Colin Jackson

Protein Engineering and Evolution. Views my own.

[Stephanie Wankowicz @stephanie_mul]

Proteins are always moving. They wiggle. They jiggle. They interact with their surroundings. That movement drives their function.

Yet the motion stays mostly invisible. We cannot understand protein function, engineer it, or correct it until we can see the motion and predict it. https://t.co/jLsPrJmvR7

[Prism Science @PrismScienceOrg]

New in BANDICOOT: color each altloc a distinct hue, so you see heterogeneity while you build. Each added alternate conformation is auto hue-shifted from the last; remove them all and the residue returns to bulk color. Configurable and open source! https://t.co/WH2TxZB19P #compbio

[Prism Science @PrismScienceOrg]

In a test case, swapping Phenix's flat bulk-solvent mask for an MD-derived map lowered cross-validated R-free from 0.147 to 0.109 in one 0.96 Å. Code here: https://t.co/Gex7Baz1lk

[Prism Science @PrismScienceOrg]

Bulk solvent fills ~half a protein crystal. Modeling this is required for a good fit to experimental data. How best to model this remains an open question. New from diffUSE: a Phenix patch to supply your own solvent map (MD, 3D-RISM, EDEN, neural nets). https://t.co/N0sRw0q9rC

[Jennifer Listgarten @jlistgarten]

Our review on AI for protein engineering is out now, about this too-fast-moving field full of hype and overclaim, yet one that is having a real impact on the world and can be described in a coherent manner without histrionics
https://t.co/woOWuyTV5R

[Jennifer Listgarten @jlistgarten]

Our new ICLR paper on leveraging “soft decomposability” of design spaces (eg protein sequence) wrt a target property (eg enzymatic activity) in order to more efficiently search through the design space. Active site vs. scaffold, for eg. @jamesbowden_ joint with @svlevine

[Jennifer Listgarten @jlistgarten]

Our new paper on leveraging ML to characterize the fitness landscape of two proteins binding through evolution, wrt geometry, epistasis, etc. The super hard work of Hanlun Jiang, Stephan Allenspach and @jamesbowden_ on our end. https://t.co/qtrURlRYyM

[Jennifer Listgarten @jlistgarten]

New, full length ProteinGuide manuscript, now spanning interpolative, extrapolative and multi-property (extending Pareto optimality) settings; comparisons to fine-tuning; and beating 7 rounds of directed evolution with just one round of ProteinGuide.
https://t.co/wIexIhNow2

[Fasan Lab @FasanLab]

Delighted to share our publication in @NatureComms on the computational design of generalist carbene transferases with tailored, stereodivergent selectivity! Great collab with Sagar Khare! Kudos to Zhuofan, Mary, and Xinkun and all other coauthors!
https://t.co/YAtfzLI0np

[Stephanie Wankowicz @stephanie_mul]

New Preprint!! We show that binding entropy can be quantitatively predicted from crystallographic ensemble models, accounting for both protein conformational entropy and solvent entropy! https://t.co/h9L4glyBYr

[Colin Jackson @Jackson_Lab]

Project started by Jack and led by Sacha

[Colin Jackson @Jackson_Lab]

https://t.co/SSytLwl6i1... most proteins are multi domain but our understanding of how architectures evolve is limited - we mapped 40K chitinases and show a stepwise grammar of domain gain/loss and localisation changes that predicts ecological strategy and physiological function

[Colin Jackson @Jackson_Lab]

https://t.co/Dstfry1pxQ Link didn’t work :(

[Colin Jackson @Jackson_Lab]

Protein design mostly targets single domains; but bio builds function by recombining domains into larger multi domain proteins. Understanding the evolutionary rules of domain assembly will be important if we want to design the level of functionality seen in many native proteins

[John B. Holbein @JohnHolbein1]

"We propose that the p-value be demoted from its threshold screening role and instead, treated continuously."

[Hongyi Xu @XUEY85]

Excited to share our latest work: Continuous Serial Electron Diffraction for High Quality Protein Structures https://t.co/oCTyL8T4uV

[Nozomi Ando @nozomi_ando]

Deeply honored to be part of the 2025 @schmidtsciences Polymath cohort! 🥳

[𝗦𝗜𝗠 @Melo2Ant]

I’m crine bro 😭

[Nature Chemical Biology @nchembio]

‘Protein evolution as a complex system’ – A new Comment discusses protein evolution in terms of complex systems theory and machine learning approaches to model the dynamics of protein evolution

https://t.co/L62p40MOQh

[Frances Arnold @francesarnold]

Really proud of this work by Jae Kennemur and Yueming Long. #Enzymes rock, with a little help from #directedevolution to do #chemistry not known in nature (and not easily done by humans).