New approach to protein fold recognition based on Delaunay tessellation of protein structure

Title: New approach to protein fold recognition based on Delaunay tessellation of protein structure

Full Record
Other Related Research

Abstract

We propose new algorithms for sequence-structure compatibility (fold recognition) searches in multidimensional sequence-structure space. Individual amino acid residues in protein structures are represented by their C{sup {alpha}} atoms; thus each protein is described as a collection of points in three-dimensional space. Delaunay tessellation of a protein generates an aggregate of space-filling, irregular tetrahedra, or Delaunay simplices. Statistical analysis of quadruplet residue compositions of all Delaunay simplices in a representative dataset of protein structures leads to a novel four body contact residue potential expressed as log likelihood factor q. The q factors are calculated for native 20 letter amino acid alphabet and several reduced alphabets. Two sequence structure compatibility functions are computed as (i) the sum of q factors for all Delaunay simplices in a given protein, or (ii) 3D-1D Delaunay tessellation profiles where the individual residue profile value is calculated as the sum of q factors for all simplices that share this vertex residue. Both threading functions have been implemented in structure-recognizes-sequence and sequence-recognizes-structure protocols for protein fold recognition. We find that both profile and total score based threading functions can distinguish both the native fold from incorrect folds for a sequence, and the native sequence from non-native sequences formore » a fold. 25 refs., 4 figs., 1 tab.« less

Authors:

Zheng, W; Cho, S J; Vaisman, I I; Tropsha, A ^[1]

Univ. of North Carolina, Chapel Hill, NC (United States)

Publication Date:: 1996-12-31

OSTI Identifier:: 549278

Report Number(s):: CONF-970132-
TRN: 97:005592-0048

Resource Type:: Conference

Resource Relation:: Conference: Pacific symposium on biocomputing `97, Kapalua, HI (United States), 6-9 Jan 1997; Other Information: PBD: 1996; Related Information: Is Part Of Pacific symposium on biocomputing `97: Proceedings; Altman, R.B. [ed.] [Stanford Univ., CA (United States). Section on Medical Informatics]; Dunker, A.K. [ed.] [Washington State Univ., Pullman, WA (United States). Dept. of Biochemistry and Biophysics]; Hunter, L. [ed.] [National Insts. of Health, Bethesda, MD (United States). National Library of Medicine]; Klein, T.E. [ed.] [California Univ., San Francisco, CA (United States). Dept. of Pharmaceutical Chemistry]; PB: 508 p.

Country of Publication:: United States

Language:: English

Subject:: 55 BIOLOGY AND MEDICINE, BASIC STUDIES; 99 MATHEMATICS, COMPUTERS, INFORMATION SCIENCE, MANAGEMENT, LAW, MISCELLANEOUS; DNA SEQUENCING; COMPATIBILITY; PROTEIN STRUCTURE; ALGORITHMS; THREE-DIMENSIONAL CALCULATIONS; NUMERICAL ANALYSIS; MATHEMATICAL MODELS; STRUCTURAL MODELS; PROTEINS; STRUCTURE-ACTIVITY RELATIONSHIPS; ELECTRONIC STRUCTURE; AMINO ACIDS; STATISTICS; ELECTRIC POTENTIAL

Citation Formats


                    Zheng, W, Cho, S J, Vaisman, I I, and Tropsha, A. New approach to protein fold recognition based on Delaunay tessellation of protein structure.  United States: N. p., 1996. 
        Web.

Copy to clipboard


                    Zheng, W, Cho, S J, Vaisman, I I, & Tropsha, A. New approach to protein fold recognition based on Delaunay tessellation of protein structure.  United States.

Copy to clipboard


                    Zheng, W, Cho, S J, Vaisman, I I, and Tropsha, A. Tue .  
        "New approach to protein fold recognition based on Delaunay tessellation of protein structure".  United States.

Copy to clipboard


                    
@article{osti_549278,

  title        = {New approach to protein fold recognition based on Delaunay tessellation of protein structure},

  author       = {Zheng, W and Cho, S J and Vaisman, I I and Tropsha, A},

  abstractNote = {We propose new algorithms for sequence-structure compatibility (fold recognition) searches in multidimensional sequence-structure space. Individual amino acid residues in protein structures are represented by their C{sup {alpha}} atoms; thus each protein is described as a collection of points in three-dimensional space. Delaunay tessellation of a protein generates an aggregate of space-filling, irregular tetrahedra, or Delaunay simplices. Statistical analysis of quadruplet residue compositions of all Delaunay simplices in a representative dataset of protein structures leads to a novel four body contact residue potential expressed as log likelihood factor q. The q factors are calculated for native 20 letter amino acid alphabet and several reduced alphabets. Two sequence structure compatibility functions are computed as (i) the sum of q factors for all Delaunay simplices in a given protein, or (ii) 3D-1D Delaunay tessellation profiles where the individual residue profile value is calculated as the sum of q factors for all simplices that share this vertex residue. Both threading functions have been implemented in structure-recognizes-sequence and sequence-recognizes-structure protocols for protein fold recognition. We find that both profile and total score based threading functions can distinguish both the native fold from incorrect folds for a sequence, and the native sequence from non-native sequences for a fold. 25 refs., 4 figs., 1 tab.},

  doi          = {},

  url          = {https://www.osti.gov/biblio/549278},
  journal      = {},
number       = ,

  volume       = ,

  place        = {United States},

  year         = {1996},

  month        = {12}

}

Copy to clipboard

Conference:

Other availability

Please see Document Availability for additional information on obtaining the full-text document. Library patrons may search WorldCat to identify libraries that hold this conference proceeding.

Save / Share:

Export Metadata

Save to My Library

Similar records in OSTI.GOV collections:

The threading approach to the inverse protein folding problem

Conference Smith, T F ; Bienkowska, J ; Rogers, B

The logic behind the threading approach to the prediction of an amino acid sequence`s expected three-dimensional fold is almost seductively simple, if not obvious. In practice, however, the threading approach has not yet lived up to our expectations. Before asking why, let`s review what is generally meant by this approach to protein fold prediction. Threading rests on two basic ideas: first, that there is a limited and rather small number of basic {open_quotes}protein domain{close_quotes} core folds or architectures that need to be modeled; and, second, that a sum over a sequence`s amino acid structural environment preferences is a sufficient indicatormore »« less
Solving Globally-Optimal Threading Problems in ''Polynomial-Time''

Conference Uberbacher, E C ; Xu, D ; Xu, Y

Computational protein threading is a powerful technique for recognizing native-like folds of a protein sequence from a protein fold database. In this paper, we present an improved algorithm (over our previous work) for solving the globally-optimal threading problem, and illustrate how the computational complexity and the fold recognition accuracy of the algorithm change as the cutoff distance for pairwise interactions changes. For a given fold of m residues and M core secondary structures (or simply cores) and a protein sequence of n residues, the algorithm guarantees to find a sequence-fold alignment (threading) that is globally optimal, measured collectively by (1)more »« less
Full Text Available
A new method for modeling and solving the protein fold recognition problem

Conference Xu, Ying ; Xu, Dong ; Uberbacher, E C

Computational recognition of native-like folds from a protein fold database is considered to be a promising alternative approach to the ab initio fold prediction. We present a new and effective method for protein fold recognition through optimally aligning (threading) an amino acid sequence and a protein fold (template). A protein fold, in our database, is represented as a series of core secondary structures, and the alignment quality is determined by three factors. They are (1) the fitness between each amino acid and the environment of its assigned (aligned) template position; (2) pairwise interaction preferences between amino acids that are spatiallymore »« less
Full Text Available
An evaluation of point-insertion sequences for incremental Delaunay tessellations

Journal Article Gonzaga de Oliveira, Sanderson L., E-mail: sanderson@dcc.ufla.br ; Nogueira, Jéssica Renata, E-mail: jessica.nogueira@ifsuldeminas.edu.br - Computational and Applied Mathematics

Currently, incremental algorithms may be seen as the lowest-cost computational methods to generate Delaunay tessellations in several point distributions. In this work, eight point-insertion sequences in incremental algorithms for generating Delaunay tessellations are evaluated. More specifically, four point-insertion sequences in incremental algorithms for generating Delaunay tessellations are proposed: with orders given by the red–black tree with in-order and level-order traversals, spiral ordering, and H-indexing. These four incremental algorithms with such sequences are compared with four incremental algorithms with point-insertion orders given by the following sequences: the Hilbert and Lebesgue curves, cut-longest-edge kd-tree, and random order. Six 2-D and seven 3-Dmore »« less
https://doi.org/10.1007/S40314-016-0358-0
Protein Structure Recognition: From Eigenvector Analysis to Structural Threading Method

Thesis/Dissertation Cao, Haibo

In this work, they try to understand the protein folding problem using pair-wise hydrophobic interaction as the dominant interaction for the protein folding process. They found a strong correlation between amino acid sequences and the corresponding native structure of the protein. Some applications of this correlation were discussed in this dissertation include the domain partition and a new structural threading method as well as the performance of this method in the CASP5 competition. In the first part, they give a brief introduction to the protein folding problem. Some essential knowledge and progress from other research groups was discussed. This partmore »« less
https://doi.org/10.2172/822060

Full Text Available

Similar Records