Assessing protein conformational sampling methods based on bivariate lag-distributions of backbone angles
KAUST DepartmentApplied Mathematics and Computational Science Program
Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
Computer Science Program
Computational Bioscience Research Center (CBRC)
Structural and Functional Bioinformatics Group
Online Publication Date2012-08-27
Print Publication Date2013-11-01
Permanent link to this recordhttp://hdl.handle.net/10754/562280
MetadataShow full item record
AbstractDespite considerable progress in the past decades, protein structure prediction remains one of the major unsolved problems in computational biology. Angular-sampling-based methods have been extensively studied recently due to their ability to capture the continuous conformational space of protein structures. The literature has focused on using a variety of parametric models of the sequential dependencies between angle pairs along the protein chains. In this article, we present a thorough review of angular-sampling-based methods by assessing three main questions: What is the best distribution type to model the protein angles? What is a reasonable number of components in a mixture model that should be considered to accurately parameterize the joint distribution of the angles? and What is the order of the local sequence-structure dependency that should be considered by a prediction method? We assess the model fits for different methods using bivariate lag-distributions of the dihedral/planar angles. Moreover, the main information across the lags can be extracted using a technique called Lag singular value decomposition (LagSVD), which considers the joint distribution of the dihedral/planar angles over different lags using a nonparametric approach and monitors the behavior of the lag-distribution of the angles using singular value decomposition. As a result, we developed graphical tools and numerical measurements to compare and evaluate the performance of different model fits. Furthermore, we developed a web-tool (http://www.stat.tamu. edu/~madoliat/LagSVD) that can be used to produce informative animations. © The Author 2012. Published by Oxford University Press.
CitationMaadooliat, M., Gao, X., & Huang, J. Z. (2012). Assessing protein conformational sampling methods based on bivariate lag-distributions of backbone angles. Briefings in Bioinformatics, 14(6), 724–736. doi:10.1093/bib/bbs052
SponsorsThis work was supported by grants from NCI (CA57030), NSF (DMS-0907170, DMS-1007618), and Award Numbers KUS-CI-016-04 and GRP-CF-2011-19-P-Gao-Huang, made by King Abdullah University of Science and Technology (KAUST).
PublisherOxford University Press (OUP)
JournalBriefings in Bioinformatics
PubMed Central IDPMC3888108
- Full cyclic coordinate descent: solving the protein loop closure problem in Calpha space.
- Authors: Boomsma W, Hamelryck T
- Issue date: 2005 Jun 28
- Predicting dihedral angle probability distributions for protein coil residues from primary sequence using neural networks.
- Authors: Helles G, Fonseca R
- Issue date: 2009 Oct 16
- A sampling approach for protein backbone fragment conformations.
- Authors: Yu JY, Zhang W
- Issue date: 2013
- Near-native protein loop sampling using nonparametric density estimation accommodating sparcity.
- Authors: Joo H, Chavan AG, Day R, Lennox KP, Sukhanov P, Dahl DB, Vannucci M, Tsai J
- Issue date: 2011 Oct
- Density Estimation for Protein Conformation Angles Using a Bivariate von Mises Distribution and Bayesian Nonparametrics.
- Authors: Lennox KP, Dahl DB, Vannucci M, Tsai JW
- Issue date: 2009 Jun 1