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Reposted by Ashar Malik

Caroline Puente-Lelievre @cpuentelelievre.bsky.social · Sep 4

Special Section in GBE: Structural Phylogenetics

Here we showcase novel work on how 3D protein structures can reshape evolutionary biology, from methods to applications.

More papers coming out soon!

@genomebiolevol.bsky.social @proteinmechanic.bsky.social

academic.oup.com/gbe/search-r...

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Ashar Malik @proteinmechanic.bsky.social · Aug 22

Third Era of Phylogenetics!

1️⃣ Era 1: Morphology 🦴
2️⃣ Era 2: Sequences 🧬
3️⃣ Era 3: 3D Structures ⚛️

Solving deep evolutionary puzzles like never before. Our new review in GBE explores what's next in #phylogenetics

academic.oup.com/gbe/article/...

#structuralbiology #evolution #AlphaFold #SciSky

Protein Structural Phylogenetics

Abstract. Protein structural phylogenetics is an interdisciplinary branch of molecular evolution that (i) uses 3D structural data to trace evolutionary his

academic.oup.com

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Reposted by Ashar Malik

bioRxivpreprint @biorxivpreprint.bsky.social · Aug 8

Quantome: A Quantum Surrogate Model for Biophysical Landscapes https://www.biorxiv.org/content/10.1101/2025.08.06.668871v1

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Reposted by Ashar Malik

bioRxiv Biophysics @biorxiv-biophys.bsky.social · Aug 8

Quantome: A Quantum Surrogate Model for Biophysical Landscapes https://www.biorxiv.org/content/10.1101/2025.08.06.668871v1

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Ashar Malik @proteinmechanic.bsky.social · Aug 7

Playing around with quantum-styled math on trivial biological problems before tackling the really hard questions. Initial signs are good, with the math behaving as expected. Next leg would be using a non-trivial dataset like missense variants.

bioRxivpreprint @biorxivpreprint.bsky.social · Aug 7

On a quantum-inspired kernel for classifying protein torsion angles https://www.biorxiv.org/content/10.1101/2025.08.05.668681v1

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Ashar Malik @proteinmechanic.bsky.social · Jun 29

Within Tagetes lemmonii, (Lemmon’s marigold) are defence molecules called thiophenes which become highly toxic when exposed to sunlight, damaging pests at the cellular level. An elegant example of how plants weaponize light to survive.

#Brisbane #nature #nikon #naturephotography #SciComm

Tagetes lemmonii, also known as Lemmon’s marigold (or mountain marigold according to Google's Brisbane result) is shown against a blurred background (bokeh).

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Ashar Malik @proteinmechanic.bsky.social · Jun 4

If you do deep evolutionary analysis - structure-aware characters can help. To ensure correct alignments - give it a try: biosig.lab.uq.edu.au/structome_al...

If you would like any features added, drop a message and will give it a shot.

#Science #Evolution #MolecularEvolution #DeepEvolution

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Ashar Malik @proteinmechanic.bsky.social · Jun 4

Explore it here: biosig.lab.uq.edu.au/structome_al...
Free to use, no login required.
Feedback welcome — especially if you're working on deep evolutionary comparisons.

🕰️ Let these structure-aware sequence alignments reveal a distant past that amino acid sequences alone couldn’t reach.

Structome-AlignViewer

Structome-AlignViewer is a tool to assess the quality of structural alignments using 3Di character encoding. It provides interactive visualization, confidence scoring, and downloadable full/trimmed al...

biosig.lab.uq.edu.au

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Ashar Malik @proteinmechanic.bsky.social · Jun 4

Using pairwise structure-aware character substitution scores across your proteins, the app computes per-column confidence, maps it to B-factors, and visualizes it in Mol*. You can spot conserved cores.

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Ashar Malik @proteinmechanic.bsky.social · Jun 4

But structure-aware alignments can mislead if divergent folds cause misalignments. That’s where Structome-AlignViewer comes in — it helps you evaluate how reliable each alignment column is, and where structural consistency holds up.

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Ashar Malik @proteinmechanic.bsky.social · Jun 4

It’s like turning protein structures into a kind of “structural FASTA.” This lets us compare, align, and analyze proteins based on shape — not just sequence.

In the past www.biorxiv.org/content/10.1...
we used this method to character-based structural phylogenetic trees.

Tertiary-interaction characters enable fast, model-based structural phylogenetics beyond the twilight zone

Protein structure is more conserved than protein sequence, and therefore may be useful for phylogenetic inference beyond the “twilight zone” where sequence similarity is highly decayed. Until recently...

www.biorxiv.org

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Ashar Malik @proteinmechanic.bsky.social · Jun 4

What are structure-aware characters?

Structure-aware characters describe 3D conformation. Each residue gets a label (by Foldseek) based on its spatial context — enabling compact, alignment-ready strings from protein structures.

#Evolution #Phylogenetics #Science

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Ashar Malik @proteinmechanic.bsky.social · Jun 4

🧵: It's out. Structome-AlignViewer, a web-based resource for evaluating protein structure-aware sequence alignments. It maps alignment columns directly onto structures and helps identify conserved regions. Feedback encouraged. www.biorxiv.org/content/10.1...

#Evolution #MolecularEvolution #Science

Structome-AlignViewer: On Confidence Assessment in Structure-Aware Alignments

Protein structure-based comparison provides a framework for uncovering deep evolutionary relationships that can escape conventional sequence-based approaches. Encoding three-dimensional protein struct...

www.biorxiv.org

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Ashar Malik @proteinmechanic.bsky.social · May 15

In a talk today thinking that science isn’t just a collection of facts it’s a method and sometimes, a philosophical tightrope.

Emeritus Professor Ross Bernard at #UQ exploring how science proceeds - via falsifiability. Not everyone agrees but a conversation worth having.

#Science #Philosophy

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Ashar Malik @proteinmechanic.bsky.social · May 11

#DecodingEvolution The Molecular Story of Life’s Transformations

#Evolution is often seen in grand transformations dinosaurs into birds, fish onto land. Uncover how tiny changes drive life’s biggest adaptations, revealing evolution’s true blueprint.

pintofscience.com.au/event/from-m...

#Pint25

Ashar Malik @proteinmechanic.bsky.social · May 11

I am speaking soon about #Evolution at a public talk series in #Brisbane (Ticket $10). Many other talks covering a range of topics. Interested in havin a fun science evening with family?

For more information vIsit and tickets: pintofscience.com.au/events/brisb...

#pintofscience #Pint25 #PintAU25

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Ashar Malik @proteinmechanic.bsky.social · Apr 14

Oldest reference I’ve ever seen while reviewing — 1667, Antonie van Leeuwenhoek.

From the first observation of bacteria under a handcrafted microscope to modern phylogenetics. Science stands on the shoulders of giants — even from 400 years ago.
#Science #Evolution #AcademicLife

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Ashar Malik @proteinmechanic.bsky.social · Apr 7

Just attending a talk by Professor Warwick from QUBIC at #BrisScience on

“Bringing Quantum to Life: How Quantum technologies may shape the future of society”.

Exciting times ahead as quantum algorithm unravel mysteries of life.

#Quantum #Science

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Ashar Malik @proteinmechanic.bsky.social · Mar 19

Interested in giving it a try?

Have a go here: biosig.lab.uq.edu.au/missenseview...

MissenseViewer: A Unified Dashboard for Missense Mutation Effects

Explore missense mutation pathogenicity predictions from ESM1b, AlphaMissense, and VESPA. Visualize substitution sites, domain contexts, and ligand-binding site relationships on protein structures.

biosig.lab.uq.edu.au

Ashar Malik @proteinmechanic.bsky.social · Mar 19

For better analysis of drug binding profiles - we integrated ligand related information as well. Would love to hear thoughts from the community! Any suggestions for improvement on this database while we work on the meta predictor?

#MissenseViewer #AI #science #AIinhealth #precisionmedicine

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Ashar Malik @proteinmechanic.bsky.social · Mar 19

Mutation impact isn’t just about sequence—it’s about where the mutation occurs in 3D space. #MissenseViewer links missense effect predictions to protein structures, helping extract structural features that can improve predictive models and deepen our understanding of mutation effects.

#AI #science

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Ashar Malik @proteinmechanic.bsky.social · Mar 19

Each predictor has strengths and weaknesses—some overpredict #pathogenicity, others miss functionally critical sites. A meta-predictor that synergizes these methods could help improve accuracy. #MissenseViewer is a first step in enabling this by providing comparative insights across predictors.

#AI

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Ashar Malik @proteinmechanic.bsky.social · Mar 19

Missense mutations impact protein function, but no single predictor is perfect. MissenseViewer integrates AlphaMissense, ESM1b, and VESPA predictions, mapping them onto protein structures to provide a richer, more interpretable view of mutation effects.

#science #health #precisionmedicine #AI

bioRxivpreprint @biorxivpreprint.bsky.social · Mar 19

On interactive spatial visualisation of pathogenicity predictions https://www.biorxiv.org/content/10.1101/2025.03.19.644131v1

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Reposted by Ashar Malik

Lorne Proteins @lorneproteins.bsky.social · Feb 10

Michael Healy is first speaker of the Anders early career investigators session. The scientists of the future (and the present!).

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Ashar Malik @proteinmechanic.bsky.social · Feb 9

Professor Frances Separovic documents her tough journey in #Science. A trailblazing scientist who defied the odds and carved her path in a time when women in science faced unimaginable barriers. Her story is a testament to the power of determination.

#WomenInScience @lorneproteins.bsky.social

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