Page 176 - Macromolecular Crystallography

MODEL BUILDING, REFINEMENT, AND VALIDATION 165

was one of the first successful approaches to auto- thenbuiltinthesesecondarystructureregionswhilst
mate construction of new protein structures from taking care not to over-interpret them. Secondary
previously seen fragments, following the syntac- structural main-chain fragments of sufficient length
tic concept of pattern recognition. FFFear (Cowtan, (15–20 residues) are slid along the sequence and the
1998) presented an elegant implementation of the best match to the side-chain density is used to assign
ESSENS idea in a fast Fourier framework that theresiduetype.Loopsarebuiltbyextendingthebuilt
allowed not only to speed-up program execution but main-chain fragments by sampling Ramachandran
also the use of structure templates in a probabilistic space.
manner. The ARP/wARP package follows the full path of
The software packages ARP/wARP (Lamzin and syntactic construction of a model starting from free
Wilson, 1993; Perrakis et al., 1997, 1999, 2001; Lamzin atoms, through candidate Cα atoms, peptide and
et al., 2001; Morris et al., 2002, 2003, 2004; Cohen et al., dipeptide units, chain fragments to sequence dock-
2004, Zwart et al., 2004), TEXTAL/CAPRA (Ioerger ing, and side-chain building. It was the first software
etal., 1999; Holtonetal., 2000; IoergerandSacchettini, package to combine most steps of model building
2002, 2003), MAID (Levitt, 2001), and RESOLVE with refinement in an iterative manner. The power
(Terwilliger, 2001, 2003a, 2003b, 2003c, 2004) aim to of ARP/wARP lies precisely in this iterative nature
deliver a complete macromolecular model starting (Perrakis et al., 1999). Although iteration is offered
from an electron density map. RESOLVE is perhaps in other packages it is de facto less important and
one of the most advanced programs in terms of less powerful due to the lack of the use of the free
implementingaproperstatisticalpattern-recognition atoms concept and the focus on a ‘snapshot’ inter-
system. A promising development of RESOLVE pretation of the current density map. The concept
involves the use of template matching of a number of ARP/wARP is different. When atoms are placed
of commonly observed density distributions to per- in electron density only the fragments that could be
form density modification. FFT-based methods are interpreted with confidence are built and refined as
employed to calculate derivatives of a log-likelihood part of the restrained atomic model. The parts that
map,andstructurefactorstatisticsarecombinedwith were less certain are still allowed to move as free
prior knowledge of density distributions to provide atoms. Atoms that do not refine well can be removed
scores, which are used to match templates to grid and density that is yet unaccounted for can be filled
points and their surrounding region to perform den- with atoms at any point. In this way, not only the
sity modification. TEXTAL uses a high-dimensional atomic parameters but the atoms themselves and the
feature space consisting of rotationally invariant connectivity between them are made part of the opti-
properties derived from the electron density. These mization that so encompasses both model building
includetheaveragedensityandhighermoments, the and refinement.
varianceovergridpoints, themomentsofinertiaand For a detailed comparison of some popular
spokes of density values (the three bonding tubes of automated model building packages, see Badger
density that are to be expected around a Cα atom). (2003). For an analysis of structural features and
TEXTALcomputesthesefeaturevectorsandattempts their relationship to model building strategies, see
to recognize the closest density pattern from a large Morris (2004). Further details should be sought in
database of precomputed patterns. After the density the original articles.
featureshavebeenmatched, thecoordinatesfromthe
database template are used to place atoms into den-
11.3.3 Automation in crystallographic structure
sity. The program MAID relies on skeletonization of
solution: decision-making systems
agivenelectrondensitymaptodeterminethepathof
the main chain. The skeleton grid points then serve An emerging goal in the field of macromolecular
as features in which secondary structural elements crystallography methods development is the overall
patterns are sought, very much like the computer automation of the time-consuming steps in structure
graphics model building steps with a program such solution. To a large extent, two software packages
as O. A stereochemically accurate atomic model is exemplified that concept at the turn of the previous