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Showing 1 to 15 of 15 for “"protein folds"”.
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A thermodynamic definition of protein folds
… in structural biology, like homology modeling, protein threading, protein fold classification, and homology detection have proven extremely useful. For example, they have provided us with evolutionary information about protein homology which has in some many cases lead directly to therapeutics. …
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From Protein Folds to Chromatin: Topological Data Analysis and Deep Learning at Multiple Scales
Across biological scales—from atomic-level protein folds to the three-dimensional architecture of chromatin—structural organization governs molecular function and regulation. We present two complementary computational frameworks that integrate geometric, topological, and spatial modeling with deep …
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Analysis of the thermodynamic determinants of protein fold specificity in the denatured state ensemble
Although the thermodynamic control of protein folding has been known for decades, a complete understanding of the thermodynamic determinants that defining protein folds is still elusive. In this regard, it is becoming clear that focusing only on the native states of protein folds will be …
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Highly Accurate Fragment Library for Protein Fold Recognition
<p>Proteins play a crucial role in living organisms as they perform many vital tasks in every living cell. Knowledge of protein folding has a deep impact on understanding the heterogeneity and molecular functions of proteins. Such information leads to crucial advances in drug design and disease …
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Data Driven Modeling of Proteins
Proteins are tiny molecular machines that perform the vast majority of the functions in living cells. In order for the protein to perform its function, it has to be able to fold from a disordered coil into a specific compact structure. Two new computational methods are developed that take advantage …
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Protein Fold Recognition Using Adaboost Learning Strategy
Protein structure prediction is one of the most important and difficult problems in computational molecular biology. Unlike sequence-only comparison, protein fold recognition based on machine learning algorithms attempts to detect similarities between protein structures which might not be …
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Photosensing with LOV: Molecular Insights into the Shared Mechanism of Light-Regulated Kinase Signaling between Plant Phototropins and Bacterial Two-Component Systems
… the plant and bacterial kinases have diverse protein folds and functions, they both share the common photosensing module. Using a combination of biophysical and biochemical techniques, I examined the properties of these light mediated proteins and provided molecular insights in which light …
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Scope: A Protein Force Field With An Artificial Neural Network Approach to Protein Refinement
<p>Protein folding is the one of the most important topics of research in Biochemistry. The understanding of how a protein folds into its three dimensional shape from its amino acid sequence is of extreme importance in medicine today because proteins play important roles in diseases such as sickle …
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Evolutionary Constraints Specifying Protein Folding and Function
Proteins are complex macromolecules that carry out biological functions while under constant mutational load and selective pressure during evolution. Consequently, evolution has generated protein families by exploring the set of sequences able to carry out a particular biological activity, …
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Improving Structural Features Prediction in Protein Structure Modeling
<p>Proteins play a vital role in the biological activities of all living species. In nature, a protein folds into a specific and energetically favorable three-dimensional structure which is critical to its biological function. Hence, there has been a great effort by researchers in both …
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Size-dependent mechanical properties of beta-structures in protein materials
Protein materials such as spider silk can be exceptionally strong, and they can stretch tremendously before failure. Notably, silks are made entirely of proteins, which owe their structure and stability to weak molecular interactions, in particular, hydrogen bonds (H-bonds). Beta-structures, a …
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Investigating Protein Folding Pathways at Atomistic Resolution: from a Small Domain to a Knotted Protein
Although protein folding has been studied for decades many open issues still resist, and we yet lack a clear and general description of the mechanisms leading from the unfolded to the folded state. In particular, it is still under debate whether proteins fold through few well-defined pathways or …
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In silico protein evolution by intelligent design: creating new and improved protein structures
Natural proteins perform a startling diversity of biological functions, but comprise a miniscule fraction of the theoretical sequence-structure space that polypeptides might occupy. The goal of protein design is to identify new free-energy minima in this sequence-structure landscape so as to expand …
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Effects of macromolecular crowding and small ions on the folding, structure, and stability of Desulfovibrio desufuricans flavodoxin
The intracellular environment in which most proteins fold and function contains a range of biomolecules that results in significant volume exclusion, thus contrasting to the dilute buffer conditions common to most in vitro studies. In addition to intracellular macromolecular crowding, cells are …
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Stability, folding and evolution of the tumour suppressor protein p16.
The tumour suppressor protein, p16, is a member of the INK4 family of inhibitors of the cyclin D-dependent kinases 4 and 6 in the pRb pathway of eukaryotic cell cycle. The 156-amino acid protein consists of four ankyrin (ANK) repeats. The ANK repeat is a ubiquitous 33-residue sequence motif that …