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ProteomicsModeling flexible protein structure with AlphaFold2 and cross-linking mass spectrometry
We propose a pipeline that combines AlphaFold2 (AF2) and crosslinking mass spectrometry (XL-MS) to model the structure of proteins with multiple conformations. The pipeline consists of two main steps: ensemble generation using AF2, and conformer selection using XL-MS data. For conformer selection, w...
ORGANISM(S): Escherichia coli 
2024-05-24 | PXD046392 | Pride
Crosslinks Monolinks Alphafold2 Idr Flexible protein 
ProteomicsMassSpecPreppy - an end-to-end solution for automated protein concentration determination and flexible sample digestion for proteomics applications
In proteomics, fast, efficient and highly reproducible sample preparation are of utmost importance, particularly in view of fast scanning mass spectrometers enabling analyses of large sample series. To address this need, we have developed the web application MassSpecPreppy that operates on the open ...
ORGANISM(S): Saccharomyces Cerevisiae Strain C13-aby.s86 Escherichia Coli K-12 (ncbitaxon:83333) Homo Sapiens (ncbitaxon:9606) 
2023-07-20 | MSV000092489 | MassIVE
UnknownDatabase searching by flexible protein structure alignment.
Not available
S-EPMC2279924 | biostudies-literature
UnknownSAXS/WAXS data of conformationally flexible ribose binding protein.
Not available
S-EPMC10764985 | biostudies-literature
GenomicsFlexible chromatin loops in the VH gene region of the Igh locus facilitate the generation of a diverse antibody repertoire
The immunoglobulin heavy-chain (Igh) locus undergoes large-scale contraction in pro-B cells, which facilitates VH-DJH recombination by juxtaposing distal VH genes next to the DJH- rearranged gene segment in the proximal Igh domain. By high-resolution mapping of long-range interactions, we now demons...
ORGANISM(S): Mus musculus 
2013-09-30 | E-GEOD-43008 | biostudies-arrayexpress
UnknownRescaling protein-protein interactions improves Martini 3 for flexible proteins in solution.
Not available
S-EPMC11300910 | biostudies-literature
UnknownA flexible, allosteric loop regulates protein activity and rewires electrostatics.
Not available
S-EPMC12459221 | biostudies-literature
ProteomicsSas20 is a highly flexible starch-binding protein in the Ruminococcus bromii cell-surface amylosome
Ruminococcus bromii is a keystone species in the human gut that has the rare ability to degrade dietary resistant starch (RS). This bacterium secretes a suite of starch-active proteins that work together within larger complexes called amylosomes that allow R. bromii to adhere to and degrade RS. Sas2...
ORGANISM(S): Bacteria Ruminococcus bromii L2-63 
2022-06-09 | PXD032013 | Pride
R. bromii 
UnknownFlexible protein-protein docking with a multitrack iterative transformer.
Not available
S-EPMC10804679 | biostudies-literature
UnknownMapache: a flexible pipeline to map ancient DNA.
Not available
S-EPMC9901408 | biostudies-literature
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