-Kettering Cancer Center, USA
Enrique Pedroso, University of Barcelona,Spain
Oliver Seitz, Humboldt-University zu Berlin, Germany
Hanadi Sleiman, McGill University, Canada
Michael Sofia, Pharmasset, USA
David N Standring, Idenix Pharmaceuticals Inc, USA
Piotr Strazewski, University Claude Bernard Lyon 1, France
Jack Szostak, Howard Hughes Medical Institute, USA

 

Features and Registration

This four-day conference will include two dedicated scientific poster sessions, trade exhibition and conference banquet among other features.   Registration fees range from CAN $ 325 to CAN $ 925.

In Nature Vs. Nature, Nature May Not Win

Repost of  

Subject: In Nature Vs. Nature, Nature May Not Win

      By GINA MARANTO
      
     S everal weeks ago, when 170 Michigan schoolchildren were infected
     with hepatitis A after eating tainted strawberries imported from
     Mexico, the nation wondered what other viruses and bacteria might
     be hitching a ride across the border on foodstuffs.
     
     Microorganisms, it turns out, are but a tiny part of a growing
     problem. Every day hordes of foreign insects, plants, and animals
     infiltrate the United States.
     
     There are 500 million plants flowing into the United States each
     year -- about 80 percent through the Port of Miami -- and tons of
     fresh fruit, vegetables and grains where alien insects can hide
     out. In Florida alone, state biologists have tallied some 1,300
     established alien plant species, some of which have despoiled
     uncounted acres.
     
     Today the scale of the international traffic in flora and fauna is
     so vast -- and the resulting hazards to agriculture and ecosystems
     potentially so great -- that there is a whole branch of science
     devoted to the militaristic sounding study of "invasion biology."
     
     How, then, should one react to the news that scientists, in an
     attempt to deal with what are variously called aliens, immigrants,
     xenophytes or, simply, introduced species, are opting to bring in
     still more exotic species? Isn't this foolhardy?
     
     For example, the U.S. Department of Agriculture is about to do a
     controlled release of the snout beetle near Loxahatchie to try to
     get rid of the Australian melaleuca, a tree which is spreading
     across the Everglades at a rate of about 35 acres a day, forming
     dense thickets that crowd out native plants. The snout beetle, also
     known as the melaleuca weevil, is one of the most tested bugs in
     history, so it probably won't wind up eating mahogany or palms
     instead of melaleuca.
     
     But the snout beetle isn't the only foreign bug that is being
     drafted to gobble up a pest. Researchers in Gainesville, Fla., have
     finished up Brazilian field tests of a parasitic fly, the phorid
     fly, that can kill non-native fire ants, which have decamped in 11
     southern states, by laying eggs upon the ants' bodies. The
     researchers hope to do outdoor tests in Gainesville this summer and
     then to turn the flies loose in nature. Spectacular Goofs
     
     This strategy, known as biological control -- fighting nature with
     nature -- has had some spectacular failures. Take the cane toad.
     Imported by Australia in the 1930s to oblige sugar cane growers --
     against the dire advice of a naturalist named Walter W. Froggatt --
     the poisonous cane toad was meant to get rid of a beetle that was
     devastating the sugar cane crops.
     
     However, explains herpetologist Walter Meshaka, Jr., supervisory
     curator at the Everglades Museum, "Beetles fly at night and were
     inaccessible to the toads." So the voracious toads ate everything
     else, having a field day in an under-exploited niche. Soon 102
     toads turned into a trillion.
     
     Or think of that staple of ecology textbooks, the Indian mongoose,
     which Hawaii imported to eat rats that were overrunning cane
     fields. Between 1883 and 1885, the mammals were brought in, leading
     not only to a small drop in the rat population but to the
     destruction of ground-nesting native birds throughout the islands.
     
     Then there was Kudzu. Although not technically a biocontrol agent,
     this Japanese plant was planted across the American South during
     the 1930s as an erosion buster; it now blankets whole landscapes,
     ruining native habitats.
     
     Or recall the arrival of tilapia, a fish meant to take care of
     hydrilla, a runaway exotic aquatic plant that clogs Florida
     waterways: The tilapia didn't make a major dent in the problem they
     were supposed to solve but they did manage to drive out native
     fish, especially large-mouth bass, the prime freshwater sport fish.
     
     It is cases like these that make ecologists frown on using
     vertebrates and amphibians as controls.
     
     Yet there have been successes, cases where insects imported to take
     care of a runaway colleague or an invasive plant have done their
     work, with limited impact on other species. Parasitic wasps have
     proved helpful in California's orchards. Beetles from Europe and
     northern African have pushed Klamath weed out of some 5 million
     acres of rangeland in the West. In the South, flea beetles have
     thwarted alien alligator weed.
     
     Peter Room, an entomologist at the Center for Tropical Pest
     Management in Brisbane, Australia, has had successes all over the
     world with a Brazilian beetle. First he cleared 500 acres in Lake
     Moondarra of a free-floating aquatic species called Salvinia
     molesta. Then, he introduced the beetle to Sri Lanka, India,
     Zambia, Kenya, Fiji and Malaysia.
     
     When the costs and benefits of the Sri Lanka project were tallied,
     the return for every $1 spent was $53, and farmers were saved 1,673
     hours of clearing salvinia for every hour of work by scientists.
     
     It's no wonder that in the 1960s, biological controls were touted
     as the "green" alternative to pesticides and herbicides. But now
     the supporters of biocontrols are duking it out with skeptical
     ecologists over what "success" and "safety" really mean.
     
     And some former supporters of biological controls, notably Daniel
     Simberloff, a biologist at Florida State University, have changed
     their minds. Mr. Simberloff suggests that the impact of biocontrols
     on natural systems has not been adequately assessed and they should
     be a last resort.
     
     Of course, as the ecologists are battling it out, exotic species
     that are not part of any controlled program are coming to our
     shores every day, with the possibility of wreaking havoc. In its
     1993 report the Office of Technology Assessment said the nation
     spends at least hundreds of millions of dollars each year to
     extirpate exotic species that endanger native species or threaten
     agriculture.
     
     Biocontrols are, naturally, also subject to the law of unintended
     consequences. Even though scientists may know a fair amount about
     an ecosystem, they can never predict with complete accuracy what
     will happen when they release a new exotic species.
     
     But after all is said and done, taking a considered risk may be
     better than sitting around while the invading hordes run riot.