lloyd@bruce.cs.monash.OZ.AU (lloyd allison) (09/27/90)
This is to request references to a package called Explore (sp?) that predicts protein tertiary structure. Lloyd Allison Department of Computer Science UUCP: lloyd@bruce.cs.monash.edu.au Monash University, Clayton or : uunet!munnari!bruce.cs.monash.edu!lloyd VICTORIA 3168, AUSTRALIA Tel : 565-5205 FAX: +61 3 565 5146
usenet@nlm.nih.gov (usenet news poster) (09/27/90)
In article <3137@bruce.cs.monash.OZ.AU> lloyd@bruce.cs.monash.OZ.AU (lloyd allison) writes: >This is to request references to a package called Explore (sp?) >that predicts protein tertiary structure. > >Lloyd Allison >Department of Computer Science UUCP: lloyd@bruce.cs.monash.edu.au >Monash University, Clayton or : uunet!munnari!bruce.cs.monash.edu!lloyd >VICTORIA 3168, AUSTRALIA Tel : 565-5205 FAX: +61 3 565 5146 EXPLOR is a Polygen product based on work by Axel Brunger and Martin Karplus using molecular dynamics and simulated annealing to refine three dimensional X-ray crystal structures. See: Brunger AT; Clore GM; Gronenborn AM; Karplus M Proc Natl Acad Sci U S A 83: 3801-5 (1986) Three-dimensional structure of proteins determined by molecular dynamics with interproton distance restraints: application to crambin. and many subsequent references. David States states@ncbi.nlm.nih.gov National Center for Biotechnology Information National Library of Medicine
Cherry@Coffee.MGH.Harvard.EDU (J. Michael Cherry) (09/27/90)
In article <3137@bruce.cs.monash.OZ.AU> lloyd@bruce.cs.monash.OZ.AU (lloyd allison) writes: > This is to request references to a package called Explore (sp?) > that predicts protein tertiary structure. > > Lloyd Allison > Department of Computer Science UUCP: lloyd@bruce.cs.monash.edu.au Sounds like you are referring to a program originally from Axel Brunger while at Harvard, now at U of Chicago I believe. See A. Brunger, Acta Cryst. A, A46, 46-57 (1990). This program like other programs from Karplus' group at Harvard are commercialized by Polygen Corp in Waltham, Massachusetts (617) 890-2888. The introduction on the X-PLOR product sheet says: "X-PLOR (tm) is a macromolecular crystal structure program which integrates x-ray diffraction data with molecular mechanics, dynamics, energy minimization, or NMR internuclear distances to aid in the solution of 3-dimensional molecular structures. The technique of simulated annealing overcomes local misplacement of flexible fragments. X-PLOR uses the CHARMm (tm) force field, modified automatically for use in high temperature dynamics simulations. The QUANTA (tm) Structure Analysis and Refinement modeling application package facilitates access to and data exchange between X-PLOR and QUANTA." X-PLOR is not meant to generate a folded protein structure from just the primary amino acid sequence. It requires structural data like an electron density map or NMR measurements as its reference. It then manipulates the coordinates to fit the structural data, as opposed to CHARMm which is generally used to fit structures to an energy function. I have no connection to Polygen Corp. I am not even a satisfied user. Mike Cherry cherry@frodo.mgh.harvard.edu Department of Molecular Biology Massachusetts General Hospital, Boston