Webbläsaren som du använder stöds inte av denna webbplats. Alla versioner av Internet Explorer stöds inte längre, av oss eller Microsoft (läs mer här: * https://www.microsoft.com/en-us/microsoft-365/windows/end-of-ie-support).

Var god och använd en modern webbläsare för att ta del av denna webbplats, som t.ex. nyaste versioner av Edge, Chrome, Firefox eller Safari osv.

Default user image.

Carsten Peterson

Expert

Default user image.

A novel approach to structure alignment

Författare

  • Mattias Ohlsson
  • Carsten Peterson
  • Markus Ringnér
  • Richard Blankenbecler

Summary, in English

A novel approach for structure alignment is presented, where the key ingredients are: (1) An error function formulation of the problem simultaneously in terms of binary (Potts) assignment variables and real-valued atomic coordinates. (2) Minimization of the error function by an iterative method, where in each iteration a mean field method is employed for the assignment variables and exact rotation/translation of atomic coordinates is performed, weighted with the corresponding assignment variables. The approach allows for extensive search of all possible alignments, including those involving arbitrary permutations. The algorithm is implemented using a C_alpha representation of the backbone and explored on different protein structure categories using the Protein Data Bank (PDB) and is successfully compared with other algorithms. The approach performs very well with modest CPU consumption and is robust with respect to choice of parameters. It is extremely generic and flexible and can handle additional user-prescribed constraints easily. Furthermore, it allows for a probabilistic interpretation of the results.

Avdelning/ar

  • Computational Biology and Biological Physics - Has been reorganised

Publiceringsår

2000-04

Språk

Engelska

Publikation/Tidskrift/Serie

LU TP 00-07

Dokumenttyp

Rapport

Ämne

  • Biophysics
  • Bioinformatics and Computational Biology

Aktiv

Published