Molecular & cellular proteomics : MCP
Aug 21, 2021
A multitude of efforts worldwide aim to create a single-cell reference map of the human body, for fundamental understanding of human health, molecular medicine, and targeted treatment. Antibody-based proteomics using immunohistochemistry (IHC) has pr...
This article reports and analyzes the results of protein contact and distance prediction by our methods in the 14th Critical Assessment of techniques for protein Structure Prediction (CASP14). A new deep learning-based contact/distance predictor was ...
Directed evolution of proteins often involves a greedy optimization in which the mutation in the highest-fitness variant identified in each round of single-site mutagenesis is fixed. The efficiency of such a single-step greedy walk depends on the ord...
The trRosetta structure prediction method employs deep learning to generate predicted residue-residue distance and orientation distributions from which 3D models are built. We sought to improve the method by incorporating as inputs (in addition to se...
International journal of molecular sciences
Aug 17, 2021
Protein Blocks (PBs) are a widely used structural alphabet describing local protein backbone conformation in terms of 16 possible conformational states, adopted by five consecutive amino acids. The representation of complex protein 3D structures as 1...
Knowledge about protein structure assignment enriches the structural and functional understanding of proteins. Accurate and reliable structure assignment data is crucial for secondary structure prediction systems. Since the 1980s, various methods bas...
Protein-protein interaction plays an important role in life activities. A more fine-grained analysis, such as residues and atoms level, will better benefit us to understand the mechanism for inter-protein interaction and drug design. The development ...
Coarse-grained (CG) models of biomolecules have been widely used in protein/ribonucleic acid (RNA) three-dimensional structure prediction, docking, drug design, and molecular simulations due to their superiority in computational efficiency. Most of t...
Journal of chemical information and modeling
Aug 10, 2021
A structure-based drug design pipeline involves the development of potential drug molecules or ligands that form stable complexes with a given receptor at its binding site. A prerequisite to this is finding druggable and functionally relevant binding...
There are more amino acid permutations within a 40-residue sequence than atoms on Earth. This vast chemical search space hinders the use of human learning to design functional polymers. Here we show how machine learning enables the de novo design of ...
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