PMID- 24866861
OWN - NLM
STAT- MEDLINE
DCOM- 20150721
LR  - 20140728
IS  - 1549-960X (Electronic)
IS  - 1549-9596 (Linking)
VI  - 54
IP  - 7
DP  - 2014 Jul 28
TI  - Protein secondary structure classification revisited: processing DSSP information 
      with PSSC.
PG  - 2166-79
LID - 10.1021/ci5000856 [doi]
AB  - A first step toward three-dimensional protein structure description is the 
      characterization of secondary structure. The most widely used program for 
      secondary structure assignment remains DSSP, introduced in 1983, with currently 
      more than 400 citations per year. DSSP output is in a one-letter representation, 
      where much of the information on DSSP's internal description is lost. Recently it 
      became evident that DSSP overlooks most pi-helical structures, which are more 
      prevalent and important than anticipated before. We introduce an alternative 
      concept, representing the internal structure characterization of DSSP as an 
      eight-character string that is human-interpretable and easy to parse by software. 
      We demonstrate how our protein secondary structure characterization (PSSC) code 
      allows for inspection of complicated structural features. It recognizes ten times 
      more pi-helical residues than does the standard DSSP. The plausibility of 
      introduced changes in interpreting DSSP information is demonstrated by better 
      clustering of secondary structures in (phi, psi) dihedral angle space. With a sliding 
      sequence window (SSW), helical assignments with PSSC remain invariant compared 
      with an assignment based on the complete structure. In contrast, assignment with 
      DSSP can be changed by residues in the neighborhood that are in fact not 
      interacting with the residue under consideration. We demonstrate how one can 
      easily define new secondary structure classification schemes with PSSC and 
      perform the classifications. Our approach works without changing the DSSP source 
      code and allows for more detailed protein characterization.
FAU - Zacharias, Jan
AU  - Zacharias J
AD  - Fachbereich Biologie, Chemie, Pharmazie/Institute of Chemistry and Biochemistry, 
      Freie Universitat Berlin , Fabeckstrasse 36A, 14195 Berlin, Germany.
FAU - Knapp, Ernst-Walter
AU  - Knapp EW
LA  - eng
PT  - Journal Article
DEP - 20140616
PL  - United States
TA  - J Chem Inf Model
JT  - Journal of chemical information and modeling
JID - 101230060
RN  - 0 (Proteins)
SB  - IM
MH  - Computational Biology/*methods
MH  - Models, Molecular
MH  - Protein Structure, Secondary
MH  - Proteins/*chemistry
EDAT- 2014/05/29 06:00
MHDA- 2015/07/22 06:00
CRDT- 2014/05/29 06:00
PHST- 2014/05/29 06:00 [entrez]
PHST- 2014/05/29 06:00 [pubmed]
PHST- 2015/07/22 06:00 [medline]
AID - 10.1021/ci5000856 [doi]
PST - ppublish
SO  - J Chem Inf Model. 2014 Jul 28;54(7):2166-79. doi: 10.1021/ci5000856. Epub 2014 
      Jun 16.