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FRAGFOLD assembles folds from a mixture of supersecondary structural fragments and short fixed length fragments taken from a library of highly resolved protein structures using a simulated annealing approach.
This potential is constructed by analyzing a set of 500 experimentally resolved protein structures (see Methods), monitoring the probability of the event that single residues or residue pairs are observed in one of the structural classes defined as follows.
Ligand-based approach is frequently applicable in the absence of experimentally resolved protein crystal structure whereas, structure-based method extract the protein bound ligand information for the generation of align model [8 10].
Five clearly resolved protein peaks (P1, P2, P3, P4 and P5) were identified (figure 2A).
The resolved protein band was subjected to in-gel digestion with trypsin followed by MALDI-TOF mass spectrometry for identification of peptide fragments.
We can then safely conclude that the Rd.HMM from X-ray resolved protein structures are highly selective, and the number of relatives present in the sequence database searched did not affect this selectivity.
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Resolved proteins were electronically blotted onto PVDF membranes (GE healthcare).
Resolved proteins were then transferred onto a PVDF membrane using a tank blotter (Bio-Rad).
The protein lysates (20 μg) from HepG2 cell or liver tissues were subjected to 10% SDS-polyacrylamide gel electrophoresis (SDS-PAGE) and the resolved proteins were transferred to polyvinylidene difluoride membranes (Millipore, Billerica, MA, USA).
Total protein (50 100 μg) was subjected to sodium dodecyl sulfate-polyacrylamide gel electrophoresis and the resolved proteins were transferred with EzFastBlot transfer buffer (ATTO) to a polyvinylidene difluoride (PVDF) transfer membrane (ATTO).
Are any of the decoy molecules ligands found in structurally resolved protein-ligand complexes?
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