title: A neural-network based method for prediction of gamma-turns in proteins from multiple sequence alignment.
abstract: In the present study, an attempt has been made to develop a method for predicting gamma-turns in proteins. First, we have implemented the commonly used statistical and machine-learning techniques in the field of protein structure prediction, for the prediction of gamma-turns. All the methods have been trained and tested on a set of 320 nonhomologous protein chains by a fivefold cross-validation technique. It has been observed that the performance of all methods is very poor, having a Matthew's Correlation Coefficient (MCC) </= 0.06. Second, predicted secondary structure obtained from PSIPRED is used in gamma-turn prediction. It has been found that machine-learning methods outperform statistical methods and achieve an MCC of 0.11 when secondary structure information is used. The performance of gamma-turn prediction is further improved when multiple sequence alignment is used as the input instead of a single sequence. Based on this study, we have developed a method, GammaPred, for gamma-turn prediction (MCC = 0.17). The GammaPred is a neural-network-based method, which predicts gamma-turns in two steps. In the first step, a sequence-to-structure network is used to predict the gamma-turns from multiple alignment of protein sequence. In the second step, it uses a structure-to-structure network in which input consists of predicted gamma-turns obtained from the first step and predicted secondary structure obtained from PSIPRED.
authors.affiliation: Institute of Microbial Technology, Sector 39A, Chandigarh, India.
authors.forename: Harpreet
authors.initials: H
authors.lastname: Kaur
authors.forename: G P S
authors.initials: GP
authors.lastname: Raghava
mesh_terms: D030562:Databases, Protein; D008958:Models, Molecular; D016571:Neural Networks, Computer; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment
chemical_list: D011506:Proteins