TL;DR: CCK-12, the next in our series of meetings for computational chemists, cheminformaticians, and molecular modelers, will be on Tuesday, September 4th, 2018, at 5 pm in the Seminar Room, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU. Free CCK-12 tickets are available.
Dear Friends and Colleagues,
Please join us for our next “Comp Chem Kitchen”, CCK-12, at 5-6 pm on Tuesday, September 4th, 2018, in the Seminar Room, Department of Biochemistry, South Parks Road, Oxford. We are very pleased to announce Prof. Alessandro Contini from the Department of Pharmaceutical Sciences, Università degli Studi di Milano, Italy, will be speaking:
- Prof. Alessandro Contini (Department of Pharmaceutical Sciences, Università degli Studi di Milano, Italy): “Nwat-MMGBSA: mixing implicit and explicit solvation for a better prediction of relative binding energies“.
— MM-PBSA is a rather popular method, often used in binding energy calculations. Both strengths and weaknesses depend on the use of implicit solvation, that abolishes the energy fluctuations due to the rearrangement of water molecules but loses the contribution of explicit interactions between solute and solvent to the binding energy. Nwat-MMGBSA is a variant of MM-PB/GBSA thought to correct this last issue. Nwat-MMGBSA is based on including a fixed number of explicit water molecules that, in each frame of a molecular dynamics (MD) trajectory, are the closest to the ligand. The method provided improvements in the correlation between predicted and experimental binding energies in both ligand-receptor1 and protein-protein complexes,2 compared to standard MM-GBSA, with a negligible increase in cost. A set of scripts has been designed to automatically perform a structure based virtual screening workflow, including library preparation, docking, parameterization, MD and Nwat-MMGBSA rescoring, using non-commercial software.3 The full workflow, using an optimized setup, takes about 2h/ligand on a standard workstation equipped with a relatively cheap GPU card. In this talk, I will present some examples, discussing strengths, weaknesses and outlooks for this method.
1. Maffucci & Contini (2013) J. Chem. Theor. Comput., 9, 2706.
2. Maffucci & Contini, (2016) J. Chem. Inf. Model., 56, 1692.
3. Maffucci, Hu, Fumagalli & Contini, (2018) Front. Chem., https://doi.org/10.3389/fchem.2018.00043.
Get in touch if you would like to give a 5 minute talk at a future CCK on your latest research or give a quick demo your latest programming project, or even to nominate someone (students, postdocs, professionals, PIs, Emeritus Professors). The talks usually resemble one of the following styles:
- an overview of computational chemistry in your research;
- a (live!) demonstration of some software that you are developing or using; or
- a summary of a computational chemistry paper, method, programming language, or tool that you’ve seen recently.
Refreshments will be provided, including beer.
We would like to thank the University of Oxford MPLS Network and Interdisciplinary Fund for making CCK possible.
Comp Chem Kitchen is a regular forum and seminar series to hear about and discuss computational methods for tackling problems in chemistry, biochemistry and drug discovery. It focuses principally on cheminformatics, computational chemistry, and molecular modelling, and overlaps with neighboring areas such as materials properties and bioinformatics.
We’re keen to encourage people involved in coding and methods development (i.e. hackers, in the original untarnished sense of the word) to join us. Our hope is that we will share best practices, even code snippets and software tools, and avoid re-inventing wheels.
In addition to local researchers, we invite speakers from industry and non-profits from time to time, and occasionally organize software demos and tutorials.
If you’re interested in giving a talk, here are some possible topics:
- Software development (e.g.: Python, C, C++, CUDA, shell, Matlab);
- Optimizing force field parameters & EVB models;
- Cheminformatics (e.g.: RDKit);
- X-ray and NMR crystallography, including small molecule and macromolecular;
- Protein & RNA modeling, including Molecular Dynamics;
- Virtual screening and Docking;
- Machine Learning;
- Quantum Methods, including DFT.
Bring your laptops, by the way, if you have something you’d like to show!
Want to speak? Ideas for speakers?
* If you have ideas for speakers, or would like to give a talk, let us know. We also invite lightning talks of 5 minutes (or fewer) from attendees, so if you have some cool code you’ve been working on and would like to demo, bring your laptop, smartphone, tablet, (wearable?) and tell us all about it. *
Please pass this message on to friends, colleagues, and students who may be interested too!
The main CCK web site is: http://compchemkitchen.org/
Follow us on Twitter: @CompChemKitchen
See you soon! We’re looking forward to seeing and hearing about the diverse range of computational molecular science that you’re cooking up…
—Garrett, Richard, Phil and Rob