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Tien Phan

@tienphan.bsky.social
49 followers 132 following 0 posts

Postdoc at Texas A&M University | Computational Biophysics | Molecular Dynamics Simulations | Machine Learning and AI

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Reposted by Tien Phan
Jan H. Jensen @janhjensen.bsky.social · 30/04/2025
Explainable GNNs in Chemistry: Combining Attribution and Uncertainty Quantification | ChemRxiv - doi.org/10.26434/che... #compchem
doi.org
Explainable GNNs in Chemistry: Combining Attribution and Uncertainty Quantification
Graph Neural Networks (GNNs) are powerful tools for predicting chemical properties, but their black-box nature can limit trust and utility. Explainability through feature attribution and awareness of ...
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 27/04/2025
AFESM: a metagenomic guide through the protein structure universe! We clustered 821M structures (AFDB&ESMatlas) into 5.12M groups; revealing biome-specific groups, only 1 new fold even after AlphaFold2 re-prediction & many novel domain combos. 🧵 🌐 afesm.foldseek.com 📄 www.biorxiv.org/content/10.1...
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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 17/04/2025
AlphaFold is amazing but gives you static structures 🧊 In a fantastic teamwork, @mcagiada.bsky.social and @emilthomasen.bsky.social developed AF2χ to generate conformational ensembles representing side-chain dynamics using AF2 💃 Code: github.com/KULL-Centre/... Colab: github.com/matteo-cagia...
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Rosana Collepardo @rcollepardo.bsky.social · 07/03/2025
In this wonderful collaboration with K Maeshima and M Shimazoe we show that H1 in living cells acts as a liquid-like glue not a driver of stiff zigzag fibers 🔥🔥🔥 Each H1 bridges multiple nucleosomes and exchanges nucleosomes frequently: boosting both compaction and dynamical behaviour of chromatin
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Rafael C. Bernardi @rcbernardi.bsky.social · 17/02/2025
🚀 First Bluesky Post! 🎉 VMD 2.0 Alpha is here! Released today at BPS 2025, this is the biggest update in 30 years—new UI, real-time ray tracing, fast surfaces, UHD & touchscreen support. Monthly updates coming in 2025! Try it now! #VMD #BPS2025 #MolecularVisualization www.ks.uiuc.edu/Research/vmd...
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Siewert-Jan Marrink @cg-martini.bsky.social · 01/02/2025
Excellent review including a comprehensive section on what Martini can do in this field: "Computational Methods for Modeling Lipid-Mediated Active Pharmaceutical Ingredient Delivery | Molecular Pharmaceutics" pubs.acs.org/doi/10.1021/...
pubs.acs.org
Computational Methods for Modeling Lipid-Mediated Active Pharmaceutical Ingredient Delivery
Lipid-mediated delivery of active pharmaceutical ingredients (API) opened new possibilities in advanced therapies. By encapsulating an API into a lipid nanocarrier (LNC), one can safely deliver APIs n...
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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 26/01/2025
Ten simple rules for developing good reading habits during graduate school and beyond To me, the most important are: Read often, read broadly (incl. older papers and outside your field), and learn to read some papers in detail and others more superficially (and quickly)
Ten simple rules for developing good reading habits during graduate school and beyond by Marcos Méndez
1: Develop the habit of reading on a daily basis
2: Read thoroughly to build a sound background understanding of your topic
3: Do not ignore the pillars of your discipline; read the classics
4: If you have to get familiar with a new topic, consider reading in chronological order
5: Avoid narrow-mindedness by reading beyond your discipline
6: Create a list of relevant journals
7: Not all interesting stuff will appear in articles; read books
8: Use a reference manager to keep track of your literature
9: Keep a long-term review for your own use as a way to remember what you read
10: Build your own library to make yourself independent and inspire others
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Karsten Rippe @karsten-rippe.bsky.social · 25/01/2025
A mechanism for maintaining and spreading H3K9me3 in heterochromatin from the Fejes Toth and Aravin labs that depends on the local H3K9me3 density: HP1 dimers recruit SetDB1 to chromatin by simultaneously binding H3K9me3 on histone H3 and auto-methylated SetDB1. www.biorxiv.org/content/10.1...
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Rosana Collepardo @rcollepardo.bsky.social · 23/01/2025
What is the multiscale structure of chromatin condensates? How does it shape thermodynamic and material properties? We address this at near-atomistic resolution🔥🔥🔥 using cryoET (Rosen & Villa labs, led by H Zhou), a new multiscale model (K Russell) and cryoET-guided sims (J Huertas & J Maristany)
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Jorge Bravo Abad @bravo-abad.bsky.social · 04/01/2025
Feng et al. propose a two-stage sampling to train electron density ML models using under 0.015% of grid points, yet achieving ∼0.001 e/ų error for broad systems (e.g., QM9, H₂O/Pt). The approach also captures field-driven charge transfers in metals with minimal cost. pubs.acs.org/doi/full/10....
pubs.acs.org
Efficient Sampling for Machine Learning Electron Density and Its Response in Real Space
Electron density is a fundamental quantity that can in principle determine all ground state electronic properties of a given system. Although machine learning (ML) models for electron density based on either an atom-centered basis or a real-space grid have been proposed, the demand for a number of high-order basis functions or grid points is enormous. In this work, we propose an efficient grid-point sampling strategy that combines targeted sampling favoring a large density and a screening of grid points associated with linearly independent atomic features. This new sampling strategy is integrated with a field-induced recursively embedded atom neural network model to develop a real-space grid-based ML model for the electron density and its response to an electric field. This approach is applied to a QM9 molecular data set, a H2O/Pt(111) interfacial system, an Au(100) electrode, and an Au nanoparticle under an electric field. The number of training points is found to be much smaller than previous models, while yielding comparably accurate predictions for the electron density of the entire grid. The resultant machine-learned electron density model enables us to properly partition partial charge onto each atom and analyze the charge variation upon proton transfer in the H2O/Pt(111) system. The machine-learning electronic response model allows us to predict charge transfer and the electrostatic potential change induced by an electric field applied to an Au(100) electrode or an Au nanoparticle.
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Diego del Alamo @delalamo.xyz · 01/01/2025
A method for integrating externally calculated potentials from any Python package of interest into OpenMM, courtesy of ByteDance, which I must stress again is the parent company of TikTok
arxiv.org
OpenMM-Python-Force: Deploying Accelerated Python Modules in Molecular Dynamics Simulation
We present OpenMM-Python-Force, a plugin designed to extend OpenMM's functionality by enabling integration of energy and force calculations from external Python programs via a callback mechanism. Duri...
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Patrick van der Wel @pcavanderwel.bsky.social · 28/12/2024
Here is the link to our new collaborative paper with Sijbren Otto and his team: "Departure from randomness: Evolution of self-replicators that can self-sort through steric zipper formation": www.sciencedirect.com/science/arti.... #Amyloid principles in self assembly
sciencedirect.com
Departure from randomness: Evolution of self-replicators that can self-sort through steric zipper formation
Darwinian evolution of self-replicating entities most likely played a key role in the emergence of life from inanimate matter. For evolution to occur,…
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Proceedings of the National Academy of Sciences @pnas.org · 27/12/2024
Researchers challenged longhorn crazy ants and humans with the same task: maneuvering a T-shaped object through two consecutive open doorways. Single humans always outperformed single ants, but ant groups could beat human groups. In PNAS: www.pnas.org/doi/10.1073/...
A group of longhorn crazy ants (top) and a group of people (bottom) tackling scaled versions of the same geometrical maneuvering puzzle.

CREDIT: Ofer Feinerman
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Bird account @dialecticbio.bsky.social · 28/12/2024
Deep learning for proteins tutorial: github.com/Graylab/DL4P...
github.com
GitHub - Graylab/DL4Proteins-notebooks: Colab Notebooks covering deep learning tools for biomolecular structure prediction and design
Colab Notebooks covering deep learning tools for biomolecular structure prediction and design - Graylab/DL4Proteins-notebooks
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Frank Noe @franknoe.bsky.social · 06/12/2024
Super excited to preprint our work on developing a Biomolecular Emulator (BioEmu): Scalable emulation of protein equilibrium ensembles with generative deep learning from @msftresearch.bsky.social ch AI for Science. www.biorxiv.org/content/10.1...
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Jean-Philip Piquemal @jppiquem.bsky.social · 08/12/2024
#compchem Good read: PLUMED Tutorials: a collaborative, community-driven learning ecosystem #compchemsky arxiv.org/abs/2412.03595
arxiv.org
PLUMED Tutorials: a collaborative, community-driven learning ecosystem
In computational physics, chemistry, and biology, the implementation of new techniques in a shared and open source software lowers barriers to entry and promotes rapid scientific progress. However, ef...
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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 07/12/2024
"Are there at least 3 simulations per simulation condition with statistical analysis?" From @commsbio.bsky.social's "Reliability and reproducibility checklist for molecular dynamics simulations" (doi.org/10.1038/s420...) IMO the number 3 is meaningless and could equally well be 1 or 1000
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Tiago Peixoto @tiago.skewed.de · 02/12/2024
Good news everyone! A new version of graph-tool is just out! @graph-tool.skewed.de graph-tool.skewed.de Graph-tool is a comprehensive and efficient Python library to work with networks, including structural, dynamical, and statistical algorithms, as well as visualization. 1/N #networkscience
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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 06/05/2024
If you're interested in reading about how I got into biophysics and protein science and what I enjoy about the field, I'm profiled this month by the Biophysical Society: www.biophysics.org/profiles/kre...
biophysics.org
Kresten Lindorff-Larsen
Kresten Lindorff-Larsen, Professor at the Linderstrøm-Lang Centre for Protein Science in the De­partment of Biology, University of Copenhagen, studied biochemistry, leading him to...
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Rommie Amaro @rommieamaro.bsky.social · 26/11/2024
A project 10 years in the making w/ Terry Sejnowski, led by @philosophaki.bsky.social Insights into ryanodine receptor activation & calcium-induced Ca2+ release from a stochastic explicit-particle 3D simulation of cardiac dyad w/ realistic TEM geometry 🧪 www.sciencedirect.com/science/arti...
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David Ryan Koes @dkoes.compstruct.org · 21/11/2024
Some fun with Boltz-1 (www.biorxiv.org/content/10.1...). I generated 1000 samples profilin (green) and compare them to the NMR structures (cyan). Samples were generated by docking 1000 random ligands. NMR structures show more conformational diversity.
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David Ryan Koes @dkoes.compstruct.org · 22/11/2024
Here is how Boltz-1 (green), DynamicBind (magenta), and GNINA (blue) dock a collection of random molecules. GNINA, using a classical sampling algorithm (MCMC) hits all concave regions while the ML samplers have distinct preferences. Boltz is the most likely to induce a fit.
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Rommie Amaro @rommieamaro.bsky.social · 18/11/2024
🚨Announcing NetSci: a super fast tool to compute correlated motion in biomolecules pubs.acs.org/doi/10.1021/... @pabloarantes.bsky.social & team also made it into a Colab notebook: colab.research.google.com/drive/1GGJKr... Give it a try & send feedback!
pubs.acs.org
NetSci: A Library for High Performance Biomolecular Simulation Network Analysis Computation
We present the NetSci program–an open-source scientific software package designed for estimating mutual information (MI) between data sets using GPU acceleration and a k-nearest-neighbor algorithm. This approach significantly enhances calculation speed, achieving improvements of several orders of magnitude over traditional CPU-based methods, with data set size limits dictated only by available hardware. To validate NetSci, we accurately compute MI for an analytically verifiable two-dimensional Gaussian distribution and replicate the generalized correlation (GC) analysis previously conducted on the B1 domain of protein G. We also apply NetSci to molecular dynamics simulations of the Sarcoendoplasmic Reticulum Calcium-ATPase (SERCA) pump, exploring the allosteric mechanisms and pathways influenced by ATP and 2′-deoxy-ATP (dATP) binding. Our analysis reveals distinct allosteric effects induced by ATP compared to dATP, with predicted information pathways from the bound nucleotide to the calcium-binding domain differing based on the nucleotide involved. NetSci proves to be a valuable tool for estimating MI and GC in various data sets and is particularly effective for analyzing intraprotein communication and information transfer.
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