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A list of all the posts and pages found on the site. For you robots out there is an XML version available for digesting as well.
Pages
About me
Martin’s homepage
Posts
Controlling PyMol from afar
Published:
Do you keep downloading .pdb and .sdf files and loading them into PyMol repeatedly?
Fine-tune generated molecular poses with a force field
Published:
Some molecular pose generation methods benefit from an energy relaxation post-processing step.
Molecular conformation generation with a DL-based force field
Published:
Deep learning (DL) methods in structural modelling are outcompeting force fields because they overcome the two main limitations to force fields methods – the prohibitively large search space for large systems and the limited accuracy of the description of the physics1.
M. Baek and D. Baker, “Deep learning and protein structure modeling,” Nat Methods, vol. 19, no. 1, pp. 13–14, Jan. 2022, doi: 10.1038/s41592-021-01360-8. ↩
Ligands of CASF-2016
Published:
CASF-2016 is a commonly used benchmark for docking tools. Unfortunately, some of the provided ligand files cannot be loaded using RDKit (version 2022.09.1) but there is an easy remedy.
Bad chemistry in old protein-ligand binding complex data set
Published:
The Astex Diverse set1 is a dataset containing the crystallized poses of 85 protein-ligand complexes. It was introduced in 2007 to address problems in previous datasets such as incorrect ligand representation.
Hartshorn, M. J. et al. Diverse, high-quality test set for the validation of protein−ligand docking performance. J. Med. Chem. 50, 726–741 (2007). ↩
portfolio
Portfolio item number 1
Short description of portfolio item number 1
Portfolio item number 2
Short description of portfolio item number 2
publications
Paper Title Number 1
Published in Journal 1, 2009
This paper is about the number 1. The number 2 is left for future work.
Recommended citation: Your Name, You. (2009). "Paper Title Number 1." Journal 1. 1(1).
Download Paper | Download Slides
Paper Title Number 2
Published in Journal 1, 2010
This paper is about the number 2. The number 3 is left for future work.
Recommended citation: Your Name, You. (2010). "Paper Title Number 2." Journal 1. 1(2).
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Paper Title Number 3
Published in Journal 1, 2015
This paper is about the number 3. The number 4 is left for future work.
Recommended citation: Your Name, You. (2015). "Paper Title Number 3." Journal 1. 1(3).
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Paper Title Number 4
Published in GitHub Journal of Bugs, 2024
This paper is about fixing template issue #693.
Recommended citation: Your Name, You. (2024). "Paper Title Number 3." GitHub Journal of Bugs. 1(3).
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talks
Talk 1 on Relevant Topic in Your Field
Published:
This is a description of your talk, which is a markdown file that can be all markdown-ified like any other post. Yay markdown!
Conference Proceeding talk 3 on Relevant Topic in Your Field
Published:
This is a description of your conference proceedings talk, note the different field in type. You can put anything in this field.
teaching
Teaching experience 1
Undergraduate course, University 1, Department, 2014
This is a description of a teaching experience. You can use markdown like any other post.
Teaching experience 2
Workshop, University 1, Department, 2015
This is a description of a teaching experience. You can use markdown like any other post.