Collective Estimation of Multiple Bivariate Density Functions With Application to Angular-Sampling-Based Protein Loop Modeling

No abstract is available for this paper.

• Publication year

  2016

• Venue

  Journal of the American Statistical Association

• Publication date

  2016-01-02

• Fields of study

  Mathematics, Computer Science

• Identifiers
  DOI 10.1080/01621459.2015.1099535
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar

• No claims are published for this paper.

• No concepts are published for this paper.

• Assessment of the assessment: Evaluation of the model quality estimates in CASP10

  2014cited by this paper
• RaptorX server: a resource for template-based protein structure modeling.

  2014cited by this paper
• Improvements to Robotics-Inspired Conformational Sampling in Rosetta

  2013influential reference
• Assessing protein conformational sampling methods based on bivariate lag-distributions of backbone angles

  2013cited by this paper
• A stochastic evolutionary model for protein structure alignment and phylogeny.

  2012cited by this paper
• UNCONSTRAINED PILOT SELECTORS FOR SMOOTHED CROSS‐VALIDATION

  2011cited by this paper
• A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions.

  2011cited by this paper
• Statistical Applications in Genetics and Molecular Biology Bayesian Statistical Studies of the Ramachandran Distribution

  2011cited by this paper
• Smoothing Spline ANOVA

  2011cited by this paper
• Probability for Statistics and Machine Learning: Fundamentals and Advanced Topics

  2011cited by this paper
• Evaluation of model quality predictions in CASP9

  2011cited by this paper
• A protein-dependent side-chain rotamer library

  2011cited by this paper
• Multivariate plug-in bandwidth selection with unconstrained pilot bandwidth matrices

  2010cited by this paper
• Modern Applied Statistics with S

  2010cited by this paper
• A Probabilistic and Continuous Model of Protein Conformational Space for Template-Free Modeling

  2010influential reference
• A DIRICHLET PROCESS MIXTURE OF HIDDEN MARKOV MODELS FOR PROTEIN STRUCTURE PREDICTION.

  2010cited by this paper
• Neighbor-Dependent Ramachandran Probability Distributions of Amino Acids Developed from a Hierarchical Dirichlet Process Model

  2010influential reference
• Predicting Local Quality of a Sequence-Structure Alignment

  2009cited by this paper
• Applying undertaker cost functions to model quality assessment

  2009cited by this paper
• Density Estimation for Protein Conformation Angles Using a Bivariate von Mises Distribution and Bayesian Nonparametrics

  2009cited by this paper
• Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling

  2009influential reference
• Evaluation of CASP8 model quality predictions

  2009cited by this paper
• Free-energy landscape of RNA hairpins constructed via dihedral angle principal component analysis.

  2009cited by this paper
• Conformation dependence of backbone geometry in proteins.

  2009cited by this paper
• Tali: Local Alignment of protein Structures Using Backbone Torsion Angles

  2008cited by this paper
• Construction of the free energy landscape of biomolecules via dihedral angle principal component analysis.

  2008cited by this paper
• QMEAN: A comprehensive scoring function for model quality assessment

  2008cited by this paper
• A generative, probabilistic model of local protein structure

  2008cited by this paper
• Assessing side-chain perturbations of the protein backbone: a knowledge-based classification of residue Ramachandran space.

  2008cited by this paper
• Toward better refinement of comparative models: Predicting loops in inexact environments

  2008cited by this paper
• Dihedral angle principal component analysis of molecular dynamics simulations.

  2007cited by this paper
• Protein Bioinformatics and Mixtures of Bivariate von Mises Distributions for Angular Data

  2007cited by this paper
• Ranking predicted protein structures with support vector regression

  2007cited by this paper
• ks: Kernel Density Estimation and Kernel Discriminant Analysis for Multivariate Data in R

  2007cited by this paper
• Spline functions on triangulations

  2007influential reference
• Long loop prediction using the protein local optimization program

  2006cited by this paper
• Importance of the CMAP correction to the CHARMM22 protein force field: dynamics of hen lysozyme.

  2006cited by this paper
• Sampling Realistic Protein Conformations Using Local Structural Bias

  2006influential reference
• Helix, sheet, and polyproline II frequencies and strong nearest neighbor effects in a restricted coil library.

  2005cited by this paper
• Dependency between consecutive local conformations helps assemble protein structures from secondary structures using Go potential and greedy algorithm

  2005cited by this paper
• The Uppsala Electron-Density Server.

  2004cited by this paper
• Energy landscape of a small peptide revealed by dihedral angle principal component analysis

  2004cited by this paper
• Protein Structure Prediction Using Rosetta

  2004influential reference
• MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes

  2004cited by this paper
• Relationships between amino acid sequence and backbone torsion angle preferences

  2004cited by this paper
• A hierarchical approach to all‐atom protein loop prediction

  2004cited by this paper
• circular: Circular Statistics, from "Topics in circular Statistics" (2001) S. Rao Jammalamadaka and A. SenGupta, World Scientific.

  2004cited by this paper
• Principal Component Analysis

  2003cited by this paper
• Smoothing Spline Anova Models

  2002cited by this paper
• Probabilistic model for two dependent circular variables

  2002cited by this paper
• Conformations of amino acids in proteins.

  2002cited by this paper
• Topics in Circular Statistics

  2001influential reference
• HMMSTR: a hidden Markov model for local sequence-structure correlations in proteins.

  2000cited by this paper
• Ab initio protein structure prediction of CASP III targets using ROSETTA

  1999cited by this paper
• Objectively judging the quality of a protein structure from a Ramachandran plot

  1997cited by this paper
• Triogram Models

  1996cited by this paper
• Kernel Smoothing

  1995cited by this paper
• Omega loops; nonregular secondary structures significant in protein function and stability

  1995cited by this paper
• Analysis of Cα geometry in protein structures

  1994cited by this paper
• Multivariate plug-in bandwidth selection

  1994cited by this paper
• Cross-Validation of Multivariate Densities

  1994cited by this paper
• Nonparametric regression and generalized linear models

  1994cited by this paper
• Smoothing Spline Density Estimation: A Dimensionless Automatic Algorithm

  1993cited by this paper
• PROCHECK: a program to check the stereochemical quality of protein structures

  1993cited by this paper
• Nonparametric Regression and Generalized Linear Models: A roughness penalty approach

  1993cited by this paper
• Multivariate Density Estimation, Theory, Practice and Visualization

  1992cited by this paper
• A simple root n bandwidth selector

  1991cited by this paper
• Large-Sample Inference for Log-Spline Models

  1990cited by this paper
• Spline Models for Observational Data

  1990cited by this paper
• Probability for statistics

  1989cited by this paper
• A distribution for dependent unit vectors

  1988cited by this paper
• Fast Computation of Fully Automated Log-Density and Log-Hazard Estimators

  1988cited by this paper
• Density Estimation for Statistics and Data Analysis

  1987cited by this paper
• Information Theory and an Extension of the Maximum Likelihood Principle

  1973cited by this paper
• Statistics of Directional Data

  1972cited by this paper
• Conformation of polypeptides and proteins.

  1968cited by this paper
• Stereochemistry of polypeptide chain configurations.

  1963cited by this paper
• Structure of Myoglobin: A Three-Dimensional Fourier Synthesis at 2 Å. Resolution

  1960cited by this paper

• Asymptotically faster estimation of high‐dimensional additive models using subspace learning

  2024cites this paper
• Torus Probabilistic Principal Component Analysis

  2020cites this paper
• Collective spectral density estimation and clustering for spatially-correlated data

  2020cites this paper
• Investigation of machine learning techniques on proteomics: A comprehensive survey.

  2019cites this paper
• Prediction of Protein Backbone Torsion Angles Using Deep Residual Inception Neural Networks

  2019cites this paper
• Enhancing Statistical Multiple Sequence Alignment and Tree Inference Using Structural Information.

  2018cites this paper
• DEEPre: sequence-based enzyme EC number prediction by deep learning

  2017cites this paper
• Nonparametric collective spectral density estimation with an application to clustering the brain signals

  2017cites this paper
• Protein Structure Classification and Loop Modeling Using Multiple Ramachandran Distributions

  2017cites this paper
• K-nearest uphill clustering in the protein structure space

  2017cites this paper
• Skewed factor models using selection mechanisms

  2016influential citation
• Bayesian protein sequence and structure alignment

  2014cites this paper