Shiva Shankar S @BioShankar
| Structural biology and Mass Spectrometry enthusiast | Protein engineering | PhD student @csir_ncl Pune, India Joined August 2015-
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Shiva Shankar S retweeted
Predicting Experimental Success in De Novo Binder Design: A Meta-Analysis of 3,766 Experimentally Characterised Binders biorxiv.org/content/10.110… #biorxiv_bioinfo
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Shiva Shankar S retweeted
A newly discovered type of immune cell found in fat tissue seems to contribute to the chronic inflammation associated with ageing go.nature.com/3I8VZbA
Shiva Shankar S retweeted
PlasmoDocking: A User-Friendly Open-Source Web Tool for Virtual Screening Targeting Plasmodium falciparum Enzymes 1. PlasmoDocking is a novel web-based platform designed to simplify and accelerate the process of virtual screening for potential antimalarial compounds. It…
Shiva Shankar S retweeted
1/ 🚀 Introducing AIDO.StructureDiffusion: A generative model for structural protein design—enabling high-quality, controllable generation of monomers, complexes, and antibodies. 🧵
Shiva Shankar S retweeted
Evaluation of De Novo Deep Learning Models on the Protein-Sugar Interactome 1. A new study evaluates the performance of various deep learning models, including AlphaFold3, Boltz-1, Chai-1, DiffDock, and RosettaFold-All Atom, on predicting noncovalent protein-carbohydrate…
Shiva Shankar S retweeted
A joint sequence-structure diffusion model for transmembrane proteins!
Shiva Shankar S retweeted
Generating Functional and Multistate Proteins with a Multimodal Diffusion Transformer 1. A groundbreaking study introduces ProDiT, a multimodal diffusion model that integrates sequence and structure modeling to design functional proteins at scale. This approach leverages the…
Shiva Shankar S retweeted
Guided docking using solvent structure information improves the prediction of protein-glycans complexes 1. A new study has made significant strides in predicting the structure of protein-carbohydrate complexes, a challenge due to the flexibility of glycans and their shallow,…
Shiva Shankar S retweeted
New content online: Two decades into the crosstalk between bone and energy metabolism bit.ly/46lB3aG
Shiva Shankar S retweeted
Targeting ceramide synthases for the development of new antifungals dlvr.it/TMtFzk
Shiva Shankar S retweeted
Great blogpost by Nick Boyd and Sam Guns from Escalante Bio (posted on the other site!) blog.escalante.bio/minibinder-des… They introduce mosaic for binder design, and show some impressive results, with 7/10 and 8/10 binders working for two targets! github.com/escalante-bio/…
Shiva Shankar S retweeted
FreeBindCraft brings open-source protein design to everyone. By replacing PyRosetta with MIT/BSD-licensed alternatives, BindCraft has been freed from its licensing constraints. Available now on Ariax! Read our announcement at ariax.bio/resources/free…
Shiva Shankar S retweeted
AlphaFold modeling uncovers global structural features of class I and class II fungal hydrophobins 1. A new study by Yang et al. leverages AlphaFold to explore the structural universe of fungal hydrophobins, revealing novel insights into their global features and potential…
Shiva Shankar S retweeted
OTMol: Robust Molecular Structure Comparison via Optimal Transport 1. A groundbreaking method named OTMol has been introduced to tackle the challenge of molecular structure comparison. This method leverages optimal transport theory to achieve robust and accurate alignment of…
Shiva Shankar S retweeted
Shivering, but not adipose tissue thermogenesis, increases as a function of mean skin temperature in cold-exposed men and women dlvr.it/TMr1ZH
Shiva Shankar S retweeted
Engineering enzymes for solvent & heat stability boosts industrial biocatalysis! #EnzymeEngineering Details： doi.org/10.1016/j.bide…
Shiva Shankar S retweeted
Very happy to share that validation of our AMP-Diffusion model that we introduced last year has been published in @CellBiomat! 🦠🥳Very thankful for our experimental collaborators @delafuentelab for testing it out! 🙏🐁 📜: cell.com/cell-biomateri… 💻: github.com/programmablebi……
Shiva Shankar S retweeted
Excited to share our latest in @CellBiomat @CellPressNews! We present a generative AI approach that designs novel antibiotics from scratch. Using diffusion models guided by a protein LM (ESM-2), we sample novel, grammar-consistent sequences and triage them with our APEX AI…
Shiva Shankar S retweeted
Online now! Code to complex: AI-driven de novo binder design dlvr.it/TMpWry
Shiva Shankar S retweeted
Unlocking longevity through the comparative biology of aging | Nature Aging nature.com/articles/s4358…
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