Literature DB >> 8673326

Algorithms for finding the axis of a helix: fast rotational and parametric least-squares methods.

J A Christopher1, R Swanson, T O Baldwin.   

Abstract

Several methods for finding the axis of a helix are presented and compared. The most accurate determines the helix axis as the axis of rotation necessary to map point i to point i + 1 of the helix. The fastest method calculates the helix axis as the best-fit line through the coordinates by a three-dimensional parametric linear least-squares algorithm, taking advantage of the sequential nature of the data.

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Year:  1996        PMID： 8673326     DOI： 10.1016/0097-8485(95)00075-5

Source DB:  PubMed          Journal:  Comput Chem        ISSN： 0097-8485


  24 in total

1.  Discovery of a significant, nontopological preference for antiparallel alignment of helices with parallel regions in sheets.

Authors:  Brandon M Hespenheide; Leslie A Kuhn
Journal:  Protein Sci       Date:  2003-05       Impact factor: 6.725

2.  Microfibrillar structure of type I collagen in situ.

Authors:  Joseph P R O Orgel; Thomas C Irving; Andrew Miller; Tim J Wess
Journal:  Proc Natl Acad Sci U S A       Date:  2006-06-02       Impact factor: 11.205

3.  Crystal structure of a human CD3-epsilon/delta dimer in complex with a UCHT1 single-chain antibody fragment.

Authors:  Kelly L Arnett; Stephen C Harrison; Don C Wiley
Journal:  Proc Natl Acad Sci U S A       Date:  2004-11-08       Impact factor: 11.205

4.  A molecular dynamics study of the bee venom melittin in aqueous solution, in methanol, and inserted in a phospholipid bilayer.

Authors:  Alice Glättli; Indira Chandrasekhar; Wilfred F van Gunsteren
Journal:  Eur Biophys J       Date:  2005-12-02       Impact factor: 1.733

5.  TRAJELIX: a computational tool for the geometric characterization of protein helices during molecular dynamics simulations.

Authors:  Mihaly Mezei; Marta Filizola
Journal:  J Comput Aided Mol Des       Date:  2006-05-10       Impact factor: 3.686

6.  The crystal structure of Bacillus subtilis YycI reveals a common fold for two members of an unusual class of sensor histidine kinase regulatory proteins.

Authors:  Eugenio Santelli; Robert C Liddington; Michael A Mohan; James A Hoch; Hendrik Szurmant
Journal:  J Bacteriol       Date:  2007-02-16       Impact factor: 3.490

7.  Collagen fibril architecture, domain organization, and triple-helical conformation govern its proteolysis.

Authors:  Shiamalee Perumal; Olga Antipova; Joseph P R O Orgel
Journal:  Proc Natl Acad Sci U S A       Date:  2008-02-14       Impact factor: 11.205

8.  Candidate cell and matrix interaction domains on the collagen fibril, the predominant protein of vertebrates.

Authors:  Shawn M Sweeney; Joseph P Orgel; Andrzej Fertala; Jon D McAuliffe; Kevin R Turner; Gloria A Di Lullo; Steven Chen; Olga Antipova; Shiamalee Perumal; Leena Ala-Kokko; Antonella Forlino; Wayne A Cabral; Aileen M Barnes; Joan C Marini; James D San Antonio
Journal:  J Biol Chem       Date:  2008-05-15       Impact factor: 5.157

9.  End-to-end and end-to-middle interhelical interactions: new classes of interacting helix pairs in protein structures.

Authors:  Tarini Shankar Ghosh; S Krishna Chaitanya; Ramasubbu Sankararamakrishnan
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2009-09-16

10.  In situ D-periodic molecular structure of type II collagen.

Authors:  Olga Antipova; Joseph P R O Orgel
Journal:  J Biol Chem       Date:  2010-01-06       Impact factor: 5.157
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