Multiscale and high-throughput exploration of protein-ligand binding

A fully funded PhD position is available in the group of Prof. Tristan Bereau (tristanbereau.com) at the Institute for Theoretical Physics, Heidelberg University. We invite applications for a position at the intersection of multiscale modeling, high-throughput molecular dynamics simulations, and machine learning to efficiently explore the chemical space of thermodynamic properties. The project will focus on protein-ligand binding, estimating ligand-binding stability for large subsets of chemical space. The starting date is negotiable, preferably Fall 2023. The position includes funds for travel, visits, and publications. Both CPU and GPU computing resources are available.

About the Role

The successful candidate will focus on the development of methodologies and applications to explore the chemical space of thermodynamic properties. Our approach uses multiscale modeling, especially transferable coarse-grained models, to efficiently reduce and navigate chemical space. The project will focus on protein-ligand binding, with ample methodological development to help solve key challenges along the way.

Relevant group publications around multiscale chemical-space exploration:

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	doi	title	journal	volume	year
	10.1021/acs.jctc.3c00201	Condensed-Phase Molecular Representation to Link Structure and Thermodynamics in Molecular Dynamics	Journal of Chemical Theory and Computation	19	2023
	10.1039/D2CB00125J	CLiB – a novel cardiolipin-binder isolated <i>via</i> data-driven and <i>in vitro</i> screening	RSC Chemical Biology	3	2022
	10.1039/D2SC00116K	Data-driven discovery of cardiolipin-selective small molecules by computational active learning	Chemical Science	13	2022
	10.1038/s41597-020-0391-0	Molecular dynamics trajectories for 630 coarse-grained drug-membrane permeations	Scientific Data	7	2020
	10.1103/PhysRevE.100.033302	Controlled exploration of chemical space by machine learning of coarse-grained representations	Physical Review E	100	2019
	10.1080/00268976.2019.1601787	Revisiting the Meyer-Overton rule for drug-membrane permeabilities	Molecular Physics	117	2019
	10.1021/acscentsci.8b00718	Drug–Membrane Permeability across Chemical Space	ACS Central Science	5	2019
	10.1063/1.4987012	<i>In silico</i> screening of drug-membrane thermodynamics reveals linear relations between bulk partitioning and the potential of mean force	The Journal of Chemical Physics	147	2017
	10.1016/j.bbrc.2017.08.095	Efficient potential of mean force calculation from multiscale simulations: Solute insertion in a lipid membrane	Biochemical and Biophysical Research Communications	498	2017

About You

The ideal candidate will possess:

1. A Master degree or a four or five-year Bachelor degree in Physics or related field. Exposure to the core Phyics courses is required for the PhD degree.
2. Motivation to tackle challenging scientific projects, Openness to trying out new ideas and concepts, Strong determination
3. Teamwork, strong communication skills, and inclusive culture
4. English proficiency, both written and oral
5. Programming and machine learning experience

Doing a PhD at Heidelberg University

As the oldest university in Germany, Heidelberg University is a world-leading institution and provides an internationally recognised and collaborative environment. Joining Heidelberg University’s Institute for Theoretical Physics will give you the opportunity to:

1. Work on exciting topics at the intersection of molecular modeling and machine learning.
2. Access state-of-the-art facilities and resources.
3. Engage with a vibrant intellectual community in Heidelberg, including Simplaix, the Interdisciplinary Center for Scientific Computing (IWR), the cluster of excellence STRUCTURES, ELLIS, the Heidelberg Institute for Theoretical Studies, and Scientific Machine Learning.
4. Live in the beautiful and historic city of Heidelberg.

We welcome applications from all individuals, regardless of their gender, ethnicity, disability, or any other protected characteristic. We encourage diversity and foster a culture of inclusion where everyone feels welcome.

Application procedure

Interested candidates should submit the following via email as a single PDF:

1. Curriculum Vitae;
2. Contact information of two supervisors/collaborators to request recommendation letters;
3. Brief summary of past research projects (one or two pages).

Applications submitted by July 31, 2023 will receive full consideration.

PhD positions require acceptance to the Heidelberg Graduate School for Physics doctoral program of the Physics department. The webpage contains a more detailed list of requirements for enrollment in the doctoral program.

For more information or to apply, please contact Prof. Tristan Bereau at bereau@thphys.uni-heidelberg.de