ANTHEPROT: a package for protein sequence analysis using a microcomputer
Comput. Appl. Biosci., 1988 A simple microcomputer package is described to make the theoretical analysis of protein sequences. Several methods designed to compare two sequences, to model proteolytic reactions and to predict the secondary structure, the hydrophobic/hydrophilic ...
G. Deléage +3 more
semanticscholar +1 more source
Improved contact prediction in proteins: Using pseudolikelihoods to infer Potts models
, 2013 Spatially proximate amino acids in a protein tend to coevolve. A protein's three-dimensional (3D) structure hence leaves an echo of correlations in the evolutionary record.
Aurell, Erik +4 more
core +1 more source
Subpar reporting of pre‐analytical variables in RNA‐focused blood plasma studies
Molecular Oncology, EarlyView.Pre‐analytical variables strongly influence the analysis of extracellular RNA (cell‐free RNA; exRNA) derived from blood plasma. Their reporting is essential to allow interpretation and replication of results. By evaluating 200 exRNA studies, we pinpoint a lack of reporting pre‐analytical variables associated with blood collection, plasma preparation ...
Céleste Van Der Schueren +16 more
wiley +1 more source
De Novo Functional Protein Sequence Generation: Overcoming Data Scarcity through Regeneration and Large Models [PDF]
arXivProteins are essential components of all living organisms and play a critical role in cellular survival. They have a broad range of applications, from clinical treatments to material engineering. This versatility has spurred the development of protein design, with amino acid sequence design being a crucial step in the process.
arxiv
Analysis of the 3′-terminal nucleotide sequence of vesicular stomatitis virus N protein mRNA [PDF]
, 1978 Duncan J. McGeoch, Nancy T. Turnbull
openalex +1 more source
, 2012 Wang-Landau sampling has been applied to investigate the thermodynamics and structural properties of a lattice hydrophobic-polar heteropolymer (the HP protein model) interacting with an attractive substrate.
Landau, David P. +2 more
core +1 more source
Molecular Oncology, EarlyView.Cancer‐associated fibroblasts (CAFs) promote cancer growth, invasion (metastasis), and drug resistance. Here, we identified functional and diverse circulating CAFs (cCAFs) in patients with metastatic prostate cancer (mPCa). cCAFs were found in higher numbers and were functional and diverse in mPCa patients versus healthy individuals, suggesting their ...
Richell Booijink +6 more
wiley +1 more source
ProtFlow: Fast Protein Sequence Design via Flow Matching on Compressed Protein Language Model Embeddings [PDF]
arXivThe design of protein sequences with desired functionalities is a fundamental task in protein engineering. Deep generative methods, such as autoregressive models and diffusion models, have greatly accelerated the discovery of novel protein sequences.
arxiv
Analysis of the code relating sequence to conformation in globular proteins. An informational analysis of the role of the residue in determining the conformation of its neighbours in the primary sequence [PDF]
, 1974 Barry Robson, Roger H. Pain
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Surfaceome: a new era in the discovery of immune evasion mechanisms of circulating tumor cells
Molecular Oncology, EarlyView.In the era of immunotherapies, many patients either do not respond or eventually develop resistance. We propose to pave the way for proteomic analysis of surface‐expressed proteins called surfaceome, of circulating tumor cells. This approach seeks to identify immune evasion mechanisms and discover potential therapeutic targets. Circulating tumor cells (
Doryan Masmoudi +3 more
wiley +1 more source