Prediction of Beta Sheets in Proteins
نویسندگان
چکیده
Most current methods for prediction of protein secondary structure use a small window of the protein sequence to predict the structure of the central amino acid. We describe a new method for prediction of the non-local structure called ,8-sheet, which consists of two or more ,8-strands that are connected by hydrogen bonds. Since,8strands are often widely separated in the protein chain , a network with two windows is introduced. After training on a set of proteins the network predicts the sheets well, but there are many false positives . By using a global energy function the ,8-sheet prediction is combined with a local prediction of the three secondary structures a-helix, ,8-strand and coil. The energy function is minimized using simulated annealing to give a final prediction.
منابع مشابه
Distributions of beta sheets in proteins with application to structure prediction.
We recently developed the Rosetta algorithm for ab initio protein structure prediction, which generates protein structures from fragment libraries using simulated annealing. The scoring function in this algorithm favors the assembly of strands into sheets. However, it does not discriminate between different sheet motifs. After generating many structures using Rosetta, we found that the folding ...
متن کاملImproved beta-protein structure prediction by multilevel optimization of nonlocal strand pairings and local backbone conformation.
Proteins with complex, nonlocal beta-sheets are challenging for de novo structure prediction, due in part to the difficulty of efficiently sampling long-range strand pairings. We present a new, multilevel approach to beta-sheet structure prediction that circumvents this difficulty by reformulating structure generation in terms of a folding tree. Nonlocal connections in this tree allow us to exp...
متن کاملA geometric construction determines all permissible strand arrangements of sandwich proteins.
For a large class of proteins called sandwich-like proteins (SPs), the secondary structures consist of two beta-sheets packed face-to-face, with each beta-sheet consisting typically of three to five beta-strands. An important step in the prediction of the three-dimensional structure of a SP is the prediction of its supersecondary structure, namely the prediction of the arrangement of the beta-s...
متن کاملBeta edge strands in protein structure prediction and aggregation.
It is well established that recognition between exposed edges of beta-sheets is an important mode of protein-protein interaction and can have pathological consequences; for instance, it has been linked to the aggregation of proteins into a fibrillar structure, which is associated with a number of predominantly neurodegenerative disorders. A number of protective mechanisms have evolved in the ed...
متن کاملپیشگویی زایمان زودرس توسط اندازهگیری میزان H.C.G-β در ترشحات سرویکوواژینال
Preterm delivery is the main cause of perinatal morbidity and mortality throughout the world. Many complications such as neonatal intraventricular hemorrhage, cerebral palsy and high cost have increased the importance of preterm delivery therefore, it is important to detect high risk women early in pregnancy in order to prevent this problem. All of the methods used for preterm deliv...
متن کامل