Database : the journal of biological databases and curation
Dec 18, 2023
The aim of the study is to establish an online database for predicting protein structures altered in ocular diseases by Alphafold2 and RoseTTAFold algorithms. Totally, 726 genes of multiple ocular diseases were collected for protein structure predict...
Interpretation of cryo-electron microscopy (cryo-EM) maps requires building and fitting 3D atomic models of biological molecules. AlphaFold-predicted models generate initial 3D coordinates; however, model inaccuracy and conformational heterogeneity o...
SUMMARY: The AlphaFold2 neural network model has revolutionized structural biology with unprecedented performance. We demonstrate that by stochastically perturbing the neural network by enabling dropout at inference combined with massive sampling, it...
Computational protein design has been demonstrated to be the most powerful tool in the last few years among protein designing and repacking tasks. In practice, these two tasks are strongly related but often treated separately. Besides, state-of-the-a...
Great improvement has been brought to protein tertiary structure prediction through deep learning. It is important but very challenging to accurately rank and score decoy structures predicted by different models. CASP14 results show that existing qua...
The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), founding member of the Worldwide Protein Data Bank (wwPDB), is the US data center for the open-access PDB archive. As wwPDB-designated Archive Keeper, RCSB PDB is ...
Recently, prediction of the structure and function of a protein from its sequence underwent a rapid increase in performance. It is primarily due to the application of machine learning methods, many of which rely on the predictive features supplied to...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2023
Homology modeling was long considered a method of choice in tertiary protein structure prediction. However, it used to provide models of acceptable quality only when templates with appreciable sequence identity with a target could be found. The thres...
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