Proteome Digestion Specificity Analysis for Rational Design of Extended Bottom-up and Middle-down Proteomics Experiments

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The rapid progress in the field of deep learning has had a significant impact on protein design. Deep learning methods have recently produced a breakthrough in protein structure prediction, leading to the availability of high-quality models for millions of ...

Proteins control nearly every facet of life on a molecular level. Proteins are formed from linear strings of amino acids, which fold into three-dimensional structures that can enact functions. Evolution has created highly efficient proteins in diverse fold ...

Scaffold-based protein libraries are designed to be both diverse and rich in functional/folded proteins. However, introducing an extended diversity while preserving stability of the initial scaffold remains a challenge. Here we developed an original approa ...

We present an in-depth analysis of selected CASP15 targets, focusing on their biological and functional significance. The authors of the structures identify and discuss key protein features and evaluate how effectively these aspects were captured in the su ...

Otoliths are calcium carbonate components of the stato-acoustical organ responsible for hearing and maintenance of the body balance in teleost fish. During their formation, control over, e.g., morphology and carbonate polymorph is influenced by complex ins ...

Local and global inference methods have been developed to infer structural contacts from multiple sequence alignments of homologous proteins. They rely on correlations in amino acid usage at contacting sites. Because homologous proteins share a common ance ...

The present application relates to a computer-implemented systems and methods for protein interaction design using surface fingerprints. The method comprises predicting at least one target interface site with high binding propensity, wherein, optionally, t ...

Glycans play an essential role in numerous physiological and pathological processes of living organisms. Despite their significant biological relevance, glycobiology remains one of the least explored fields of biochemistry. The intrinsic isomeric complexit ...

The high isomeric complexity of glycans makes them particularly difficult to analyze. While ultra-high-resolution ion mobility spectrometry(IMS) can offer rapid baseline separation of many glycan isomers,their unambiguous identification remains a challengi ...

The structural elucidation of metabolite molecules is important in many branches of the life sciences. However, the isomeric and isobaric complexity of metabolites makes their identification extremely challenging, and analytical standards are often require ...

Proteome Digestion Specificity Analysis for Rational Design of Extended Bottom-up and Middle-down Proteomics Experiments

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A new age in protein design empowered by deep learning

De novo designed proteins: a study in engineering novel folds and functions

Design of an artificial phage-display library based on a new scaffold improved for average stability of the randomized proteins

Protein target highlights in CASP15: Analysis of models by structure providers

First paleoproteome study of fossil fish otoliths and the pristine preservation of the biomineral crystal host

Impact of phylogeny on structural contact inference from protein sequence data

Systems and methods for de novo design of protein interactions with learned surface fingerprints

Combining ion mobility spectrometry and cryogenic ion spectroscopy with enzymatic digestion/synthesis for the study of N-linked glycans

Using Hadamard Transform Multiplexed IR Spectroscopy Together with a Segmented Ion Trap for the Identification of Mobility-Selected Isomers

New Approach for the Identification of Isobaric and Isomeric Metabolites