Sign in

Farzin Sohraby

@farzinsohraby.bsky.social
16 followers 24 following 0 posts

Computational Structural Biologist working with Enhanced Sampling Molecular Dynamics simulation, ligand (un)binding and protein design.

PostsRepliesMedia
Reposted by Farzin Sohraby
Ariane Nunes Alves @anunesalves.bsky.social · 31/07/2025
This paper is now accepted at JPC Letters! pubs.acs.org/doi/10.1021/... @unisyscat.bsky.social @tuberlin.bsky.social #compchem
pubs.acs.org
Symmetric Ligand Binding Pathways and Dual-State Bottleneck in [NiFe] Hydrogenases from Unbiased Molecular Dynamics
[NiFe] hydrogenases make up a family of enzymes that can be used to produce biofuel, thus making them important for industrial applications. In this work, we utilized unbiased molecular dynamics simu...
1136
Reposted by Farzin Sohraby
Ariane Nunes Alves @anunesalves.bsky.social · 08/08/2025
Tour with my research group yesterday at the Natural History Museum in Berlin! With T. rex skull in the back! @farzinsohraby.bsky.social
051
Reposted by Farzin Sohraby
Ariane Nunes Alves @anunesalves.bsky.social · 03/06/2025
We also observe that the main bottleneck for ligand binding can shift between two states with different bottleneck widths, a feature which can be exploited to modulate the access of small molecules to the catalytic site of [NiFe] hydrogenases. (3/3)
041
Reposted by Farzin Sohraby
Ariane Nunes Alves @anunesalves.bsky.social · 03/06/2025
We observe path symmetry for binding and unbinding, and we propose the used of the pathway probabilities presented as a benchmark for enhanced sampling methods which investigate protein-ligand binding. (2/3)
151
Reposted by Farzin Sohraby
Ariane Nunes Alves @anunesalves.bsky.social · 03/06/2025
New manuscript from my group! @farzinsohraby.bsky.social and I investigated H2 binding to / unbinding from [NiFe] hydrogenases using unbiased MD simulations. (1/3) @unisyscat.bsky.social @tuberlin.bsky.social #compchem doi.org/10.26434/che...
doi.org
Symmetric Ligand Binding Pathways and Dual-State Bottleneck in [NiFe] Hydrogenases from Unbiased Molecular Dynamics
[NiFe] hydrogenases are a family of enzymes that can be used to produce biofuel, thus making them important for industrial applications. In this work, we utilized unbiased molecular dynamics (UMD) sim...
1204
Reposted by Farzin Sohraby
Ariane Nunes Alves @anunesalves.bsky.social · 23/05/2025
Lunch with my group today to say goodbye to Laura (off to a PhD in Belgium) and to welcome Chiara and Philipp!
1151
Reposted by Farzin Sohraby
Ariane Nunes Alves @anunesalves.bsky.social · 08/01/2025
New year, new paper! Our paper presenting PathInHydro, a set of machine learning models to identify unbinding paths for gas molecules in [NiFe] hydrogenases, is now out in JCIM! #compchem pubs.acs.org/doi/10.1021/...
0233
Reposted by Farzin Sohraby
Carolyn Bertozzi @carolynbertozzi.bskyverified.social · 27/03/2025
We are seeking to hire a lab tech, this is an HHMI funded position, please share the job posting: hhmi.wd1.myworkdayjobs.com/en-US/Extern...
hhmi.wd1.myworkdayjobs.com
Lab Administration Research Technician- Bertozzi Lab
Primary Work Address: Beckman Center, Stanford, CA, 94305-5323 Current HHMI Employees, click here to apply via your Workday account. We are currently looking for a highly motivated Lab Administration ...
08777
Reposted by Farzin Sohraby
Ariane Nunes Alves @anunesalves.bsky.social · 15/03/2025
The CECAM workshop "Predicting and understanding drug-target binding kinetics via molecular simulations", organized by @herrflow.bsky.social, @rebecca-wade.bsky.social, Giovanni Bottegoni and me, ended last Wednesday.
1204