PMID- 17069644
OWN - NLM
STAT- PubMed-not-MEDLINE
DCOM- 20070808
LR  - 20200930
IS  - 1748-7188 (Electronic)
IS  - 1748-7188 (Linking)
VI  - 1
DP  - 2006 Oct 27
TI  - Reconstructing protein structure from solvent exposure using tabu search.
PG  - 20
AB  - BACKGROUND: A new, promising solvent exposure measure, called 
      half-sphere-exposure (HSE), has recently been proposed. Here, we study the 
      reconstruction of a protein's Calpha trace solely from structure-derived HSE 
      information. This problem is of relevance for de novo structure prediction using 
      predicted HSE measure. For comparison, we also consider the well-established 
      contact number (CN) measure. We define energy functions based on the HSE- or 
      CN-vectors and minimize them using two conformational search heuristics: Monte 
      Carlo simulation (MCS) and tabu search (TS). While MCS has been the dominant 
      conformational search heuristic in literature, TS has been applied only a few 
      times. To discretize the conformational space, we use lattice models with various 
      complexity. RESULTS: The proposed TS heuristic with a novel tabu definition 
      generally performs better than MCS for this problem. Our experiments show that, 
      at least for small proteins (up to 35 amino acids), it is possible to reconstruct 
      the protein backbone solely from the HSE or CN information. In general, the HSE 
      measure leads to better models than the CN measure, as judged by the RMSD and the 
      angle correlation with the native structure. The angle correlation, a measure of 
      structural similarity, evaluates whether equivalent residues in two structures 
      have the same general orientation. Our results indicate that the HSE measure is 
      potentially very useful to represent solvent exposure in protein structure 
      prediction, design and simulation.
FAU - Paluszewski, Martin
AU  - Paluszewski M
AD  - Department of Computer Science, University of Copenhagen, Universitetsparken 1, 
      2100 Copenhagen, Denmark. palu@diku.dk
FAU - Hamelryck, Thomas
AU  - Hamelryck T
FAU - Winter, Pawel
AU  - Winter P
LA  - eng
PT  - Journal Article
DEP - 20061027
PL  - England
TA  - Algorithms Mol Biol
JT  - Algorithms for molecular biology : AMB
JID - 101265088
PMC - PMC1635054
EDAT- 2006/10/31 09:00
MHDA- 2006/10/31 09:01
PMCR- 2006/10/27
CRDT- 2006/10/31 09:00
PHST- 2006/03/30 00:00 [received]
PHST- 2006/10/27 00:00 [accepted]
PHST- 2006/10/31 09:00 [pubmed]
PHST- 2006/10/31 09:01 [medline]
PHST- 2006/10/31 09:00 [entrez]
PHST- 2006/10/27 00:00 [pmc-release]
AID - 1748-7188-1-20 [pii]
AID - 10.1186/1748-7188-1-20 [doi]
PST - epublish
SO  - Algorithms Mol Biol. 2006 Oct 27;1:20. doi: 10.1186/1748-7188-1-20.