Departmental Cores (DC)

Molecular Modeling Core

The Core specializes in techniques for the display and analysis of macromolecular structures of proteins and nucleic acids. It offers molecularmodeling capabilities at several levels. Access is provided to several important databases, e.g., the RCSB Protein Data Bank (PDB), Cambridge Crystallography Data Bank (CSD), Genbank, EMBL, Swissprot.

Sequence analysis and comparison tools allow the display, editing, transforming and analysis of protein and nucleic acid sequence data. This includes homology searches, multiple sequence alignments, the enumeration of the product of digestion by given enzymes and secondary structure prediction based on empirical rules. Homology modeling can also be performed.

Analysis of molecular structure can be performed by quantum-mechanical methods to obtain, among others, the electronic structure, molecular properties and a description of electrostatic interactions. They also provide theoretical estimates of optimum molecular geometries, energies of reactions, and are useful in evaluating spectroscopic data.

Macromolecular associations, e.g. protein-protein or protein-DNA interactions, can be studied with the aid of high-resolution graphics display systems: optimal interactions can be determined, and conformational searches can be performed. Specialized computational and graphical tools are also available for the analysis of structural and energetic properties. These enable studies of structure-function relations, e.g., from consequences of mutations. Molecular simulation methods provide useful tools for description of molecular mechanisms, and are also used in conjunction with x-ray and NMR experiments for macromolecular structure determination.

All of the calculations can be performed either by using a sophisticated graphical interface that allows the user to build the system from preprogrammed building blocks, to import data from databases, or by logging on to one of the mainframe computers and executing the requisite programs. The resulting structures can be viewed in 2D or 3D renderings.

The computers in the facility include several Silicon Graphics (SGI) workstations, a 12-CPU multiprocessor server (SGI Power Challenge), a 'farm' of several 4CPU SGI O200 servers and Compaq Alpha servers, all networked. The graphics workstations are accessible 24 hours a day.

Assistance in the use of the Core is also available in the form of a facility guide a Unix/Linux survival guide and a list of the software in our library containing extensive on-line documentations, as well as tutorials and consultations.