Formulation of probabilistic models of protein structure in atomic detail using the reference ratio method

Jan B. Valentin, Christian Andreetta, Wouter Boomsma, Sandro Bottaro, Jesper Ferkinghoff-Borg, Jes Frellsen, Kanti V. Mardia, Pengfei Tian, Thomas Hamelryck

Research output: Contribution to journalJournal articleResearchpeer-review

Abstract

We propose a method to formulate probabilistic models of protein structure in atomic detail, for a given amino acid sequence, based on Bayesian principles, while retaining a close link to physics. We start from two previously developed probabilistic models of protein structure on a local length scale, which concern the dihedral angles in main chain and side chains, respectively. Conceptually, this constitutes a probabilistic and continuous alternative to the use of discrete fragment and rotamer libraries. The local model is combined with a nonlocal model that involves a small number of energy terms according to a physical force field, and some information on the overall secondary structure content. In this initial study we focus on the formulation of the joint model and the evaluation of the use of an energy vector as a descriptor of a protein's nonlocal structure; hence, we derive the parameters of the nonlocal model from the native structure without loss of generality. The local and nonlocal models are combined using the reference ratio method, which is a well-justified probabilistic construction. For evaluation, we use the resulting joint models to predict the structure of four proteins. The results indicate that the proposed method and the probabilistic models show considerable promise for probabilistic protein structure prediction and related applications. © 2013 Wiley Periodicals, Inc.
Original languageEnglish
JournalProteins: Structure, Function, and Bioinformatics
Volume82
Issue number2
Pages (from-to)288-299
Number of pages12
ISSN0887-3585
DOIs
Publication statusPublished - 2014

Keywords

  • Algorithms
  • Amino Acid Sequence
  • Bacterial Proteins
  • Bayes Theorem
  • Hydrogen Bonding
  • Models, Molecular
  • Models, Statistical
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • Structural Homology, Protein
  • Thermodynamics
  • IgG Fc-binding protein, Streptococcus
  • proteins
  • 04500, Mathematical biology and statistical methods
  • 10060, Biochemistry studies - General
  • 10064, Biochemistry studies - Proteins, peptides and amino acids
  • 10515, Biophysics - Biocybernetics
  • Computational Biology
  • Bayesian model mathematical and computer techniques
  • probabilistic model mathematical and computer techniques
  • reference ratio method mathematical and computer techniques
  • statistical protein structure prediction mathematical and computer techniques
  • Biochemistry and Molecular Biophysics
  • Models and Simulations
  • BIOCHEMISTRY
  • BIOPHYSICS
  • CONTACT MAP PREDICTION
  • FORCE-FIELD
  • STATISTICAL POTENTIALS
  • FOLDING SIMULATIONS
  • NEURAL-NETWORKS
  • CHALLENGES
  • ENSEMBLES
  • PROFILES
  • ENERGIES
  • DYNAMICS
  • Bayesian models
  • Disordered proteins
  • Protein structure prediction
  • Reference ratio method
  • Template-free modeling

Fingerprint Dive into the research topics of 'Formulation of probabilistic models of protein structure in atomic detail using the reference ratio method'. Together they form a unique fingerprint.

Cite this