Protein folding by Cohen, F

“…<p>Recent studies of the relationship between protein sequence and protein structure are reviewed. A detailed discussion of past attempts to predict the structure of a protein from its amino acid sequence, the protein folding problem, is presented and the strengths and weaknesses of these methods are examined. …”

Membrane simulations of OpcA: gating in the loops? by Bond, P, Derrick, J, Sansom, MS

“…The results suggest that the crystal environment may constrain the membrane protein structure in a nonphysiological state. The presence of lipids and physiological salt concentrations result in changes in the conformation of the extracellular loops of OpcA, leading to opening of a pore, and to modulation of the molecular surface implicated in recognition of proteoglycan. …”

Enhancing Evolutionary Couplings with Deep Convolutional Neural Networks by Liu, Yang, Ye, Qing, Peng, Jian, Palmedo, Peter Franklin, Berger Leighton, Bonnie

“…Through substantially improving the precision-recall behavior of contact prediction, DeepContact suggests we are near a paradigm shift in template-free modeling for protein structure prediction. Many protein structures of interest remain out of reach for both computational prediction and experimental determination. …”
Get full text
Get full text

Insight of brain degenerative protein modifications in the pathology of neurodegeneration and dementia by proteomic profiling by Adav, Sunil Shankar, Sze, Siu Kwan

“…Previous studies have established dementia as a ‘proteinopathy’ caused by detrimental changes in brain protein structure and function that promote misfolding, aggregation, and deposition as insoluble amyloid plaques. …”
Get full text
Get full text

Evolutionary modelling of biological structures by Golden, M

“…ETDBN uses a dihedral angle representation of protein structure, and models the evolutionary trajectory between a pair of protein structures using an angular diffusion process on the two-dimensional torus. …”

Computational Method for Drug Target Search and Application in Drug Discovery by Chen, Yuzong, Li, Zerong, Ung, C.Y.

“…Ligand-protein inverse docking has recently been introduced as a computer method for identification of potential protein targets of a drug. A protein structure database is searched to find proteins to which a drug can bind or weakly bind. …”
Get full text

Cotranslational protein folding - fact or fiction? by Deane, C, Dong, M, Huard, F, Lance, B, Wood, G

“…Motivation: Experimentalists have amassed extensive evidence over the past four decades that proteins appear to fold during production by the ribosome. Protein structure prediction methods, however, do not incorporate this property of folding. …”

Photoinduced, family-specific, site-selective cleavage of TIM-barrel proteins. by Floyd, N, Oldham, N, Eyles, C, Taylor, S, Filatov, D, Brouard, M, Davis, B

“…Nonenzymatic, chemical methods for the controlled cleavage of proteins at predictable sites in a site-specific manner are rare and of strong potential utility in clean, post-translational manipulation of protein structure for use in, for example, proteomics, sequencing, and tagged-protein production. …”

The prospects of quantum computing in computational molecular biology by Outeiral Rubiera, C, Strahm, M, Shi, J, Morris, G, Benjamin, SC, Deane, CM

“…There are potential benefits across the entire field, from the ability to process vast amounts of information and run machine learning algorithms far more efficiently, to algorithms for quantum simulation that are poised to improve computational calculations in drug discovery, to quantum algorithms for optimization that may advance fields from protein structure prediction to network analysis. However, these exciting prospects are susceptible to “hype,” and it is also important to recognize the caveats and challenges in this new technology. …”

Data set augmentation allows deep learning-based virtual screening to better generalize to unseen target classes and highlight important binding interactions by Scantlebury, J, Brown, N, von Delft, F, Deane, CM

“…Current deep learning methods for structure-based virtual screening take the structures of both the protein and the ligand as input but make little or no use of the protein structure when predicting ligand binding. Here, we show how a relatively simple method of data set augmentation forces such deep learning methods to take into account information from the protein. …”

Preparation and characterization of edible films from fish water-soluble proteins by Iwata, K, Ishizaki, S, Handa, A, Tanaka, M

“…It was revealed that FWSP had to be denatured somehow to unfold the protein structure, and the interaction of FWSP molecules, particularly through disulfide linkages, was attributed to the formation of films. …”

A review of the human Sigma-1 Receptor structure by Ossa, F, Schnell, J, Ortega-Roldan, J

“…Newly reported structures of the human S1R in ligand-bound states provides essential insights into small molecule binding in the context of the overall protein structure. The structure also raises many interesting questions and provides an excellent starting point for understanding the molecular tricks employed by this small membrane receptor to modulate a large number of signaling events. …”

Cotranslational protein folding--fact or fiction? by Deane, C, Dong, M, Huard, F, Lance, B, Wood, G

“… MOTIVATION: Experimentalists have amassed extensive evidence over the past four decades that proteins appear to fold during production by the ribosome. Protein structure prediction methods, however, do not incorporate this property of folding. …”

Isolation and characterization of a MAGE gene family in the Xp21.3 region. by Muscatelli, F, Walker, A, De Plaen, E, Stafford, A, Monaco, A

“…However, the gene and predicted protein structure are conserved, suggesting a similar function. …”

Iterative SE(3)-transformers by Fuchs, FB, Wagstaff, E, Dauparas, J, Posner, I

“…When manipulating three-dimensional data, it is possible to ensure that rotational and translational symmetries are respected by applying so-called SE(3)-equivariant models. Protein structure prediction is a prominent example of a task which displays these symmetries. …”

Systematic benchmarking of deep-learning methods for tertiary RNA structure prediction by Bahai, Akash, Kwoh, Chee Keong, Mu, Yuguang, Li, Yinghui

“…Despite advancements, the accuracy of computational methods remains modest, especially when compared to protein structure prediction. Deep learning methods, while successful in protein structure prediction, have shown some promise for RNA structure prediction as well, but face unique challenges. …”
Get full text

Exploiting whole-PDB analysis in novel bioinformatics applications by Ramraj, V

“…<p>The Protein Data Bank (PDB) is the definitive electronic repository for experimentally-derived protein structures, composed mainly of those determined by X-ray crystallography. …”

Protein loop structure prediction by Choi, Y

“…<p>This dissertation concerns the study and prediction of loops in protein structures.</p><p> Proteins perform crucial functions in living organisms. …”

Structural determination of improved methanol-tolerant mutant from Geobacillus zalihae T1 lipase by x-ray crystallography by Medam @ Hamdan, Siti Hajar

“…It showed that the substitution of amino acid S2 and A384 with cysteine could enhance the stability of the enzyme by promoting the formation of disulphide bond to tighten the both terminal ends of the protein structure. The substitution of amino acid cysteine showed the changes on the active site distance (S113, D317, and H358), however, it was not affected the lipase activity and folding of protein structure. …”
Get full text

Electronic polarization effects on protein pdb 2khk. by Chew, Xiu Qian.

“…Our study reveals that the protein structure obtained under PPC simulation is similar to the native state discovered by NMR method and it corresponds to the lowest-energy conformation of the protein. …”
Get full text