A protein backbone structure is designable if a substantial number of amino acid sequences exist that autonomously fold into it. It has been suggested that the designability of backbones is governed mainly by side chain-independent or side chain type...
The task of protein sequence design is central to nearly all rational protein engineering problems, and enormous effort has gone into the development of energy functions to guide design. Here, we investigate the capability of a deep neural network mo...
Journal of chemical information and modeling
Feb 7, 2022
The application of deep learning to generative molecule design has shown early promise for accelerating lead series development. However, questions remain concerning how factors like training, data set, and seed bias impact the technology's utility t...
DeepMind released AlphaFold 2.0 in 2020, an artificial intelligence model to predict the structure of proteins, which could mean that proteins can be characterized without the need for tedious and costly lab analysis.
Journal of computational biology : a journal of computational molecular cell biology
Jan 21, 2022
Template-based modeling (TBM), including homology modeling and protein threading, is one of the most reliable techniques for protein structure prediction. It predicts protein structure by building an alignment between the query sequence under predict...
Protein structure prediction (PSP) has achieved significant progress lately via prediction of inter-residue distances using deep learning models and exploitation of the predictions during conformational search. In this context, prediction of large in...
Short hydrogen bonds (SHBs), whose donor and acceptor heteroatoms lie within 2.7 Ã…, exhibit prominent quantum mechanical characters and are connected to a wide range of essential biomolecular processes. However, exact determination of the geometry an...
Highly accurate protein structure predictions by deep neural networks such as AlphaFold2 and RoseTTAFold have tremendous impact on structural biology and beyond. Here, we show that, although these deep learning approaches have originally been develop...
In biological systems, Glutamic acid is a crucial amino acid which is used in protein biosynthesis. Carboxylation of glutamic acid is a significant post-translational modification which plays important role in blood coagulation by activating prothrom...