title: Highly accurate sequence-based prediction of half-sphere exposures of amino acid residues in proteins.
abstract: Solvent exposure of amino acid residues of proteins plays an important role in understanding and predicting protein structure, function and interactions. Solvent exposure can be characterized by several measures including solvent accessible surface area (ASA), residue depth (RD) and contact numbers (CN). More recently, an orientation-dependent contact number called half-sphere exposure (HSE) was introduced by separating the contacts within upper and down half spheres defined according to the Cα-Cβ (HSEβ) vector or neighboring Cα-Cα vectors (HSEα). HSEα calculated from protein structures was found to better describe the solvent exposure over ASA, CN and RD in many applications. Thus, a sequence-based prediction is desirable, as most proteins do not have experimentally determined structures. To our best knowledge, there is no method to predict HSEα and only one method to predict HSEβ.
  
  
  
  This study developed a novel method for predicting both HSEα and HSEβ (SPIDER-HSE) that achieved a consistent performance for 10-fold cross validation and two independent tests. The correlation coefficients between predicted and measured HSEβ (0.73 for upper sphere, 0.69 for down sphere and 0.76 for contact numbers) for the independent test set of 1199 proteins are significantly higher than existing methods. Moreover, predicted HSEα has a higher correlation coefficient (0.46) to the stability change by residue mutants than predicted HSEβ (0.37) and ASA (0.43). The results, together with its easy Cα-atom-based calculation, highlight the potential usefulness of predicted HSEα for protein structure prediction and refinement as well as function prediction.
  
  
  
  The method is available at http://sparks-lab.org
  
  
  
  yuedong.yang@griffith.edu.au or yaoqi.zhou@griffith.edu.au
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Signal Processing Laboratory, School of Engineering, Griffith University, Brisbane, Australia.
authors.forename: Rhys
authors.initials: R
authors.lastname: Heffernan
authors.affiliation: Signal Processing Laboratory, School of Engineering, Griffith University, Brisbane, Australia, Institute for Integrated and Intelligent Systems, Griffith University, Brisbane, Australia, Medical Research Center (MRC), Department of Psychiatry, University of Iowa, Iowa City, USA.
authors.forename: Abdollah
authors.initials: A
authors.lastname: Dehzangi
authors.affiliation: Signal Processing Laboratory, School of Engineering, Griffith University, Brisbane, Australia.
authors.forename: James
authors.initials: J
authors.lastname: Lyons
authors.affiliation: Signal Processing Laboratory, School of Engineering, Griffith University, Brisbane, Australia.
authors.forename: Kuldip
authors.initials: K
authors.lastname: Paliwal
authors.affiliation: Institute for Integrated and Intelligent Systems, Griffith University, Brisbane, Australia, School of Engineering and Physics, University of the South Pacific, Private Mail Bag, Laucala Campus, Suva, Fiji.
authors.forename: Alok
authors.initials: A
authors.lastname: Sharma
authors.affiliation: Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, Shandong 253023, China.
authors.forename: Jihua
authors.initials: J
authors.lastname: Wang
authors.affiliation: Institute for Integrated and Intelligent Systems, Griffith University, Brisbane, Australia, National ICT Australia (NICTA), Brisbane, Australia and.
authors.forename: Abdul
authors.initials: A
authors.lastname: Sattar
authors.affiliation: Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, Shandong 253023, China, Institute for Glycomics and School of Information and Communication Technique, Griffith University, Parklands Dr. Southport, QLD 4222, Australia.
authors.forename: Yaoqi
authors.initials: Y
authors.lastname: Zhou
authors.affiliation: Institute for Glycomics and School of Information and Communication Technique, Griffith University, Parklands Dr. Southport, QLD 4222, Australia.
authors.forename: Yuedong
authors.initials: Y
authors.lastname: Yang
mesh_terms: D000595:Amino Acid Sequence; D000596:Amino Acids; D008958:Models, Molecular; D011506:Proteins / Q000737:chemistry*; D012997:Solvents
chemical_list: D000596:Amino Acids; D011506:Proteins; D012997:Solvents