Ariane Nunes Alves
@anunesalves.bsky.social
Computational Biochemist (ligand binding kinetics, crowding) Lead Researcher at the Brazilian Center for Research in Energy and Materials Associate Editor at the Journal of Chemical Information and Modeling Brazilian in Germany
I wrote to Director Bhattacharya with an idea about how to convert these "scientific freedom" lectures into something potentially useful. 1/3
I am happy to share that the work from Daniil Lepikhov, Laura Sandner and me to predict Michaelis constants (Km) for enzyme-substrate complexes using deep learning is now available at Digital Discovery! #compchem pubs.rsc.org/en/Content/A...
Leveraging active site information for deep learning prediction of enzyme–substrate Michaelis constants
The Michaelis constant (KM) is a key parameter in enzymology. Its experimental measurement is often low-throughput and costly, but machine learning can identify patterns to make predictions in a high-...
pubs.rsc.org
The article with the summary of the CECAM workshop on binding kinetics by @anunesalves.bsky.social, @rebecca-wade.bsky.social and Giovanni Bottegioni is now published Open Access at Drug Discovery Today – you may find it under www.sciencedirect.com/science/arti... #drugdiscovery #kinetics
Where do we go from here? Current state of drug–target binding kinetics and a roadmap to their establishment in drug discovery campaigns
Because of the observation that kinetic rates can be better correlated with in vivo drug efficacy than simple affinities, significant efforts have bee…
sciencedirect.com
A man at a meeting I attended recently made a big deal about how his office door doesn't say "Professor", just his name, and that's how he encourages healthy research culture. I pointed out that that works for him because, unlike me, he probably won't be mistaken for his own secretary.
Dr Lindsey Fitzharris@drlindseyfitz.bsky.social · 4mo agoAh, I see the internet is determined to continue showing its ass this weekend. A woman spends years earning her degree only to be told that if she uses her title, she's pretentious.
Excited to share this paper from @yiechanglin.bsky.social showing how lipids can move between bacterial membranes along the bridge like protein TamB. Also happy to be able to post the cool movie. 🎥🌟 #MDsimulations #StructuralBiology doi.org/10.1016/j.bp...
We got internal info today that hints at what at least ERC thinks is a good (=their only) idea to counter the proposal flood: vastly stricter resubmission criteria! Retroactively even! 🤬
Caroline Lynn Kamerlin ☀️@lynnkamerlin.bsky.social · 6mo agoMy latest #OpenAccess column in EMBO Reports discusses the perfect storm of hypercompetition, score compression and AI co-authorship for grant success rates, turning prestigious funding schemes into functional lotteries. 1/
I am very happy to share that I am back at the Federal University of ABC, Brazil, to start my research group, the Computational Multiscale Modelling of Organic and Biomolecules laboratory (CMOBio Lab). Now you can contact me in renato.cunha@ufabc.edu.br #compchem #newpi #researcher
I am happy to share that I am back to my home country, Brazil, to be a lead researcher at the Brazilian Center for Research in Energy and Materials (CNPEM)! My research group will keep working on binding kinetics, and on the development of methods to simulate the cell cytoplasm. #compchem
Happy to share the review that @apoorvam.bsky.social, Vanessa and I wrote about recent trends in modeling and simulation of biological phenomena in crowded and cell-like environments! I really like this topic, for me this is the future of #compchem. arxiv.org/abs/2603.26974
Recent advances in modeling and simulation of biological phenomena in crowded and cellular environments
While experiments and computer simulations to study biological phenomena are usually performed in diluted in vitro conditions, such phenomena happen inside the cellular cytoplasm, an environment dense...
arxiv.org
We did a new major #RDKit release yesterday. v2026.03.1 is out and the conda-forge builds are available. As always, especially with major releases, be sure to read the "Backwards incompatible changes" section of the release notes! github.com/rdkit/rdkit/...
Release 2026_03_1 (Q1 2026) Release · rdkit/rdkit
Release_2026.03.1 (Changes relative to Release_2025.09.1) Acknowledgements (Note: I'm no longer attempting to manually curate names. If you would like to see your contribution acknowledged with you...
github.com
👀 "In the absence of true prospective validations of Boltz-2 usage to select hit compounds from docking screens, we therefore advise remaining very skeptical with respect to affinity predictions outputted by this AI cofolding program (...)" pubs.acs.org/doi/10.1021/...
Assessing Boltz-2 Performance for the Binding Classification of Docking Hits
The recently released Boltz-2 cofolding model is generating high expectations by enabling both protein–ligand structure and binding affinity predictions. When applied to a recently described and chall...
pubs.acs.org
Apply now! The 2026 call for the EMBO Young Investigator Programme is now open with a deadline of 1 April 12:00 midday CEST. 🧪 More info here: https://www.embo.org/funding/fellowships-grants-and-career-support/young-investigator-programme/ #LifeSciences #research #funding
⭐️ Registration and Abstract submission is open for the "3rd BioExcel Conference on Advances in Biomolecular Simulations" 🗓️ 27 - 30 September 2026 📍 Brno, Czechia ℹ️ More info: bioexcel.eu/hzr0 #molecularsimulation #moleculardynamics #AI #compchem #drugdesign #molecule #computing #conference
ERC starting grant eligibility window increased to 10 years post-PhD defense: www.ukro.ac.uk/news/changes...
Changes to the 2026 and 2027 ERC Work Programmes
With the upcoming ERC Work Programme 2026 this July, several changes to the submission of applications and the evaluation of proposals will apply. The main novelties for 2026 and 2027 are are summaris...
ukro.ac.uk
📢 Applications for Google Summer of Code (GSoC) are open now through March 31, 2026. Spend 12+ weeks coding with experienced mentors and earn a stipend. Read more at goo.gle/gsoc-2026-ap... #GSoC #OpenSource #GoogleSummerofCode #StudentPrograms
goo.gle
Google Summer of Code 2026 applications are now open
goo.gle
We are hiring a postdoc in computational biophysics and machine learning studies of intrinsically disordered proteins We aim to study the function of IDPs by combining CG MD, ML and bioinformatics in collaboration with @tanjamittag.bsky.social & @rhp-lab.bsky.social tinyurl.com/REWIRE-PD
You asked, we listened. Millions of AI-predicted protein complex structures are now available in the #AlphaFold Database. This spans homodimers from 20 of the most studied species, including humans, as well as the World Health Organization’s priority pathogens list. www.ebi.ac.uk/about/news/t...
So... A friend was supposed to give a PURELY SCIENTIFIC talk at NIH within the next couple of weeks and it was cancelled because of a "new process" where all speakers/talks have to be CLEARED BY A POLITICAL APPOINTEE.
a large screen shows a man 's face and says ingsoc
ALT: a large screen shows a man 's face and says ingsoc
media.tenor.com
I am happy to share a perspective that @herrflow.bsky.social, Giovanni Bottegoni, Rebecca Wade and I wrote to summarize the discussions the participants of our recent CECAM workshop had about ligand binding kinetics. #compchem chemrxiv.org/doi/full/10....
Where do we go from here? Current state of drug-target binding kinetics and a roadmap to their establishment in drug discovery campaigns | ChemRxiv
Due to the observation that kinetic rates can be better correlated with in vivo drug efficacy than simple affinities, significant efforts have been made to develop experimental and computational methods to predict drug-target residence times over the last ...
chemrxiv.org
We're hiring! Are you a chemist looking for editorial opportunities in India? Communications Chemistry is looking for an Associate or Senior Editor to join our team in Springer Nature's Pune or New Dehli offices. springernature.wd3.myworkdayjobs.com/SpringerNatu... #chemjobs #chemsky
Associate or Senior Editor, Communications Chemistry
About Springer Nature Group Springer Nature opens the doors to discovery for researchers, educators, clinicians, and other professionals. Every day, around the globe, our imprints, books, journals, pl...
springernature.wd3.myworkdayjobs.com
📝From 2023, the Review "Advances in computational methods for ligand binding kinetics" from Farzin Sohraby and Ariane Nunes-Alves: www.cell.com/trends/bioch...
Advances in computational methods for ligand binding kinetics
In recent years, it has become apparent that calculating binding kinetic rates and understanding the binding mechanism of drugs to their target proteins can be helpful in drug design [1–3]. For instan...
cell.com
PhD positions in my lab (AI for Science), but with special preference for people who complement our current activities or are enthusiastic about contributing to our on going work. Looking for technically strong, independent and proactive candidates. www.chalmers.se/en/about-cha...
Vacancies
chalmers.se
Hello bluesky, I'm a theoretical chemist at University of Bayreuth. My group works on atomistic modeling of energy materials with electronic structure methods and ML. I'm hoping to connect to other #compchem and #materials folks!
👉 Join our 'Computer Simulation and Theory of Macromolecules' #workshop in #Hünfeld 🇩🇪 to discuss recent advances in #theory and application of #biomolecular #simulations and contribute to promoting the exchange among the communities of Germany and beyond. #MD @mpi-nat.bsky.social t1p.de/d0lrv
On my way to Aachen for the 5th German workshop on structural predictions of membrane proteins: from ion channels to G protein-coupled receptors. I will talk about drug transporters and Toll-like receptors tomorrow. #compchem
The work from @apoorvam.bsky.social, Mariona, Max, Chiara and me elucidating the role of molecular glues in stabilizing water-mediated hydrogen bonds is now out at ChemPhysChem! #compchem dx.doi.org/10.1002/cphc...
Molecular Glues Stabilize Water‐Mediated Hydrogen Bonds in Ternary Complexes
The molecular glues modulate the pattern and stability of water-mediated hydrogen bonds between the proteins of ternary complexes.
dx.doi.org
Ariane Nunes Alves@anunesalves.bsky.social · 11mo agoHappy to share the manuscript from @apoorvam.bsky.social, Mariona, Max, Chiara and me, where we used molecular dynamics simulations to investigate the effects of molecular glues over protein-protein complexes involving FKBP. arxiv.org/abs/2510.26806 #compchem
