local predictions
consistency restrictions
version
single residue
bonds
plausible predictions
ab initio predictions
computational experience
factor approximation
restriction
residues
structure
loop
secondary structure
consistency
experience
articles
metric spaces
packing
biological instances
set packing
simple problems
16-34
fact
2022-09-02T15:52
instances
false
space
MAX SNP
Consistent Sets of Secondary Structures in Proteins
Abstract
Ab initio predictions of secondary structures in proteins have to combine local predictions, based on short fragments of the protein sequence, with consistency restrictions, as not all locally plausible predictions may be simultaneously true.
We use the fact that secondary structures are patterns of hydrogen bonds and that a single residue can participate in hydrogen bonds of at most one secondary structure. Consistency of fixed-sized pieces of secondary structures is the easiest to approximate and we formalize it as 1-2 matching problem. Consistency of entire secondary structures is a version of set packing. We also investigate how to form a simple problem if we add the requirement that the secondary structure and the loops that connect them fit together in a metric space.
Every problem that we investigated is MAX-SNP hard and it has a constant factor approximation. Computational experience suggests that in biological instances, we can find nearly optimal solutions using heuristics.
2007-11-10
https://doi.org/10.1007/s00453-007-9068-8
requirements
consistent set
article
protein
initio predictions
2007-11-10
protein sequences
approximation
pieces
set
solution
hydrogen bonds
short fragments
heuristics
problem
patterns
constant factor approximation
prediction
sequence
optimal solution
fragments
matching problem
https://scigraph.springernature.com/explorer/license/
10.1007/s00453-007-9068-8
doi
Physical Chemistry (incl. Structural)
Springer Nature
Algorithmica
0178-4617
1432-0541
dimensions_id
pub.1042850308
1
Springer Nature - SN SciGraph project
Jeong
Jieun
Berman
Piotr
53
The Pennsylvania State University, University Park, PA, USA
The Pennsylvania State University, University Park, PA, USA
Chemical Sciences