Tootfinder

interactome_figeys: Figeys human interactome (2007)
A network of human proteins and their binding interactions. Nodes represent proteins and an edge represents an interaction between two proteins, as inferred using a mass spectrometry‐based approach.
This network has 2239 nodes and 6452 edges.
Tags: Biological, Protein interactions, Unweighted

interactome_yeast: Coulomb yeast interactome (2005)
A network of protein-protein binding interactions among yeast proteins. Nodes represent proteins found in yeast (Saccharomyces cerevisiae) and an edge represents a binding interaction between two proteins.
This network has 1870 nodes and 2277 edges.
Tags: Biological, Protein interactions, Unweighted

Plant-Based Proteins Are Cheaper Than Meat Right Now #plantbased

Plant-Based Proteins Are Cheaper Than Meat Right Now
A new report has found that as the price of animal products skyrockets in the UK, certain plant-based proteins are now cheaper than meat

interactome_stelzl: Stelzl human interactome (2005)
A network of human proteins and their binding interactions. Nodes represent proteins and an edge represents an interaction between two proteins, as inferred via high-throughput Y2H experiments using bait and prey methodology.
This network has 1706 nodes and 6207 edges.
Tags: Biological, Protein interactions, Unweighted

🎨 Mix insect, plant and cultivated proteins for healthier, greener, tastier food, say experts
https://phys.org/news/2025-09-insect-cultivated-proteins-healthier-greener.html

Mix insect, plant and cultivated proteins for healthier, greener, tastier food, say experts
Reducing industrial animal use can help to shrink our carbon footprint and boost health—but doing so means we need nutritious meat alternatives that are also tasty and affordable.

interactome_yeast: Coulomb yeast interactome (2005)
A network of protein-protein binding interactions among yeast proteins. Nodes represent proteins found in yeast (Saccharomyces cerevisiae) and an edge represents a binding interaction between two proteins.
This network has 1870 nodes and 2277 edges.
Tags: Biological, Protein interactions, Unweighted

Profluent, which wants to use AI for protein design in drug discovery, raised $106M led by Bezos Expeditions and Altimeter, bringing its total funding to $150M (Amy Feldman/Forbes)
http://www.forbes.com/sites/amyfeldman/20

Jeff Bezos Is Backing An AI Startup Aiming To Make Proteins Programmable
Profluent has raised $106 million to scale up use of its AI models for biology in drug development and agriculture.

interactome_yeast: Coulomb yeast interactome (2005)
A network of protein-protein binding interactions among yeast proteins. Nodes represent proteins found in yeast (Saccharomyces cerevisiae) and an edge represents a binding interaction between two proteins.
This network has 1870 nodes and 2277 edges.
Tags: Biological, Protein interactions, Unweighted

drosophila_flybi: Fruit fly protein interactions (Drosophila melanogaster)
Binary protein-protein interactions (PPIs) for Drosophila melanogaster, containing 8723 PPIs among 2939 proteins. The iteractions were identified using a yeast two-hybrid (Y2H) analysis.
This network has 2939 nodes and 8723 edges.
Tags: Biological, Protein interactions, Unweighted

interactome_pdz: PDZ-domain interactome (2005)
A network of PDZ-domain-mediated protein–protein binding interactions, extracted from the PDZBase database. Nodes represent proteins and an edge represents a binding interaction between two proteins.
This network has 212 nodes and 244 edges.
Tags: Biological, Protein interactions, Unweighted

🥫 Artificial proteins offer new path for fast, sustainable and biocompatible energy storage devices
https://techxplore.com/news/2025-11-artificial-proteins-path-fast-sustainable.html

Artificial proteins offer new path for fast, sustainable and biocompatible energy storage devices
Researchers have managed to modify a class of proteins to give them the ability to transport and store electricity. These proteins can be used to create sustainable, efficient and biocompatible conducting materials. These materials are highly stable and easy to process, which means they can be incorporated into industrial processes.

@… at least, some proof of your existence.
"In a twist, the findings lend credence to the Australian folk hoax of the “drop bear,” a ferocious, carnivorous variety of koala said to fall upon its victims from the canopy. Paleontologists think Thylacoleo was an adept climber and ambush predator that could dive upon its prey from tree branches or roc…

I would like everyone who is calling to ban animal meat to realize that many people have food allergies or reactions—often especially to proteins found in plant-based simulated meat (gluten, corn, soy, etc.).
Can we please keep this all inclusive and not a fight that's done on the backs of disabled people?
Thanks for coming to my TED talk.

interactome_figeys: Figeys human interactome (2007)
A network of human proteins and their binding interactions. Nodes represent proteins and an edge represents an interaction between two proteins, as inferred using a mass spectrometry‐based approach.
This network has 2239 nodes and 6452 edges.
Tags: Biological, Protein interactions, Unweighted

Doctors made a custom CRISPR therapy to treat an infant with a rare genetic disease
A baby, named KJ, was born with a deficiency in carbamoyl phosphate synthetase 1 (CPS1).
This deficiency means his liver couldn’t convert ammonia
– which is made naturally when the body breaks down proteins
– into urea, damaging his brain and liver.
Babies born with CPS1 deficiency often end up staying in the hospital until they’re eligible for a liver transplant.
They h…

Interaction Dynamics of Borrelia Surface Proteins with Fibronectin
Kavindi Madduma Hewage, Carlos Munoz, Mehmet Ozdogan, Catherine A. Brissette, Nuri Oncel
https://arxiv.org/abs/2510.11931

Interaction Dynamics of Borrelia Surface Proteins with Fibronectin
Lyme disease, caused by the bacterium Borrelia burgdorferi, is a significant public health concern in North America, with approximately 500,000 cases reported annually in the United States. The dissemination of B. burgdorferi from the initial tick bite site to various tissues is facilitated by surface adhesins that bind to extracellular matrix (ECM) proteins such as fibronectin (Fn). This study investigates the binding dynamics of B. burgdorferi surface proteins RevA, BBK32, BmpA, OspA, and Osp…

Weekend #Plankton Factoid 🦠🦐
Tintinnids ("tinkling bells") are ciliates found in fresh and saltwater known for their characteristic vase-shaped shell called a lorica. These are formed of tough proteins, incorporating minerals from the water and vary considerably by species. The shell offers protection and optimizes feeding on phytoplankton, bacteria and flagellates. These small pro…

interactome_figeys: Figeys human interactome (2007)
A network of human proteins and their binding interactions. Nodes represent proteins and an edge represents an interaction between two proteins, as inferred using a mass spectrometry‐based approach.
This network has 2239 nodes and 6452 edges.
Tags: Biological, Protein interactions, Unweighted

reactome: Joshi-Tope human protein interactome (2005)
A network of human proteins and their binding interactions, extracted from Reactome project. Nodes represent proteins and an edge represents a binding interaction between two proteins.
This network has 6327 nodes and 147547 edges.
Tags: Biological, Protein interactions, Unweighted
https:/…

🌞 Tiny engine runs hotter than the sun to probe the frontiers of thermodynamics
#physics

Tiny engine runs hotter than the sun to probe the frontiers of thermodynamics
Scientists have created the world's hottest engine running at temperatures hotter than those reached in the sun's core. The team from King's College London and collaborators believe their platform could provide an unparalleled understanding of the laws of thermodynamics on a small scale, and provide the foundation for a new, efficient way to compute how proteins fold—the subject of last year's Nobel Prize in Chemistry.

Impact of Force Field Polarization on Correlated Motions of Proteins
Ana Milinski (IGBMC), Annick Dejaegere (IGBMC), Roland Stote (IGBMC)
https://arxiv.org/abs/2510.04897 https:…

Impact of Force Field Polarization on Correlated Motions of Proteins
Correlated motions of proteins underpin many physiological mechanisms, such as substrate binding, signal transduction, enzymatic activity and allostery. These motions arise from low frequency collective movements of biomolecules and have mostly been studied using molecular dynamics simulations. Here, we present the effects of two different empirical energy force fields used for molecular dynamics simulations on correlated motions -- the non-polarizable CHARMM 36m additive force field and the po…

interactome_figeys: Figeys human interactome (2007)
A network of human proteins and their binding interactions. Nodes represent proteins and an edge represents an interaction between two proteins, as inferred using a mass spectrometry‐based approach.
This network has 2239 nodes and 6452 edges.
Tags: Biological, Protein interactions, Unweighted

Effect of ice nucleating proteins on the structure-property relationships of ice: A molecular dynamics study
A. K. Shargh, C. D. Stiles, J. A. El-Awady
https://arxiv.org/abs/2510.04892

Effect of ice nucleating proteins on the structure-property relationships of ice: A molecular dynamics study
Ice-nucleating proteins (INPs) are a unique class of biological macromolecules that catalyze the freezing of supercooled water far more efficiently than homogeneous nucleation. Their remarkable efficiency has motivated applications across diverse sectors, including agricultural frost protection, food processing and packaging, biomedical cryopreservation, and even strategies for mitigating glacier ice loss. The ice-nucleation performance of INPs and the mechanical behavior of the ice they produc…

reactome: Joshi-Tope human protein interactome (2005)
A network of human proteins and their binding interactions, extracted from Reactome project. Nodes represent proteins and an edge represents a binding interaction between two proteins.
This network has 6327 nodes and 147547 edges.
Tags: Biological, Protein interactions, Unweighted
https:/…

interactome_yeast: Coulomb yeast interactome (2005)
A network of protein-protein binding interactions among yeast proteins. Nodes represent proteins found in yeast (Saccharomyces cerevisiae) and an edge represents a binding interaction between two proteins.
This network has 1870 nodes and 2277 edges.
Tags: Biological, Protein interactions, Unweighted

Current flu vaccines induce immune defenses that target hemagglutinin,
one of the proteins jutting from the surface of a flu virus.
However, the outer portion of hemagglutinin changes quickly.
Researchers are trying several strategies to zero in on more stable parts of the viruses.
By analyzing multiple virus variants, Ross and his team identified sections of hemagglutinin that stay constant and then combined them to make vaccines. -- In their 2025 study, vaccines cre…

A Vaccine Big Shot - Lasker Foundation
OCT 14, 2025Read about Lasker Laureate Thomas Francis, who developed vaccines against influenza types A and B.

interactome_yeast: Coulomb yeast interactome (2005)
A network of protein-protein binding interactions among yeast proteins. Nodes represent proteins found in yeast (Saccharomyces cerevisiae) and an edge represents a binding interaction between two proteins.
This network has 1870 nodes and 2277 edges.
Tags: Biological, Protein interactions, Unweighted

🧠 A molecular atlas of the hippocampus: Mapping RNAs and proteins at synaptic resolution
https://medicalxpress.com/news/2025-09-molecular-atlas-hippocampus-rnas-proteins.html

A molecular atlas of the hippocampus: Mapping RNAs and proteins at synaptic resolution
Researchers at the Max Planck Institute for Brain Research have mapped the molecular landscape of the mouse hippocampus, a region central to learning and memory. By combining RNA and protein profiling with advanced methods to isolate brain regions and synapses, the team identified thousands of molecules with distinct spatial patterns.

interactome_stelzl: Stelzl human interactome (2005)
A network of human proteins and their binding interactions. Nodes represent proteins and an edge represents an interaction between two proteins, as inferred via high-throughput Y2H experiments using bait and prey methodology.
This network has 1706 nodes and 6207 edges.
Tags: Biological, Protein interactions, Unweighted

interactome_pdz: PDZ-domain interactome (2005)
A network of PDZ-domain-mediated protein–protein binding interactions, extracted from the PDZBase database. Nodes represent proteins and an edge represents a binding interaction between two proteins.
This network has 212 nodes and 244 edges.
Tags: Biological, Protein interactions, Unweighted

interactome_stelzl: Stelzl human interactome (2005)
A network of human proteins and their binding interactions. Nodes represent proteins and an edge represents an interaction between two proteins, as inferred via high-throughput Y2H experiments using bait and prey methodology.
This network has 1706 nodes and 6207 edges.
Tags: Biological, Protein interactions, Unweighted

Modeling Protein Diffusion Across ER-Nuclear Envelope Junctions Reveals Efficient Transport via Simple Diffusion
Sara Merino-Aceituno, Carmela Moschella, Shotaro Otsuka, Christian Schmeiser, Julia Scholz
https://arxiv.org/abs/2510.09479

Modeling Protein Diffusion Across ER-Nuclear Envelope Junctions Reveals Efficient Transport via Simple Diffusion
The endoplasmic reticulum (ER) is the largest continuous membrane-bound organelle in the cell and plays a central role in the synthesis and turnover of many lipids and proteins. It connects directly to the nucleus through specialized contact points known as ER-nuclear envelope (NE) junctions. In our recent study, we found that these ER-NE junctions are both narrow and infrequent, measuring less than 20 nanometers in diameter and occurring at a frequency of approximately 0.1 per square micromete…

interactome_stelzl: Stelzl human interactome (2005)
A network of human proteins and their binding interactions. Nodes represent proteins and an edge represents an interaction between two proteins, as inferred via high-throughput Y2H experiments using bait and prey methodology.
This network has 1706 nodes and 6207 edges.
Tags: Biological, Protein interactions, Unweighted

Adaptive Protein Design Protocols and Middleware
Aymen Alsaadi, Jonathan Ash, Mikhail Titov, Matteo Turilli, Andre Merzky, Shantenu Jha, Sagar Khare
https://arxiv.org/abs/2510.06396

Adaptive Protein Design Protocols and Middleware
Computational protein design is experiencing a transformation driven by AI/ML. However, the range of potential protein sequences and structures is astronomically vast, even for moderately sized proteins. Hence, achieving convergence between generated and predicted structures demands substantial computational resources for sampling. The Integrated Machine-learning for Protein Structures at Scale (IMPRESS) offers methods and advanced computing systems for coupling AI to high-performance computing…

interactome_stelzl: Stelzl human interactome (2005)
A network of human proteins and their binding interactions. Nodes represent proteins and an edge represents an interaction between two proteins, as inferred via high-throughput Y2H experiments using bait and prey methodology.
This network has 1706 nodes and 6207 edges.
Tags: Biological, Protein interactions, Unweighted

reactome: Joshi-Tope human protein interactome (2005)
A network of human proteins and their binding interactions, extracted from Reactome project. Nodes represent proteins and an edge represents a binding interaction between two proteins.
This network has 6327 nodes and 147547 edges.
Tags: Biological, Protein interactions, Unweighted
https:/…

Constructing a Nanopipette-based DNA Electro-Mechanical Device
Cengiz J. Khan, Oliver J. Irving, Rand A. Al-Waqfi, Giorgio Ferrari, Tim Albrecht
https://arxiv.org/abs/2510.10515

Constructing a Nanopipette-based DNA Electro-Mechanical Device
Solid-state nanopore and nanopipette sensors are powerful devices for the detection, quantification and structural analysis of biopolymers such as DNA and proteins, especially in carrier-enhanced resistive-pulse sensing. However, hundreds of different molecules typically need to be sampled from solution and analysed to obtain statistically robust information. This limits the applicability of such sensors and complicates associated workflows. Here, we present a new strategy to trap DNA structure…

interactome_vidal: Vidal human interactome (2005)
A network of human proteins and their binding interactions. Nodes represent proteins and an edge represents a binding interaction between two proteins, as tested using a high-throughput yeast two-hybrid (Y2H) system.
This network has 3133 nodes and 6726 edges.
Tags: Biological, Protein interactions, Unweighted

interactome_figeys: Figeys human interactome (2007)
A network of human proteins and their binding interactions. Nodes represent proteins and an edge represents an interaction between two proteins, as inferred using a mass spectrometry‐based approach.
This network has 2239 nodes and 6452 edges.
Tags: Biological, Protein interactions, Unweighted

interactome_figeys: Figeys human interactome (2007)
A network of human proteins and their binding interactions. Nodes represent proteins and an edge represents an interaction between two proteins, as inferred using a mass spectrometry‐based approach.
This network has 2239 nodes and 6452 edges.
Tags: Biological, Protein interactions, Unweighted

interactome_stelzl: Stelzl human interactome (2005)
A network of human proteins and their binding interactions. Nodes represent proteins and an edge represents an interaction between two proteins, as inferred via high-throughput Y2H experiments using bait and prey methodology.
This network has 1706 nodes and 6207 edges.
Tags: Biological, Protein interactions, Unweighted

Replaced article(s) found for physics.chem-ph. https://arxiv.org/list/physics.chem-ph/new
[1/1]:
- Data-Error Scaling Laws in Machine Learning on Combinatorial Mutation-prone Sets: Proteins and Sm...
Vanni Doffini, O. Anatole von Lilienfeld, Michael A. Nash

Models of topological barriers and molecular motors of bacterial DNA
Marc Joyeux
https://arxiv.org/abs/2510.05790 https://arxiv.org/pdf/2510.05790

Models of topological barriers and molecular motors of bacterial DNA
Bacterial genomes are partitioned into kilobases long domains that are topologically independent from each other, meaning that change of DNA superhelicity in one domain does not propagate to neighbours. This is made possible by proteins like the LacI repressor, which behave like topological barriers and block the diffusion of torsion along the DNA. Other proteins, like DNA gyrases and RNA polymerases, called molecular motors, use the energy released by the hydrolysis of ATP to apply forces and/…

interactome_pdz: PDZ-domain interactome (2005)
A network of PDZ-domain-mediated protein–protein binding interactions, extracted from the PDZBase database. Nodes represent proteins and an edge represents a binding interaction between two proteins.
This network has 212 nodes and 244 edges.
Tags: Biological, Protein interactions, Unweighted

Fast and Interpretable Protein Substructure Alignment via Optimal Transport
Zhiyu Wang, Bingxin Zhou, Jing Wang, Yang Tan, Weishu Zhao, Pietro Li\`o, Liang Hong
https://arxiv.org/abs/2510.11752

Fast and Interpretable Protein Substructure Alignment via Optimal Transport
Proteins are essential biological macromolecules that execute life functions. Local motifs within protein structures, such as active sites, are the most critical components for linking structure to function and are key to understanding protein evolution and enabling protein engineering. Existing computational methods struggle to identify and compare these local structures, which leaves a significant gap in understanding protein structures and harnessing their functions. This study presents PLAS…

interactome_yeast: Coulomb yeast interactome (2005)
A network of protein-protein binding interactions among yeast proteins. Nodes represent proteins found in yeast (Saccharomyces cerevisiae) and an edge represents a binding interaction between two proteins.
This network has 1870 nodes and 2277 edges.
Tags: Biological, Protein interactions, Unweighted

interactome_stelzl: Stelzl human interactome (2005)
A network of human proteins and their binding interactions. Nodes represent proteins and an edge represents an interaction between two proteins, as inferred via high-throughput Y2H experiments using bait and prey methodology.
This network has 1706 nodes and 6207 edges.
Tags: Biological, Protein interactions, Unweighted

interactome_vidal: Vidal human interactome (2005)
A network of human proteins and their binding interactions. Nodes represent proteins and an edge represents a binding interaction between two proteins, as tested using a high-throughput yeast two-hybrid (Y2H) system.
This network has 3133 nodes and 6726 edges.
Tags: Biological, Protein interactions, Unweighted

interactome_stelzl: Stelzl human interactome (2005)
A network of human proteins and their binding interactions. Nodes represent proteins and an edge represents an interaction between two proteins, as inferred via high-throughput Y2H experiments using bait and prey methodology.
This network has 1706 nodes and 6207 edges.
Tags: Biological, Protein interactions, Unweighted

Isotropy and Geometry of Pretrained Protein LMs
Sheikh Azizul Hakim, Kowshic Roy, M Saifur Rahman
https://arxiv.org/abs/2510.10655 https://arxiv.org/pdf/25…

Isotropy and Geometry of Pretrained Protein LMs
Large pretrained language models have transformed natural language processing, and their adaptation to protein sequences -- viewed as strings of amino acid characters -- has advanced protein analysis. However, the distinct properties of proteins, such as variable sequence lengths and lack of word-sentence analogs, necessitate a deeper understanding of protein language models (LMs). We investigate the isotropy of protein LM embedding spaces using average pairwise cosine similarity and the IsoSco…

Ohta-Kawasaki Model Reveals Patterns on Multicomponent Vesicles
Wangbo Luo, Zhonghua Qiao, Yanxiang Zhao
https://arxiv.org/abs/2510.02688 https://arxiv.org…

Ohta-Kawasaki Model Reveals Patterns on Multicomponent Vesicles
We present a new mechanochemical modeling framework to explore the shape deformation and pattern formation in multicomponent vesicle membranes. In this framework, the shape of the membrane is described by an elastic bending model, while phase separation of membrane-bound activator proteins is determined by an Ohta-Kawasaki (OK) model. The coupled dynamics consist of an overdamped force-balanced equation for the membrane geometry and an OK-type advection-reaction-diffusion equation on the deform…

interactome_pdz: PDZ-domain interactome (2005)
A network of PDZ-domain-mediated protein–protein binding interactions, extracted from the PDZBase database. Nodes represent proteins and an edge represents a binding interaction between two proteins.
This network has 212 nodes and 244 edges.
Tags: Biological, Protein interactions, Unweighted

🔦 Engineered protein switches may lead to safer, smarter medicines
#biology

Engineered protein switches may lead to safer, smarter medicines
A new way to potentially control when drugs are active or inactive in the body is introduced in a study reported Sept. 24 in Nature. The research showed that, instead of controlling how tightly proteins bind to partner molecules, scientists can now directly control how long they stay bound. This advance has broad implications for developing safer medicines.

interactome_vidal: Vidal human interactome (2005)
A network of human proteins and their binding interactions. Nodes represent proteins and an edge represents a binding interaction between two proteins, as tested using a high-throughput yeast two-hybrid (Y2H) system.
This network has 3133 nodes and 6726 edges.
Tags: Biological, Protein interactions, Unweighted

reactome: Joshi-Tope human protein interactome (2005)
A network of human proteins and their binding interactions, extracted from Reactome project. Nodes represent proteins and an edge represents a binding interaction between two proteins.
This network has 6327 nodes and 147547 edges.
Tags: Biological, Protein interactions, Unweighted
https:/…

interactome_yeast: Coulomb yeast interactome (2005)
A network of protein-protein binding interactions among yeast proteins. Nodes represent proteins found in yeast (Saccharomyces cerevisiae) and an edge represents a binding interaction between two proteins.
This network has 1870 nodes and 2277 edges.
Tags: Biological, Protein interactions, Unweighted

PRISM: Enhancing Protein Inverse Folding through Fine-Grained Retrieval on Structure-Sequence Multimodal Representations
Sazan Mahbub, Souvik Kundu, Eric P. Xing
https://arxiv.org/abs/2510.11750

PRISM: Enhancing Protein Inverse Folding through Fine-Grained Retrieval on Structure-Sequence Multimodal Representations
Designing protein sequences that fold into a target three-dimensional structure, known as the inverse folding problem, is central to protein engineering but remains challenging due to the vast sequence space and the importance of local structural constraints. Existing deep learning approaches achieve strong recovery rates, yet they lack explicit mechanisms to reuse fine-grained structure-sequence patterns that are conserved across natural proteins. We present PRISM, a multimodal retrieval-augme…

interactome_vidal: Vidal human interactome (2005)
A network of human proteins and their binding interactions. Nodes represent proteins and an edge represents a binding interaction between two proteins, as tested using a high-throughput yeast two-hybrid (Y2H) system.
This network has 3133 nodes and 6726 edges.
Tags: Biological, Protein interactions, Unweighted

interactome_stelzl: Stelzl human interactome (2005)
A network of human proteins and their binding interactions. Nodes represent proteins and an edge represents an interaction between two proteins, as inferred via high-throughput Y2H experiments using bait and prey methodology.
This network has 1706 nodes and 6207 edges.
Tags: Biological, Protein interactions, Unweighted

reactome: Joshi-Tope human protein interactome (2005)
A network of human proteins and their binding interactions, extracted from Reactome project. Nodes represent proteins and an edge represents a binding interaction between two proteins.
This network has 6327 nodes and 147547 edges.
Tags: Biological, Protein interactions, Unweighted
https:/…

Space-filling discrete helices
Jayanth R. Banavar, Achille Giacometti, Trinh X. Hoang, Amos Maritan, Tatjana \v{S}krbi\'c
https://arxiv.org/abs/2510.07011 https://

Space-filling discrete helices
Proteins are linear chain molecules that play a central role in life and health. Protein native state folds are modular assemblies of space-filling building blocks of α-helices, \{beta}-sheets and tight turns. Here we deduce the structures of a countable set of space-filling helical forms of a uniform discrete thick string from first principles with no additional input or adjustable parameters. These forms occur in correspondence with the natural numbers, loosely analogous to the energy levels…

interactome_pdz: PDZ-domain interactome (2005)
A network of PDZ-domain-mediated protein–protein binding interactions, extracted from the PDZBase database. Nodes represent proteins and an edge represents a binding interaction between two proteins.
This network has 212 nodes and 244 edges.
Tags: Biological, Protein interactions, Unweighted

interactome_yeast: Coulomb yeast interactome (2005)
A network of protein-protein binding interactions among yeast proteins. Nodes represent proteins found in yeast (Saccharomyces cerevisiae) and an edge represents a binding interaction between two proteins.
This network has 1870 nodes and 2277 edges.
Tags: Biological, Protein interactions, Unweighted

drosophila_flybi: Fruit fly protein interactions (Drosophila melanogaster)
Binary protein-protein interactions (PPIs) for Drosophila melanogaster, containing 8723 PPIs among 2939 proteins. The iteractions were identified using a yeast two-hybrid (Y2H) analysis.
This network has 2939 nodes and 8723 edges.
Tags: Biological, Protein interactions, Unweighted

interactome_stelzl: Stelzl human interactome (2005)
A network of human proteins and their binding interactions. Nodes represent proteins and an edge represents an interaction between two proteins, as inferred via high-throughput Y2H experiments using bait and prey methodology.
This network has 1706 nodes and 6207 edges.
Tags: Biological, Protein interactions, Unweighted

interactome_yeast: Coulomb yeast interactome (2005)
A network of protein-protein binding interactions among yeast proteins. Nodes represent proteins found in yeast (Saccharomyces cerevisiae) and an edge represents a binding interaction between two proteins.
This network has 1870 nodes and 2277 edges.
Tags: Biological, Protein interactions, Unweighted

UniOTalign: A Global Matching Framework for Protein Alignment via Optimal Transport
Yue Hu, Zanxia Cao, Yingchao Liu
https://arxiv.org/abs/2510.06554 https://

UniOTalign: A Global Matching Framework for Protein Alignment via Optimal Transport
Protein sequence alignment is a cornerstone of bioinformatics, traditionally approached using dynamic programming (DP) algorithms that find an optimal sequential path. This paper introduces UniOTalign, a novel framework that recasts alignment from a fundamentally different perspective: global matching via Optimal Transport (OT). Instead of finding a path, UniOTalign computes an optimal flow or transport plan between two proteins, which are represented as distributions of residues in a high-dime…

interactome_yeast: Coulomb yeast interactome (2005)
A network of protein-protein binding interactions among yeast proteins. Nodes represent proteins found in yeast (Saccharomyces cerevisiae) and an edge represents a binding interaction between two proteins.
This network has 1870 nodes and 2277 edges.
Tags: Biological, Protein interactions, Unweighted

interactome_stelzl: Stelzl human interactome (2005)
A network of human proteins and their binding interactions. Nodes represent proteins and an edge represents an interaction between two proteins, as inferred via high-throughput Y2H experiments using bait and prey methodology.
This network has 1706 nodes and 6207 edges.
Tags: Biological, Protein interactions, Unweighted

reactome: Joshi-Tope human protein interactome (2005)
A network of human proteins and their binding interactions, extracted from Reactome project. Nodes represent proteins and an edge represents a binding interaction between two proteins.
This network has 6327 nodes and 147547 edges.
Tags: Biological, Protein interactions, Unweighted
https:/…

reactome: Joshi-Tope human protein interactome (2005)
A network of human proteins and their binding interactions, extracted from Reactome project. Nodes represent proteins and an edge represents a binding interaction between two proteins.
This network has 6327 nodes and 147547 edges.
Tags: Biological, Protein interactions, Unweighted
https:/…

interactome_pdz: PDZ-domain interactome (2005)
A network of PDZ-domain-mediated protein–protein binding interactions, extracted from the PDZBase database. Nodes represent proteins and an edge represents a binding interaction between two proteins.
This network has 212 nodes and 244 edges.
Tags: Biological, Protein interactions, Unweighted

interactome_yeast: Coulomb yeast interactome (2005)
A network of protein-protein binding interactions among yeast proteins. Nodes represent proteins found in yeast (Saccharomyces cerevisiae) and an edge represents a binding interaction between two proteins.
This network has 1870 nodes and 2277 edges.
Tags: Biological, Protein interactions, Unweighted

interactome_vidal: Vidal human interactome (2005)
A network of human proteins and their binding interactions. Nodes represent proteins and an edge represents a binding interaction between two proteins, as tested using a high-throughput yeast two-hybrid (Y2H) system.
This network has 3133 nodes and 6726 edges.
Tags: Biological, Protein interactions, Unweighted

interactome_stelzl: Stelzl human interactome (2005)
A network of human proteins and their binding interactions. Nodes represent proteins and an edge represents an interaction between two proteins, as inferred via high-throughput Y2H experiments using bait and prey methodology.
This network has 1706 nodes and 6207 edges.
Tags: Biological, Protein interactions, Unweighted

interactome_figeys: Figeys human interactome (2007)
A network of human proteins and their binding interactions. Nodes represent proteins and an edge represents an interaction between two proteins, as inferred using a mass spectrometry‐based approach.
This network has 2239 nodes and 6452 edges.
Tags: Biological, Protein interactions, Unweighted

reactome: Joshi-Tope human protein interactome (2005)
A network of human proteins and their binding interactions, extracted from Reactome project. Nodes represent proteins and an edge represents a binding interaction between two proteins.
This network has 6327 nodes and 147547 edges.
Tags: Biological, Protein interactions, Unweighted
https:/…

interactome_pdz: PDZ-domain interactome (2005)
A network of PDZ-domain-mediated protein–protein binding interactions, extracted from the PDZBase database. Nodes represent proteins and an edge represents a binding interaction between two proteins.
This network has 212 nodes and 244 edges.
Tags: Biological, Protein interactions, Unweighted

interactome_yeast: Coulomb yeast interactome (2005)
A network of protein-protein binding interactions among yeast proteins. Nodes represent proteins found in yeast (Saccharomyces cerevisiae) and an edge represents a binding interaction between two proteins.
This network has 1870 nodes and 2277 edges.
Tags: Biological, Protein interactions, Unweighted

interactome_yeast: Coulomb yeast interactome (2005)
A network of protein-protein binding interactions among yeast proteins. Nodes represent proteins found in yeast (Saccharomyces cerevisiae) and an edge represents a binding interaction between two proteins.
This network has 1870 nodes and 2277 edges.
Tags: Biological, Protein interactions, Unweighted

interactome_figeys: Figeys human interactome (2007)
A network of human proteins and their binding interactions. Nodes represent proteins and an edge represents an interaction between two proteins, as inferred using a mass spectrometry‐based approach.
This network has 2239 nodes and 6452 edges.
Tags: Biological, Protein interactions, Unweighted

interactome_pdz: PDZ-domain interactome (2005)
A network of PDZ-domain-mediated protein–protein binding interactions, extracted from the PDZBase database. Nodes represent proteins and an edge represents a binding interaction between two proteins.
This network has 212 nodes and 244 edges.
Tags: Biological, Protein interactions, Unweighted

interactome_pdz: PDZ-domain interactome (2005)
A network of PDZ-domain-mediated protein–protein binding interactions, extracted from the PDZBase database. Nodes represent proteins and an edge represents a binding interaction between two proteins.
This network has 212 nodes and 244 edges.
Tags: Biological, Protein interactions, Unweighted

interactome_pdz: PDZ-domain interactome (2005)
A network of PDZ-domain-mediated protein–protein binding interactions, extracted from the PDZBase database. Nodes represent proteins and an edge represents a binding interaction between two proteins.
This network has 212 nodes and 244 edges.
Tags: Biological, Protein interactions, Unweighted

drosophila_flybi: Fruit fly protein interactions (Drosophila melanogaster)
Binary protein-protein interactions (PPIs) for Drosophila melanogaster, containing 8723 PPIs among 2939 proteins. The iteractions were identified using a yeast two-hybrid (Y2H) analysis.
This network has 2939 nodes and 8723 edges.
Tags: Biological, Protein interactions, Unweighted

interactome_pdz: PDZ-domain interactome (2005)
A network of PDZ-domain-mediated protein–protein binding interactions, extracted from the PDZBase database. Nodes represent proteins and an edge represents a binding interaction between two proteins.
This network has 212 nodes and 244 edges.
Tags: Biological, Protein interactions, Unweighted

drosophila_flybi: Fruit fly protein interactions (Drosophila melanogaster)
Binary protein-protein interactions (PPIs) for Drosophila melanogaster, containing 8723 PPIs among 2939 proteins. The iteractions were identified using a yeast two-hybrid (Y2H) analysis.
This network has 2939 nodes and 8723 edges.
Tags: Biological, Protein interactions, Unweighted

drosophila_flybi: Fruit fly protein interactions (Drosophila melanogaster)
Binary protein-protein interactions (PPIs) for Drosophila melanogaster, containing 8723 PPIs among 2939 proteins. The iteractions were identified using a yeast two-hybrid (Y2H) analysis.
This network has 2939 nodes and 8723 edges.
Tags: Biological, Protein interactions, Unweighted

interactome_pdz: PDZ-domain interactome (2005)
A network of PDZ-domain-mediated protein–protein binding interactions, extracted from the PDZBase database. Nodes represent proteins and an edge represents a binding interaction between two proteins.
This network has 212 nodes and 244 edges.
Tags: Biological, Protein interactions, Unweighted

interactome_pdz: PDZ-domain interactome (2005)
A network of PDZ-domain-mediated protein–protein binding interactions, extracted from the PDZBase database. Nodes represent proteins and an edge represents a binding interaction between two proteins.
This network has 212 nodes and 244 edges.
Tags: Biological, Protein interactions, Unweighted

drosophila_flybi: Fruit fly protein interactions (Drosophila melanogaster)
Binary protein-protein interactions (PPIs) for Drosophila melanogaster, containing 8723 PPIs among 2939 proteins. The iteractions were identified using a yeast two-hybrid (Y2H) analysis.
This network has 2939 nodes and 8723 edges.
Tags: Biological, Protein interactions, Unweighted

drosophila_flybi: Fruit fly protein interactions (Drosophila melanogaster)
Binary protein-protein interactions (PPIs) for Drosophila melanogaster, containing 8723 PPIs among 2939 proteins. The iteractions were identified using a yeast two-hybrid (Y2H) analysis.
This network has 2939 nodes and 8723 edges.
Tags: Biological, Protein interactions, Unweighted

drosophila_flybi: Fruit fly protein interactions (Drosophila melanogaster)
Binary protein-protein interactions (PPIs) for Drosophila melanogaster, containing 8723 PPIs among 2939 proteins. The iteractions were identified using a yeast two-hybrid (Y2H) analysis.
This network has 2939 nodes and 8723 edges.
Tags: Biological, Protein interactions, Unweighted

drosophila_flybi: Fruit fly protein interactions (Drosophila melanogaster)
Binary protein-protein interactions (PPIs) for Drosophila melanogaster, containing 8723 PPIs among 2939 proteins. The iteractions were identified using a yeast two-hybrid (Y2H) analysis.
This network has 2939 nodes and 8723 edges.
Tags: Biological, Protein interactions, Unweighted

drosophila_flybi: Fruit fly protein interactions (Drosophila melanogaster)
Binary protein-protein interactions (PPIs) for Drosophila melanogaster, containing 8723 PPIs among 2939 proteins. The iteractions were identified using a yeast two-hybrid (Y2H) analysis.
This network has 2939 nodes and 8723 edges.
Tags: Biological, Protein interactions, Unweighted