Talking with NVIDIA

We are pleased that Paul Graham, Senior Solutions Architect and Alan Gray, Senior Developer Technology Engineer from NVIDIA are going to give an online talk about GPUs and accelerating biomolecular simulations on 10 March 2021. Details and registration (by 8 March) at www.ccpbiosim.ac.uk/gpu2021.

Special Seminar on Entropy

This was the first CCPBioSim Special Seminar. Richard Henchman (University of Manchester) spoke about Entropy Analysis of Molecular Systems over Every Degree of Freedom. In case you missed it, want to watch it again, or want to share with friends, the recording is now available to view at https://youtu.be/Q5WKnayisHU.

Abstract: The stability and flexibility of biomolecules are inherent to their properties and function. Entropy is central to both these quantities, first because it is a key component of the free energy, which governs stability, and second because it expresses the probability distribution over all degrees of freedom in a single number. While there are methods to evaluate entropy for specific cases and while there are many partial measures of molecular
flexibility, a general way to evaluate the entropy and full probability distribution is lacking for systems of biomolecular interest. To address this, we present the Multiscale Cell Correlation (MCC) method [1-2] which calculates entropy in a multiscale fashion in terms of cells of correlated units. We apply it to two cases: host-guest complexes [3] and proteins [4]. Binding free energies in the recent SAMP8 Challenge give a 1 kcal mol−1 error, and protein entropies closely match values from normal mode analysis. MCC explains how entropy is distributed over all degrees of freedom in each system. For binding, as expected, the entropy loss of the binding guest is offset by the gain in the released water. In proteins, entropy in the polymer chain is found to be comparable to that within the residues, and the residue entropy is largely independent of solvent exposure due to a compensation between conformational and vibrational entropy.
[1] J. Higham, S. Chou, F. Gräter, R. H. Henchman, Mol. Phys., 2018, 116, 1965.
[2] H. S. Ali, J. Higham, R. H. Henchman, Entropy, 2020, 21, 750.
[3] H. S. Ali, A. Chakravorty, J. Kalayan, S. P. de Visser, R. H. Henchman, submitted.
[4] A. Chakravorty, J. Higham, R. H. Henchman, J. Chem. Inf. Model., 2020, 60, 5540.

SlimMD

We are delighted to announce the release of our easy-to-use repository of MD simulation trajectories slimMD.

All trajectory files are smaller than 1GB, and are named so as to be automatically read by VMD for your convenience.

They can be accessed from the “slimMD” tab at the top of the CCPBioSim webpage.

Alternatively, you can do directly to the trajectories here:

https://www.ccpbiosim.ac.uk/slimmd

and provide feedback on slimMD here:

https://www.ccpbiosim.ac.uk/slimmd/slimmd-feedback

If there are simulations you would like to see in slimMD which are not yet available, then you can request trajectories from our wider community here:

https://www.ccpbiosim.ac.uk/slimmd/slimmd-trajectory-request

If you have a simulation trajectory you would like to donate, then we would be very grateful! You can find instructions and the upload form here:

https://www.ccpbiosim.ac.uk/slimmd/slimmd-submit

Enjoy – and please do let us know how you get on!!

HPC and Covid-19

Syma Khalid and Jon Essex gave a seminar hosted by ARCHER2 UK National Supercomputing Service in November 2020 about the work that HECBioSim has been doing to help the fight against Covid-19. This is a great introduction to the science behind the virus and the role of computational research in finding potential treatments. The talk can be seen here.

Online Training Week October 2020

This October CCPBioSim hosted our first online training week. There were three plenary research seminars by Syma Khalid (University of Southampton), Prem Chapagain (Florida International University, USA) and Viv Kendon (Durham University; Chair of CCP-QC). The other sessions were: Introduction to Software Installation for Biomolecular Simulations, The Basics of Biomolecular Simulations, Seeing Biomolecules with VMD, Setting up an AMBER Simulation, Trusting Your Simulations, Structural Bioinformatics of Variants: Principles and Tools to Study Genetic Variants in the Context of Protein Structure, Validating Biomolecular Structures with ISOLDE, Docking with HADDOCK, How to Interpret Your Docking Scores: A Medicinal Chemistry Perspective, BioSimSpace in Jupyter, Materials Modelling Force Fields: Successes and Limitations, When Cryo-EM Meets Biomolecular Simulations, Large Scale Modelling with DL_MESO, and Modelling Enzymes with QM/MM. Our training programme was colour coded to help participants decide which sessions were best for them (inspired by the coding of mountain bike trails and ski slopes). Green is easy, blue is intermediate and red is advanced. Recordings (with the speakers permission) of many of the lectures are available on our YouTube channel.

 

Everything went smoothly including the scaling up of our containerised cloud resources. There were 450 registered participants with up to 187 joining at any one time. This resulted in 1122 training days. Our usual in-person training events typically have 20-40 participants, so being able to reach so many people was exciting. We had participants from Asia, Europe, Africa, South America, and North America. It was great to have so many people, but a bit hard to juggle the different time zones. The feedback was very positive. Quotes from the participants included "The workshop was a great success. I like how well you have adapted it for more massive online event, while the participants were still well supported." "It was absolutely informative, interactive and very motivating" "Wonderful. Please continue to provide such training courses. Many thanks!"

 

We would like to thank all the participants and lecturers for making the event a great success!

Imperial Physics of Life Seminar Series

The Physics of Life Network at Imperial College London is hosting a seminar series. These online seminars are available to anyone who is interested (not just members of the college). The first talk will be by Prof Margaret Gardel (University of Chicago) on 18 September 2020,15:00 - 16:00 (British time). See the link below for full details.

https://www.imperial.ac.uk/physics-of-life/physics-of-life-seminar-series/

 

Community Letter

A Community Letter Regarding Sharing Biomolecular Simulation Data for COVID-19 can be found here. The community aims to support open science and high quality reproducible computational biology.

COVID-19 Molecular Structure and Therapeutics Hub

MolSSI and BioExcel have gathered structures, models and simulations relating to the SARS-CoV-2 corona virus.

60th Anniversary Meeting of the British Biophysical Society

The British Biophysical Society is holding a virtual meeting the week beginning 14 September 2020. More information can be found here. There are satellite meetings on bacterial cell envelopes and small angle scattering.

Save the Date - Training

CCPBioSim will be hosting a virtual training week 5 - 9 October 2020. The event page has all the details. Registration will open in early September.