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Tag: LDDT
MHC-Fine: Fine-tuned AlphaFold for Precise MHC-Peptide Complex Prediction
Abstract The precise prediction of Major Histocompatibility Complex (MHC)-peptide complex structures is pivotal for understanding cellular immune responses and advancing vaccine design. In this study, we enhanced AlphaFold’s capabilities by fine-tuning it with a specialized dataset comprised by exclusively high-resolution MHC-peptide crystal structures. This tailored approach aimed to address the…
New study validates AlphaFold2 for predicting mutation effects in proteins
Proteins, the workhorses of biology, are encoded by DNA sequences and are responsible for vital functions within cells. Since the first experimental measurement of a protein structure was made by John Kendrew in the 1950s, protein’s ability to fold into complex three-dimensional structures has long been a subject of scientific…
Testing the limits of AlphaFold2’s accuracy in predicting protein structure
Figure 1. A: Overlaid wild-type (grey) and mutant (color), experimental (orange), and predicted (blue) structures of H-NOX protein. B: Wild-type protein with residues colored by strain (a measure of structural deformation), Si; the location of the mutation (residue 71 is mutated from alanine (A) to glycine (G)) is indicated. C:…
Inhibition of providencia vermicola FabD
Introduction Microbial resistance has become a problem in the contemporary medical environment due to the inadequate development of new antibiotics and the asinine prescription of antibiotics in both developed and developing nations. Antimicrobial resistance (AMR), which affects wealthy and developing nations, is a global concern.1 AMR is a problem for…
Enhancing alphafold-multimer-based protein complex structure prediction with MULTICOM in CASP15
The comparison between MULTICOM servers and other CASP15 server assembly predictors According to the CASP15 official assessment (see the official ranking predictioncenter.org/casp15/zscores_multimer.cgi), MULTICOM_qa and MULTICOM_deep servers ranked 3rd and 5th among all CASP15 assembly server predictors. The MULTICOM human predictors (MULTICOM_human and MULTICOM) ranked 7th and 10th among all CASP15…
Antiviral type III CRISPR signalling via conjugation of ATP and SAM
Cloning Supplementary Table 1 shows the synthetic gene, DNA and RNA oligonucleotide sequences used in this study. The synthetic genes encoding B.fragilis Cas6, CorA, NrN and C. botulinum SAM lyase purchased as g-blocks (IDT) were codon-optimized for expression in E. coli C43 (DE3) via the vector pEhisV5TEV, which encodes eight…
The Protein Structure Prediction Revolution and Its Implications for Medicine: 2023 Albert Lasker Basic Medical Research Award | Health Informatics | JAMA
The 2023 Albert Lasker Basic Medical Research Award has been presented to Demis Hassabis, PhD, and John Jumper, PhD, for the invention of AlphaFold, a revolutionary technology for predicting the 3-dimensional structure of proteins. Protein folding is one of the most important and complex organizing forces within the human cell,…
New algorithm reveals similarities between proteins across species
Researchers from the European Bioinformatics Institute (EMBL-EBI), ETH Zurich’s Institute of Molecular Systems Biology, and Seoul National University’s School of Biological Sciences have made significant strides in protein research. They harnessed the power of AlphaFold’s vast database of AI-predicted 3D protein structures, shedding light on protein evolution and human immunity…
Revealing the secrets of protein evolution using the AlphaFold database
Revealing the secrets of protein evolution using the AlphaFold database. Credit: Karen Arnott/EMBL-EBI By developing an efficient way to compare all predicted protein structures in the AlphaFold database, researchers have revealed similarities between proteins across different species. This work aids our understanding of protein evolution and has uncovered new insights…
Clustering-predicted structures at the scale of the known protein universe
Structural clustering algorithm The clustering procedure is similar to MMseqs2’s clustering but, instead of using sequences, Foldseek’s 3Di alphabet (Extended Data Fig. 1) was used to represent the structures as one-dimensional sequences. The clustering algorithm combines Linclust17 and cascaded MMseqs2 (ref. 42) clustering. The pipeline applies this strategy to allow for efficient…
The wheat stem rust resistance gene Sr43 encodes an unusual protein kinase
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…
An unusual tandem kinase fusion protein confers leaf rust resistance in wheat
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…
Using NovaFold AI to Streamline Structure Prediction with AlphaFold 2 | DNASTAR
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…
lDDT for nucleic acids
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…
A-Prot: protein structure modeling using MSA transformer | BMC Bioinformatics
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,…
Install alphafold on the local machine, get out of docker.
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…
highly accurate protein structure prediction with alphafold
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…
How to calculate LDDT score for protein structure ?
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…