25) and a less confident prediction of CrgA–SecG interaction that fell slightly below our cut-off. Outer-membrane β-barrel assembly machinery of P. aeruginosa and Vibrio cholerae In Gram-negative bacteria, the β-barrel assembly machinery (BAM) is essential for the folding and insertion of...
(HA) with controlled molecular weights is challenging due to the poorly understood function of the HA synthase (HAS). Here, the authors characterise and engineer HAS and conduct strain engineering to expand the molecular weight range and achieve high titres of both high and low molecular weight ...
Due to the extreme class-imbalance in the dataset, an adjustment to the decision threshold is necessary to reflect this bias and obtain optimal performance. As such, we assessed the stability of model predictions using the optimal prediction threshold (\tau _{opt}), the threshold yielding the m...
The variables that were analyzed include: year (PDB release date), protein molecular weight, protein taxonomic domain (prokaryotic or eukaryotic), protein type (alpha-helical or beta-barrel), protein class, structure determination method, solubilization detergent, structure determination detergent or non...
Qi YJ, Klein-Seetharaman J, Bar-Joseph Z: Random forest similarity for protein-protein interaction prediction from multiple sources. 2005, Singapore: World Scientific Publ Co Pte Ltd Google Scholar Shi M-G, Xia J-F, Li X-L, Huang D-S: Predicting protein-protein interactions from sequence...
We propose a new method to train deep learning protein structure prediction models using molecular dynamics force fields to work toward these goals. Our custom PyTorch loss function, OpenMM-Loss, represents the potential energy of a predicted structure. OpenMM-Loss can be applied to any all-atom ...
protein structure prediction with precision. Contribute to mqcomplab/PRIME development by creating an account on GitHub.
Protein folding has become a tractable problem with the significant advances in deep learning-driven protein structure prediction. Here we propose FoldPAthreader, a protein folding pathway prediction method that uses a novel folding force field model by
Mooney C, Haslam NJ, Holton TA, Pollastri G, Shields DC (2013) PeptideLocator: prediction of bioactive peptides in protein sequences. Bioinformatics 29:1120–1126 Article CAS Google Scholar Mora-Gutierrez A, Farrell HMJ, Attaie R, McWhinney VJ, Wang C (2007) Influence of bovine and capr...
Conners SB, Montero CI, Comfort DA, Shockley KR, Johnson MR, Chhabra SR, Kelly RM: An expression-driven approach to the prediction of carbohydrate transport and utilization regulons in the hyperthermophilic bacterium Thermotoga maritima. J Bacteriol 2005, 187(21):7267–7282. 10.1128/JB.187.21.726...