Tag: LDDT

Mutant collection development We mutagenized 2,700 seeds of the wheat–Th. elongatum introgression line RWG34 containing Sr43 (ref. 29). Dry seeds were incubated for 16 h with 200 ml of a 0.8% (w/v) EMS solution with constant shaking on a Roller Mixer (Model SRT1, Stuart Scientific) to ensure maximum homogenous exposure of the…

Plant material Bread wheat accessions Transfer (TA5524), WL711, TA5605, Ae. umbellulata accession TA1851 and Ae. triuncialis accession TA10438 were obtained from the Wheat Genetics Resource Center (WGRC). TcLr9 (Transfer/6*Thatcher) is a near-isogenic line carrying Lr9 from Transfer in the genetic background of the susceptible wheat line Thatcher. TcLr9 and TA5605…

NovaFold AI prediction software from DNASTAR is designed to streamline the entire AlphaFold 2 workflow, with no need to buy a specialized computer. In addition, both the prediction setup and downstream analysis take only a few minutes of hands-on time. Before showing the simple step-by-step workflow, we want to explain…

Forum:lDDT for nucleic acids 0 Can lDDT score be calculated for nucleic acids such as RNA from pdbs? When I use RNA structures, I get the following error: “ERROR: No valid distance to check in the reference structure(s). Please check that the first chain of the reference structure(s) contains a…

Benchmarking contact prediction First, we benchmarked the long-range contact prediction performance of A-Prot using the FM and FM/TBM targets of CASP13 [24]. The benchmark results show that the performance of our model outperforms that of the existing methods (Table 1). We compared the precision of our model’s top L/5, L/2,…

AlphaFold This package provides an implementation of the inference pipeline of AlphaFold v2.0. This is a completely new model that was entered in CASP14 and published in Nature. For simplicity, we refer to this model as AlphaFold throughout the rest of this document. Any publication that discloses findings arising from…

In: StatPearls [Internet]. team at our virtual booth on the exhibitor tab. Published online 22 07; DOI: 10.1038/s41586-021-03819-2. Extended Data Fig. Found insideAn important feature of this work is the S-plus subroutines provided for analyzing actual data sets. Coupled with the discussion of new theoretical research, the book should benefit…

Forum:How to calculate LDDT score for protein structure ? 1 I am using molecular dynamic simulation and would like to measure LDDT score for protein structure. There is an online server for doing this but I couldn’t find any python code to do it as I am using an open-source…