Tag: I-TASSER
Ancient origin and constrained evolution of the division and cell wall gene cluster in Bacteria
Miyakawa, T., Matsuzawa, H., Matsuhashi, M. & Sugino, Y. Cell wall peptidoglycan mutants of Escherichia coli K-12: existence of two clusters of genes, mra and mrb, for cell wall peptidoglycan biosynthesis. J. Bacteriol. 112, 950–958 (1972). Article CAS PubMed PubMed Central Google Scholar Ayala, J. A., Garrido, T., De Pedro,…
New Algorithms That Harnessed Protein-folding Power in 2022
Big pharma companies have been researching protein folding for a long time now. Discoveries and innovations in the field can revolutionise the development of drug and other biological advancement. Recently, the development of the COVID-19 vaccine was also supported by tackling this issue. Protein folding prediction process involves a combination…
A novel causative functional mutation in GATA6 gene is responsible for familial dilated cardiomyopathy as supported by in silico functional analysis
Pérez-Serra, A. et al. Genetic basis of dilated cardiomyopathy. Int. J. Cardiol. 224, 461–472 (2016). PubMed Article Google Scholar Petropoulou, E. et al. Digenic inheritance of mutations in the cardiac troponin (TNNT2) and cardiac beta myosin heavy chain (MYH7) as the cause of severe dilated cardiomyopathy. Eur. J. Med. Genet….
Function of SYDE C2-RhoGAP family as signaling hubs for neuronal development deduced by computational analysis
Hallam, S. J., Goncharov, A., McEwen, J., Baran, R. & Jin, Y. Syd-1, a presynaptic protein with PDZ, C2 and rhoGAP-like domains specifies axon identity in C. elegans. Nat. Neurosci. 5, 1137–1146 (2002). CAS PubMed Google Scholar Xu, Y. & Quinn, C. C. SYD-1 promotes multiple developmental steps leading to…
DNASTAR Releases NovaFold AI Powered by AlphaFold 2
February 28, 2022, Madison, WI DNASTAR® announced today a new release of their leading protein structure prediction software, NovaFold, that incorporates the award-winning AlphaFold 2 AI system developed by Google-owned DeepMind. AlphaFold 2 was the top-ranked protein structure prediction method in the CASP14 challenge in 2020, significantly outperforming the other…
Shaping modern human skull through epigenetic, transcriptional and post-transcriptional regulation of the RUNX2 master bone gene
Study of RUNX2 locus in modern and ancient humans The sequences of the RUNX2 locus (Chr6:45,318,000–45,670,000 hg38, for a total of 352.000 bases) have been aligned in AMH and ancient species’ (Neandertal and Denisovan) genomes to map the changes occurred during recent evolution. We have identified 459 and 470 changes…
rosetta fold vs alphafold 2
S. Both AlphaFold and Xu use simple folding engines L-BFGS (L- Broyden–Fletcher–Goldfarb– Shanno (BFGS)) and CNS (Crystallography and NMR System), respectively, i.e., improvements come from a better energy potential using distributional information. The phase problem is a problem, to the point that in the past decade, several structures, such as M-PMV…
Interpreting I-TASSER output
Interpreting I-TASSER output 1 Hi, Recently, i have received a protein structure result from I-TASSER. Here i have few questions to interpret the result: What does it mean by solvent accessibility value (0 to 9)? Does it mean near to 9 is more accessible to solvents? And if it likes…
The LpoA activator is required to stimulate the peptidoglycan polymerase activity of its cognate cell wall synthase PBP1a
Significance Class A penicillin-binding proteins (aPBPs) assemble the bacterial cell wall and are the targets of penicillin and related β-lactam antibiotics. In gram-negative bacteria, the aPBPs require outer membrane lipoproteins to function. However, little is known about how these proteins promote the activity of their cognate synthases in cells. Here,…
