From biorxiv.org
Orthrus: an AI-powered, cloud-ready, and open-source hybrid approach for metaproteomics
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While metaproteomics provides invaluable insight into microbial communities and functions, significant bioinformatics challenges persist due to data complexity and the limitations of database searching. We introduce Orthrus, a hybrid approach combining transformer-based de novo sequencing...
20h ago
From doi.org
MarkerDB 2.0: a comprehensive molecular biomarker database for 2025
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Abstract. MarkerDB (https://markerdb.ca) has become a leading resource for comprehensive information on molecular biomarkers. Over the past 3 years, the da
11h ago
From frontiersin.org
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The identification of effective, selective biomarkers and therapeutics is dependent on truly deep, comprehensive analysis of proteomes at the proteoform leve...
12h ago
From biorxiv.org
Characterising Protein Search Drift using exhaustive protein search and Alphafold2
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In this paper we present the first exhaustive analysis of iterative protein search drift and show how such results may impact downstream modelling. Assembling and extracting evolutionary information from families of related proteins is a core challenge in the studey of molecular evolution. For...
14h ago
From biorxiv.org
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Many proteins can exist in multiple conformational states in vivo to achieve distinct functional roles. These states include alternative conformations, variable PTMs, and association with interacting protein, nucleotide, and ligand partners. Quantitative chemical cross-linking of live cells,...
15h ago
From biorxiv.org
InterPLM: Discovering Interpretable Features in Protein Language Models via Sparse Autoencoders
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Protein language models (PLMs) have demonstrated remarkable success in protein modeling and design, yet their internal mechanisms for predicting structure and function remain poorly understood. Here we present a systematic approach to extract and analyze interpretable features from PLMs using...
15h ago
From biorxiv.org
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The human genome has been the subject of intense scrutiny by experimental and manual curation projects for more than two decades. Novel coding genes have been proposed from large-scale RNASeq, ribosome profiling and proteomics experiments. Here we carry out an in-depth analysis of an entire...
16h ago
From springer.com
Decoding Ubiquitin Modifications by Mass Spectrometry
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Protein ubiquitination is a critical and widely distributed post-translational modification (PTM) involved in the regulation of almost every cellular process and pathway in cells, such as proteostasis, DNA repair, trafficking, and immunity. Mass spectrometry...
on Sat, 1AM
From biorxiv.org
TopLib: Building and searching top-down mass spectral libraries for proteoform identification
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Mass spectral library search is a widely used approach for spectral identification in mass spectrometry (MS)-based proteomics. While numerous methods exist for building and searching bottom-up mass spectral libraries, there is a lack of software tools for top-down mass spectral libraries. To...
on Sat, 1AM
From arxiv.org
Computational Methods to Investigate Intrinsically Disordered Proteins and their Complexes
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In 1999 Wright and Dyson highlighted the fact that large sections of the proteome of all organisms are comprised of protein sequences that lack globular folded structures under physiological conditions. Since then the biophysics community has made significant strides in unraveling the intricate...
on Sep 6