Gerrit G. Langer

Assessment of automatic ligand building in ARP/wARP

The performance of the ligand-building module of the ARP/wARP software suite is assessed through a large-scale test on known protein–ligand complexes. The results provide a detailed benchmark and guidelines for future improvements.

Modelling bound ligands in protein crystal structures

Methods for automated identification and building of protein-bound ligands in electron-density maps are described. An error model of the geometrical features of the molecular structure of a ligand based on a lattice distribution of positional parameters is obtained via simulation and is used for the construction of an approximate likelihood scoring function. This scoring function combined with a graph-based search technique provides a flexible model-building scheme and its application shows promising initial results. Several ligands with sizes ranging from 9 to 44 non-H atoms have been identified in various X-ray structures and built in an automatic way using a minimal amount of prior stereochemical knowledge.

Visual automated macromolecular model building

The molecular viewer ArpNavigator allows easy execution of ARP/wARP model-building routines while model-update steps are shown in real time, rendering the whole process transparent to the user.

SPINE workshop on automated X-ray analysis: a progress report

The Structural Proteomics In Europe (SPINE) consortium contained a workpackage to address the automated X-ray analysis of macromolecules. The aim of this workpackage was to increase the throughput of three-dimensional structures while maintaining the high quality of conventional analyses. SPINE was able to bring together developers of software with users from the partner laboratories. Here, the results of a workshop organized by the consortium to evaluate software developed in the member laboratories against a set of bacterial targets are described. The major emphasis was on molecular-replacement suites, where automation was most advanced. Data processing and analysis, use of experimental phases and model construction were also addressed, albeit at a lower level.

Interpretation of very low resolution X-ray electron-density maps using core objects

The interpretation of a 20 Å resolution electron-density map using segmentation and pattern-recognition-based identification of domain shapes is described.

Remote services for model building in macromolecular crystallography

A server to run remote ARP/wARP jobs for automated model building in macromolecular crystallography was set up at EMBLHamburg, based on a 16 processor Linux Cluster. The project aimed to provide a user-friendly service for macromolecular crystallographers, with the following intentions: 1) to allow users to go far beyond routine data acqusition. 2) to obtain data for software development and project tracking 3) to provide users with the latest executables 4). to provide users with CPU power. The server was opened to the community in July 2004. This paper will describe the way remote job submission is carried out. An example will be given to lead the reader through the process. Statistics on the number of jobs run at the cluster, type and frequency of software and hardware errors, and a variety of other lessons learnt will be presented. Plans for scaling up and improvement of the services will also be described. m03.p05