Francesco Costa
@atsocf.bsky.social
🧬 Isopeptor enables reliable detection and geometry evaluation of these covalent links using a template-based strategy powered by pyJess.
🔍 The tool demonstrates a precision of 1.0 and recall of 0.947 in identifying incorrectly modelled isopeptide bonds in PDB structures.
🔍 The tool demonstrates a precision of 1.0 and recall of 0.947 in identifying incorrectly modelled isopeptide bonds in PDB structures.
March 20, 2025 at 10:55 AM
🧬 Isopeptor enables reliable detection and geometry evaluation of these covalent links using a template-based strategy powered by pyJess.
🔍 The tool demonstrates a precision of 1.0 and recall of 0.947 in identifying incorrectly modelled isopeptide bonds in PDB structures.
🔍 The tool demonstrates a precision of 1.0 and recall of 0.947 in identifying incorrectly modelled isopeptide bonds in PDB structures.
We show that using high plDDT models as templates can increase the speed of AlphaFold2 as implemented in ColabFold, potentially reducing computational costs and carbon footprint. 5/7
December 9, 2024 at 1:57 PM
We show that using high plDDT models as templates can increase the speed of AlphaFold2 as implemented in ColabFold, potentially reducing computational costs and carbon footprint. 5/7
We introduced a novel "Best Pick" strategy that combines predictions made with and without multiple sequence alignment (MSA) information, selecting the model with the highest average plDDT. 4/7
December 9, 2024 at 1:57 PM
We introduced a novel "Best Pick" strategy that combines predictions made with and without multiple sequence alignment (MSA) information, selecting the model with the highest average plDDT. 4/7
This observation led us to explore whether low-confidence predictions could be improved using high-confidence templates from the same protein family. About one-third of low-confidence structures can be "rescued" to reasonable confidence levels using this method. 3/7
December 9, 2024 at 1:57 PM
This observation led us to explore whether low-confidence predictions could be improved using high-confidence templates from the same protein family. About one-third of low-confidence structures can be "rescued" to reasonable confidence levels using this method. 3/7
By observing the plDDT distribution within protein domain families, we noticed a certain degree of heterogeneity in the confidence of AlphaFold2 predictions. 2/7
December 9, 2024 at 1:57 PM
By observing the plDDT distribution within protein domain families, we noticed a certain degree of heterogeneity in the confidence of AlphaFold2 predictions. 2/7