Simultaneous optimization of biomolecular energy functions on features from small molecules and macromolecules. J. Chem. Theory Comput. 12, 6201–6212 (2016). CAS PubMed PubMed Central Google Scholar Chaudhury, S., Lyskov, S. & Gray, J. J. PyRosetta: a script-based interface for ...
Article Open access 13 September 2023 The ClusPro AbEMap web server for the prediction of antibody epitopes Article 15 May 2023 Computational optimization of antibody humanness and stability by systematic energy-based ranking Article 07 August 2023 Change...
Besides, the binding energy for each peptide-Keap1 interaction is calculated to estimate the strength and stability of the interactions (Fig. 1d). 3.2. Design of peptide-binding keap1 protein using deep generative models Using the deep generative model pipeline, we designed peptides aimed at ...
From the 30,000 decoys calculated, the 10 lowest energy models were selected to represent the final NMR ensemble structure. The structure calculation was considered converged because the lowest energy models clustered within less than 2 Å from the model with the lowest energy. Final structures...
Park, H. et al. Simultaneous optimization of biomolecular energy functions on features from small molecules and macromolecules.J. Chem. Theory Comput.12, 6201–6212 (2016). CASPubMedPubMed CentralGoogle Scholar Chaudhury, S., Lyskov, S. & Gray, J. J. PyRosetta: a script-based interface fo...
(E), the FARFAR2 model is the best of five low-energy cluster centers after clustering 5,000 models with a 3.0 Å radius; in (F) to (J), the FARFAR2 model is the best of five low-energy cluster centers after clustering 400 models with a 2.0 Å radius. In each case, model ...
Nevertheless, phylogenetic analysis of the candidate HGTs revealed incongruent gene trees, with candidate HGTs clustering with genes from potential donors, including bacteria, unicellular algae, and fungi. This suggests that candidate horizontally transferred genes in S. rosetta were acquired from multiple ...
In contrast, there are remarkable similarities between centenarians. A clustering of centenarians in certain areas of the world may be observed, these are referred to as blue zones (Evert et al.2003). Whilst the habitants in a blue zone may share a common genetic background, they also exhibit...