Protein Engineering and Evolution. Views my own.
Joined August 2013
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Colin Jackson retweeted
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. prismscience.org
Colin Jackson retweeted
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! diffuse.science/post/bandico… #compbio
Colin Jackson retweeted
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: github.com/jmholton/phenix_u…
Colin Jackson retweeted
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). thestacks.org/publications/m…
Colin Jackson retweeted
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
science.org/eprint/666XRGRCV…
Colin Jackson retweeted
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
I'm excited to share our ICLR paper on how leveraging decomposability can enable more efficient scientific design, with @jlistgarten and @svlevine. We were motivated by protein design in particular. Check out the blog post: james-bowden.github.io/dado/.
Colin Jackson retweeted
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. science.org/doi/10.1126/scie…
Colin Jackson retweeted
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.
arxiv.org/abs/2505.04823
Colin Jackson retweeted
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!
nature.com/articles/s41467-0…
Colin Jackson retweeted
New Preprint!! We show that binding entropy can be quantitatively predicted from crystallographic ensemble models, accounting for both protein conformational entropy and solvent entropy! biorxiv.org/content/10.64898…
biorxiv.org/content/10.6... 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
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
Colin Jackson retweeted
"We propose that the p-value be demoted from its threshold screening role and instead, treated continuously."
Colin Jackson retweeted
Excited to share our latest work: Continuous Serial Electron Diffraction for High Quality Protein Structures biorxiv.org/content/10.1101/…
Colin Jackson retweeted
Deeply honored to be part of the 2025 @schmidtsciences Polymath cohort! 🥳
Congratulations to Nozomi Ando, @CornellChem professor! She's been named a @schmidtsciences Polymath, part of a global cohort of 8 scientists & engineers with “remarkable track records, promising futures and a desire to expand their research portfolios."
as.cornell.edu/news/nozomi-a…
ALT Person posing in a lab
Colin Jackson retweeted
‘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
nature.com/articles/s41589-0…
Colin Jackson retweeted
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).
#Enzymatic Stereodivergent Synthesis of Azaspiro[2.y]alkanes by Jennifer L. Kennemur, Yueming Long, Catherine J. Ko, Anuvab Das, and @francesarnold at @CaltechCCE in @J_A_C_S pubs.acs.org/doi/10.1021/jac…
