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MAESTROweb: a web server for structure-based protein stability prediction. Bioinformatics 32, 1414–1416 (2016). CAS PubMed Google Scholar Frappier, V., Chartier, M. & Najmanovich, R. J. ENCoM server: exploring protein conformational space and the effect of mutations on protein function and...
The (PS)2-v2 server is an easy-to-use web server (Figure2). Users input the query protein sequence in FASTA format. The server provides three modes (Automatic, Manual and 'Use this template') for choosing template(s) (Figure2A). The default mode is 'Automatic'. In this mode, (PS)...
Analysis of the KRT8 sequence using the protein disorder prediction server (PrDOS), which predicts natively disordered protein regions, identifies the head (residues 1–90) and tail (residues 399–483) domains as likely disordered (Fig. 3a). We expressed and purified the head domain of KRT8 (...
Protein structure prediction on the Web - a case study using the Phyre server 热度: Resampling Methods for Protein Structure Prediction 热度: SCRATCH:aproteinstructureandstructuralfeature predictionserver J.Cheng,A.Z.Randall,M.J.SweredoskiandP.Baldi* ...
In this latter case, the web server requires only pasting of a protein sequence in a raw format. We therefore introduce I-Mutant2.0 as a unique and valuable helper for protein design, even when the protein structure is not yet known with atomic resolution. AVAILABILITY: http://gpcr.biocomp....
Here we present DynaMut, a web server implementing two distinct, well established normal mode approaches, which can be used to analyze and visualize protein dynamics by sampling conformations and assess the impact of mutations on protein dynamics and stability resulting from vibrational entropy changes....
SCRATCH: a protein structure and structural feature prediction server. Nucl Acids Res. 2005;33(suppl 2):W72–6. Article CAS Google Scholar Pollastri G, Baldi P, Fariselli P, Casadio R. Prediction of coordination number and relative solvent accessibility in proteins. Proteins. 2002;47:142–...
Application of the prediction method to a new independent test set. To further test the stability of our KMC simulations and rule out the possibility of model over-fitting during machine learning, an inde- pendent test set of 10 complexes was collected; the detailed information for this set...
Protein structure prediction pipelines based on artificial intelligence, such as AlphaFold2, have achieved near-experimental accuracy. These advanced pipelines mainly rely on multiple sequence alignments (MSAs) as inputs to learn the co-evolution information from the homologous sequences. Nonetheless, sear...