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WESTPA Software @WestpaSoftware

Moved @westpasoftware.bsky.social. Highly scalable software for weighted ensemble simulations with any dynamics engine, including MD and systems biology.

Joined January 2019
  • Tweets 56
  • Following 83
  • Followers 253
Photos and videos
WESTPA Software retweeted
Darian@darianyang
27 Mar 2025
The bulk of my thesis work was recently published! We used 19F NMR and weighted ensemble simulations among other methods to explore hidden dimer states of the HIV-1 capsid protein. If this sounds interesting to you, see the full paper here: pnas.org/doi/10.1073/pnas.24…
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WESTPA Software retweeted
Dhiman Ray@DhimanRay16
9 Dec 2024
Just out in @JChemPhys! Integrating Weighted Ensemble (@WestpaSoftware) with OPES-Flooding for accurate and efficient calculation of rare-event kinetics involving barrier crossing and diffusion (e.g. protein folding, ligand binding) @uoCHandBIC #compchem doi.org/10.1063/5.0239303
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Check out this recent publication from the @agrossfield lab where they used WESTPA to determine the effects of system size on free energy landscapes of a phase-separating ternary lipid bilayer! pubs.aip.org/aip/jcp/article…

System size effects on the free energy landscapes from molecular dynamics of phase-separating...

The “lipid raft” hypothesis proposes that cell membranes contain distinct domains of varying lipid compositions, where “rafts” of ordered lipids and cholesterol

pubs.aip.org
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WESTPA Software retweeted
Rommie Amaro@RommieAmaro
10 Oct 2024
New work on protein design... 🚨S2 immunogen design using advanced simulation @WestpaSoftware WE MD--> opening mechanism--> design--> stabilized protein--> cryoEM structure immunology @xandra_nuqui @LCasalino88 @McLellan_Lab @ChandranLab nature.com/articles/s41467-0…
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We are excited to share this collaboration between the Gardner and Chong labs in which weighted ensemble simulations are combined with NMR and ensemble docking! jbc.org/article/S0021-9258(2…

Identification of small-molecule ligand-binding sites on and in the ARNT PAS-B domain

Transcription factors are challenging to target with small-molecule inhibitors due to their structural plasticity and lack of catalytic sites. Notable exceptions include naturally ligand-regulated...

jbc.org
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WESTPA Software retweeted
JCIM & JCTC Journals@JCIM_JCTC
16 Aug 2024
#HighlightOfTheWeek Animated time-evolution of a 2D probability distribution obtained using WEDAP, a python package to plot molecular simulation data. Work by @darianyang and @ltchong. #compchem pubs.acs.org/doi/10.1021/acs…
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We're excited to see Shirley Ahn's group using WESTPA to explore optimizing weighted ensemble simulations with cumulative distribution functions! pubs.aip.org/aip/jcp/article…

Optimization of the resampling method in the weighted ensemble simulation toolkit with paralleliz...

Molecular dynamics (MD) simulations are powerful tools for studying the dynamic behavior of molecular systems at the atomic level. MD simulations provide insigh

pubs.aip.org
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Having trouble visualizing your data from WESTPA? Try WEDAP! A user-friendly plotting package from @darianyang and @ltchong (1/4) pubs.acs.org/doi/10.1021/acs…

WEDAP: A Python Package for Streamlined Plotting of Molecular Simulation Data

Given the growing interest in path sampling methods for extending the time scales of molecular dynamics (MD) simulations, there has been great interest in software tools that streamline the generat...

pubs.acs.org
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more replies
You can even use WEDAP to make gifs! (3/4)
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Want to try it out? Just run: "pip install wedap" - PyPI: pypi.org/project/wedap/ - GitHub: github.com/darianyang/wedap - Docs Page: darianyang.github.io/wedap (4/4)
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WESTPA Software retweeted
Gabriel Monteiro da Silva@GMondaSilva
28 May 2024
Thrilled to share that my thesis manuscript is out! Here, we used WESTPA2 to show that mutations in Abl1 lead to drug resistance by dramatically shifting relative state populations, impacting the conformational search step of binding. Link below: biorxiv.org/content/10.1101/…

Compound Mutations in the Abl1 Kinase Cause Inhibitor Resistance by Shifting DFG Flip Mechanisms...

The intrinsic dynamics of most proteins are central to their function. Protein tyrosine kinases such as Abl1 undergo significant conformational changes that modulate their activity in response to...

biorxiv.org
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WESTPA Software retweeted
Lillian Chong@ltchong
2 May 2024
It's finally out! Outstanding work by @atbogetti @mczwier using @WestpaSoftware @ambermdprog
J. Am. Chem. Soc.@J_A_C_S
1 May 2024
Revisiting Textbook Azide-Clock Reactions: A “Propeller-Crawling” Mechanism Explains Differences in Rates | Journal of the American Chemical Society @ltchong @PittChem @PittTweet #Azide #Clock #PropellerCrawling #Mechanism #Rates pubs.acs.org/doi/10.1021/jac…
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Another great BPS with both vintage and fresh WESTPA developers/users from the @ltchong @RommieAmaro @DMZuckermanLab @Terrasztain and Ahn Labs!
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WESTPA Software retweeted
MolSSI@MolSSI_NSF
7 Feb 2024
Register now for the free WESTPA Workshop @Pitt_Chemistry, June 20-21. Explore rare event simulations like protein folding, ligand binding, & chemical reactions with our open-source software. Perfect for those using AMBER, NAMD, GROMACS, etc. Reg info: forms.gle/6gJF6jJ72iexbDTq8

Registration for WESTPA workshop - CLOSED

Please join us for this year's WESTPA workshop at the University of Pittsburgh, June 20-21, 2024. We will be celebrating the 10th anniversary of WESTPA! WESTPA is an open-source, highly-scalable...

docs.google.com
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Using WE simulations and experiments, @ChongLabPitt and the Horne lab explore the atomistic folding pathways of protein mimetics pubs.rsc.org/en/content/arti…

Effects of altered backbone composition on the folding kinetics and mechanism of an ultrafast-fol...

Sequence-encoded protein folding is a ubiquitous biological process that has been successfully engineered in a range of oligomeric molecules with artificial backbone chemical connectivity. A remark...

pubs.rsc.org
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Want to see WE / WESTPA applied towards understanding the free-energy landscape of phase separation in lipid bilayers? Check it out:
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WESTPA Software retweeted
Saxena Lab@Saxena_Lab
29 Aug 2023
Beyond coarse-grained modeling: Seconds-timescale protein conformational change measured using Cu(II)-based EPR and weighted ensemble MD simulations. @ltchong Congratulations to Xiaowei and @AnthonyBogetti on this work, now published in Protein Science: onlinelibrary.wiley.com/doi/…
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Congrats to one of our core WESTPA developers Jeremy Leung for receiving a MolSSI software fellowship!
MolSSI@MolSSI_NSF
28 Jul 2023
We loved having our 2023-24 MolSSI Software Fellows with us last week! We thank Jessica Nash @jessica_a_nash and the other MolSSI Software Scientists for another inspired week of programming and mentorship!
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Brossard and Corcelli just published their first paper using WESTPA! They investigated the mechanism for binding a small molecule to the minor groove of DNA. pubs.acs.org/doi/10.1021/acs…

Molecular Mechanism of Ligand Binding to the Minor Groove of DNA

Although DNA–ligand binding is pervasive in biology, little is known about molecular-level binding mechanisms. Using all-atom, explicit-solvent molecular dynamics simulations in conjunction with...

pubs.acs.org
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