Latest news for the Scientific Computing Research Unit
Prof Kevin Naidoo one of twenty of the country’s leading scholars and scientists was inaugurated as a Member of the Academy of Science of South Africa (ASSAf) at the annual Awards Ceremony on 10 October 2018. He is one of the four UCT scientists honoured by ASSAf.
The Nobel Prize in Medicine 2018 was awarded jointly to cancer researchers James P. Allison and Tasuku Honjo who discovered a cancer therapy that works by inhibition of negative immune regulation. Both researchers independently discovered methods of "removing the brakes" or stimulating the immune system to fight cancer - now called immune checkpoint therapy.
One of the proteins responsible, Programmed Death-1 (PD-1) protein, binds sialic acid confirming the critical role of carbohydrates in the fight against cancer (read more about this sialic acid binding immunoglobulin (Ig)-like lectin).
The 2018 Scientific Computing International Lecture Series (SCILS) visiting scholar will be Dr Niclas Karlsson (PI of Glyco Inflammatory Group at the University of Gothenburg, Sweden)
Dr Karlsson a Glycobioinformatician will present a departmental lecture titled "Osteoarthritis - A life science glycoproblem".
Dr Karlsson is the PI on the UniCarb-DB database that stores, integrates and processes data from manually annotated ms spectra glyco fragments.
The Scientific Computing Research Unit will be a hosting a workshop – “Molecular Dynamics using BRIDGE” at the 2018 CHPC National Conference. This will take place on the 6th December at the Century City Convention Centre. For more info see http://bit.ly/2C4ybCW. Please register on Google Forms and on the CHPC registration page:
Hope to see you there! Tweet to us at @scicompute with the #bridge #galaxy #chpc2018 hashtags.
INDABA 9Sunday, 02 September 2018 - Friday, 07 September 2018
Presenting at the INDABA 9 ConferenceProf Kevin Naidoo - Multidimensional Reaction Dynamics of Enzyme Catalysis Dr Chris Barnett - Computational Cancer Glycobiology: Simulation, Analysis and Visualisation
BXQ-350 is a first-of-its-kind cancer treatment that weaponizes the special mechanics of cancer to destroy it. Discovered by Xiaoyang Qi - Professor of Medicine, Co-Division Chief for Basic Science Research - BXQ-350 is a protein which can fuse to the walls of cancerous cells, causing those cells to die off.
The South African Health Minister Aaron Motsoaledi acknowledged that the national healthcare system is battling a rise in cancer cases. Some patients die before receiving treatment (Read full article).
We are developing cancer diagnostics with a focus on early detection, read more about our research.
See our Unsupervised Learning method "Denoising Autoencoder Self-Organising Map" (DASOM) although developed for the Early Cancer Diagnostics Project it is universally applicable to a wide range of applications. DASOM integrates autoencoders into a hierarchically organised hybrid model where the front-end component is a grid of topologically ordered neurons. The model maintains clustering properties but by extending and enhancing its visualisation capacity it enables an inclusion and analysis of the intermediate representative space. Download the paper for free at https://authors.elsevier.com/a/1X5v~3BBjKVz76
Prof Levitt one of the 2013 Nobel Prize laureates visited the Scientific Computing Research Unit in November 2017. Prof Levitt’s diverse interests have included RNA & DNA modelling, protein folding simulation, classification of protein folds & protein geometry, antibody modelling, x-ray refinement, antibody humanisation, side-chain geometry, torsional normal mode, molecular dynamics in solution, secondary structure prediction, aromatic hydrogen bonds, structure databases, and mass spectrometry.
We are thankful that Prof Levitt took time out of his busy schedule to engage with the students and trust he enjoyed discussing their research projects.
Public Lecture by Prof Michael Levitt, Stanford University
Birth & Future of Multiscale Modeling
Date: Friday 17th November, 2017
Venue: PD Hahn Lecture Theatre 3
Public Lecture available at http://media.uct.ac.za/engage/theodul/ui/core.html?id=4796c0df-188d-4220-bc7e-e221e5cf711a
Born in South Africa in 1947, Prof Levitt was awarded the 2013 Nobel Prize for Chemistry (shared with Martin Karplus and Arieh Warshel). Prof Levitt’s diverse interests have included RNA & DNA modelling, protein folding simulation, classification of protein folds & protein geometry, antibody modelling, x-ray refinement, antibody humanisation, side-chain geometry, torsional normal mode, molecular dynamics in solution, secondary structure prediction, aromatic hydrogen bonds, structure databases, and mass spectrometry. He has a passion in helping today’s young scientists gain the recognition and independence that his generation enjoyed.
In his talk, Prof Levitt will review how the development of multiscale models for complex chemical systems began in 1967. These same multiscale models have become increasingly popular in applications that range from simulation of atomic protein motion, to protein folding and explanation of enzyme catalysis.
October is Breast Cancer Awareness Month, which is an annual campaign to increase awareness of the disease
This is relevant to our research unit as we aim to classify cancer at the genetic and molecular (Glycan) level. Using our mechanistic understanding of glycosylation and glycolysis of tumours we design leads for molecular classes of Cancer. SCRU laboratories collaborate closely with medicinal laboratories as well as human biology laboratories to translate basic research findings into new clinical strategies for diagnosis and therapy.
Professor Jonathan W. Essex (Director of Research, Computational Systems Chemistry, Chemistry Department, University of Southampton) has been invited as part of the SCILS.
He will present a DEPARTMENTAL LECTURE on Protein-Ligand Binding by Free Energy Simulations: Issues, Successes and Failures.
Further information about Prof Essex and his research is available at https://www.southampton.ac.uk/chemistry/jessex/