Results 261 to 270 of about 13,913,476 (302)

The protein secondary structure flexibility

2008
Modeling protein flexibility is a long standing challenge in computational biology with a special impact to protein docking. Relating problems are protein structures alignment and identification of flexible and rigid protein regions, as well as a general definition of a region degree of flexibility.
Šikić, Krešimir, Tomić, Sanja, Jeren, Branko   +2 more
openaire   +3 more sources

Prediction of super-secondary structure in proteins

Nature, 1983
Various methods for the prediction of secondary structure from amino acid sequence can consistently achieve on average 60% accuracy when tested for several proteins. Improvement on this value has proved difficult, despite increasing the size of the data set and refining predictive techniques.
W R, Taylor, J M, Thornton
openaire   +2 more sources

Protein secondary structure

International Journal of Peptide and Protein Research, 1982
A secondary structure prediction technique is proposed which includes nucleation site determination through multiplication of conformational preference parameters as well as weighting factors to represent structurally stabilizing short range interactions.
J, Palau, P, Argos, P, Puigdomenech
openaire   +2 more sources

Chemogenomics with Protein Secondary-Structure Mimetics

2009
During molecular recognition of proteins in biological systems, helices, reverse turns, and beta-sheets are dominant motifs. Often there are therapeutic reasons for blocking such recognition sites, and significant progress has been made by medicinal chemists in the design and synthesis of semirigid molecular scaffolds on which to display amino acid ...
Garland R, Marshall, Daniel J, Kuster, Ye, Che   +2 more
openaire   +2 more sources

Recognition of super-secondary structure in proteins

Journal of Molecular Biology, 1984
A procedure to recognize super-secondary structure in protein sequences is described. An idealized template, derived from known super-secondary structures, is used to locate probable sites by matching with secondary structure probability profiles. We applied the method to the identification of beta alpha beta units in beta/alpha type proteins with 75 ...
W R, Taylor, J M, Thornton
openaire   +2 more sources

Searching on the Secondary Structure of Protein Sequences

2002
In spite of the many decades of progress in database research, surprisingly scientists in the life sciences community still struggle with inefficient and awkward tools for querying biological data sets. This work highlights a specific problem involving searching large volumes of protein data sets based on their secondary structure.
Laurie Hammel, Jignesh M. Patel
openaire   +2 more sources

Protein Secondary Structure Analysis in the Cloud

Proceedings of the 6th International Workshop on Parallelism in Bioinformatics, 2018
Many biological problems, such finding recurring geometrical patterns in the secondary structures of protein pairs, are often solved by using parallel applications running on HPC systems that, thanks to their powerful architecture and high number of CPUs, can yield good performance.
Marco Ferretti, Luigi Santangelo
openaire   +2 more sources

Evaluating Predictions of Secondary Structure in Proteins

Biochemical and Biophysical Research Communications, 1994
To learn how secondary structure assignments diverge during divergent evolution, pairs of proteins with solved crystal structures were aligned and their assignments compared as a function of evolutionary distance. Residues assigned in one structure to a helix or a strand are frequently paired with residues assigned in the other to a coil.
T F, Jenny, S A, Benner
openaire   +2 more sources

A mathematical model for secondary structure in proteins

13th IEEE International Conference on BioInformatics and BioEngineering, 2013
We propose a new mathematical model for secondary structure in proteins. Our model is inspired by percolation theory on binary strings. What sets us apart from similar work on the subject is our attempt to deviate from a data mining approach (which is mostly the trend is science these days). Therefore, in predicting secondary structures, we make it our
Alexey Nikolaev, Saad Mneimneh
openaire   +2 more sources

Protein Secondary Structure

2010
There are several methods available that can be used to gain information on secondary structure, apart from X-ray crystallography, which remains the ‘gold standard’.
openaire   +1 more source