where can i find good molecular dynamics simulations papers without experimental (wet lab) counterparts. This is for computational biologist without a wet lab set up. Given that most journals require computational works supported or validated by experimental work. Wonder if there are journal that consider pure computational works without experimental work. Particularly interested in areas of protein-ligand, ion channel, membrane simulation etc.
I don't think it necessarily has to do with the journal. Good MD research gets published when it either:
A) is corroborated by wet lab, experimental data (like Stéphane Abel
said), and/orB) uses best practices for MD simulations to quantify uncertainty and sampling quality of your system
It seems like you want option B.
I have found Daniel Zuckerman's blog < http://statisticalbiophysicsblog.org/ > very helpful in understanding issues relevant to MD simulations.
I think the Best Practices checklists laid out in the papers from LiveCoMS (Living Journal of Computational Molecular Science) are a good place to start a MD-only research project. Here are a few:
Best Practices for Foundations in Molecular Simulations: https://bit.ly/2HPkcmv
Best Practices for Quantification of Uncertainty & Sampling Quality in Molecular Simulations: https://bit.ly/2H2Vj5a
Simulation Best Practices for Lipid Membranes: https://bit.ly/2J5isGj
Scientific Reports ( impact factor 4.122) accepts articles without wet lab experiments. But they ask to perform at least 50ns molecular dynamics simulation with specific software e.g. GROMACS.
I don't think it necessarily has to do with the journal. Good MD research gets published when it either:
A) is corroborated by wet lab, experimental data (like Stéphane Abel
said), and/orB) uses best practices for MD simulations to quantify uncertainty and sampling quality of your system
It seems like you want option B.
I have found Daniel Zuckerman's blog < http://statisticalbiophysicsblog.org/ > very helpful in understanding issues relevant to MD simulations.
I think the Best Practices checklists laid out in the papers from LiveCoMS (Living Journal of Computational Molecular Science) are a good place to start a MD-only research project. Here are a few:
Best Practices for Foundations in Molecular Simulations: https://bit.ly/2HPkcmv
Best Practices for Quantification of Uncertainty & Sampling Quality in Molecular Simulations: https://bit.ly/2H2Vj5a
Simulation Best Practices for Lipid Membranes: https://bit.ly/2J5isGj
I can only suggest you, ACS JCIM. You need a good story, attractive graphicsl representstion even you perform 100ns. Maybe i am wrong, but i saw numerous cases recently.
Many journals will take it. The key is importance for the general audience (HIV vs an obscure protein) and the quality of work. Additionally, they require at least 100 ns simulation time to interpret results.
Unfortunately for many journals, reviewers are not up to the task. The big name journals are OK but the rest neeeds a "retooling".
For other articles than original research (e.g. reviews, perspectives, etc), I would say most journals welcome molecular dynamics presented in the paper.
- Badges
- Science topic
- Similar topics
- Bioinformatics
- Bioinformatics and Computational Biology