title: FLEXc: protein flexibility prediction using context-based statistics, predicted structural features, and sequence information.
abstract: BACKGROUND
  The fluctuation of atoms around their average positions in protein structures provides important information regarding protein dynamics. This flexibility of protein structures is associated with various biological processes. Predicting flexibility of residues from protein sequences is significant for analyzing the dynamic properties of proteins which will be helpful in predicting their functions.
  
  
  RESULTS
  In this paper, an approach of improving the accuracy of protein flexibility prediction is introduced. A neural network method for predicting flexibility in 3 states is implemented. The method incorporates sequence and evolutionary information, context-based scores, predicted secondary structures and solvent accessibility, and amino acid properties. Context-based statistical scores are derived, using the mean-field potentials approach, for describing the different preferences of protein residues in flexibility states taking into consideration their amino acid context. The 7-fold cross validated accuracy reached 61 % when context-based scores and predicted structural states are incorporated in the training process of the flexibility predictor.
  
  
  CONCLUSIONS
  Incorporating context-based statistical scores with predicted structural states are important features to improve the performance of predicting protein flexibility, as shown by our computational results. Our prediction method is implemented as web service called "FLEXc" and available online at: http://hpcr.cs.odu.edu/flexc .
authors: Department of Electrical Engineering & Computer Science, Texas A&M University-Kingsville, Kingsville, TX, 78363, USA. ashraf.yaseen@tamuk.edu.
authors: Ashraf
authors: A
authors: Yaseen
authors: Department of Electrical Engineering & Computer Science, Texas A&M University-Kingsville, Kingsville, TX, 78363, USA.
authors: Mais
authors: M
authors: Nijim
authors: Department of Mathematics & Computer Science, Fisk University, Nashville, TN, 37208, USA.
authors: Brandon
authors: B
authors: Williams
authors: Department of Mathematics & Computer Science, Fisk University, Nashville, TN, 37208, USA.
authors: Lei
authors: L
authors: Qian
authors: School of Information Science and Engineering, Central South University, Changsha, 410083, China.
authors: Min
authors: M
authors: Li
authors: School of Information Science and Engineering, Central South University, Changsha, 410083, China.
authors: Jianxin
authors: J
authors: Wang
authors: Department of Computer Science, Old Dominion University, Norfolk, VA, 23529, USA.
authors: Yaohang
authors: Y
authors: Li
mesh_terms: D000595:Amino Acid Sequence; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D016571:Neural Networks, Computer; D018583:Pliability; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D012984:Software; D013223:Statistics as Topic
chemical_list: D011506:Proteins