Section 25.1.7. Graphics and model building

AMBER (Assisted Model Building with Energy Refinement; Cornell et al., 1995) is a molecular-dynamics and energy-minimization program. AMBER refers to two things: a molecular-mechanical force field for the simulation of biomolecules (which is in general use in a variety of simulation programs) and a package of molecular-simulation programs which includes source code and demonstrations.

Location: http://amber.scripps.edu/ . Operating systems: UNIX, SGI, SUN etc. Type: source code and binary. Languages: Fortran and C. Distribution: commercial.

CHARMM (Chemistry at HARvard Molecular Mechanics; Brooks et al., 1983; MacKerell et al., 1998) is a program for macromolecular simulations, including energy minimization, molecular dynamics and Monte Carlo simulations.

Location: http://yuri.harvard.edu/ . Operating systems: UNIX, SGI, SUN etc. Type: source code. Language: C. Distribution: minor licence fee for academic users.

Insight II is a 3D graphical environment for molecular modelling. Insight II creates, modifies, manipulates, displays and analyses molecular systems and related data, and provides the core requirements for all Insight II software modules. Its powerful user interface enables the seamless flow of data between a wide range of scientific applications. The Insight II environment integrates builder modules, development tools, force fields, simulation and visualization tools with tools specifically developed for applications in the life and materials sciences.

Location: http://www.msi.com/life/products/insight/index.html . Operating systems: SGI and IBM UNIX systems. Type: binary. Distribution: commercial.

MidasPlus (formerly Midas) (Ferrin et al., 1988) is an advanced molecular-modelling system developed by the Computer Graphics Laboratory (CGL) at the University of California, San Francisco. The system can be used for display and manipulation of macromolecules such as proteins and nucleic acids. Ancillary programs allow for such features as computation of molecular surfaces and electrostatic potentials and generation of publication-quality space-filling images with multiple light sources and shadows. To address the needs of the structure-based drug-design community, MidasPlus has been developed with an emphasis on the interactive selection, manipulation and docking of drugs and receptors. Although quite powerful in this application, the system is also somewhat specialized in this respect: it requires three-dimensional atomic coordinate data for the structures being displayed and expects the primary structure to be based on linear chains of subunits such as amino acids or nucleic acids. Using MidasPlus for complex inorganic compounds or large polymers with many cross-links is another application.

Location: http://www.cgl.ucsf.edu/Outreach/midasplus/ . Operating systems: SGI, DEC Alpha, NeXT, IBM RS6000 and LINUX. Type: source code. Distribution: minor licence fee for academic users.

MODELLER (Sali & Blundell, 1993) is most frequently used for homology or comparative modelling of protein three-dimensional structure. The user provides an alignment of a sequence to be modelled with known related structures and MODELLER will automatically calculate a full-atom model. More generally, MODELLER models protein 3D structure by satisfaction of spatial restraints. In principle, the restraints can be derived from a number of different sources. These include homologous structures (comparative modelling), NMR experiments (NMR refinement), rules of secondary-structure packing (combinatorial modelling), cross-linking experiments, fluorescence spectroscopy, image reconstruction in electron microscopy, site-directed mutagenesis, intuition, residue–residue and atom–atom potentials of mean force, etc. The output of MODELLER is a 3D structure of a protein that satisfies these restraints as well as possible. The optimization is carried out by the variable-target function procedure employing methods of conjugate gradients and molecular dynamics with simulated annealing. MODELLER can also do several other tasks, including multiple comparison of protein sequences and/or structures, clustering, and searching of sequence databases. MODELLER is also available as part of QUANTA (Section 25.1.7.8), Insight II (Section 25.1.7.3) and Weblab GeneExplorer.

Location: http://salilab.org/modeller/modeller.html . Operating system: UNIX. Type: source code and binary. Language: Fortran. Distribution: free academic.

MOLMOL is a molecular graphics program for display, analysis and manipulation of three-dimensional structures of biological macromolecules, with special emphasis on nuclear magnetic resonance (NMR) solution structures of proteins and nucleic acids. MOLMOL has a graphical user interface with menus, dialogue boxes and online help. The display possibilities include conventional presentations, as well as novel schematic drawings, with the option of displaying different presentations in one view. Covalent molecular structures can be modified by addition or removal of individual atoms and bonds. The three-dimensional structure can be manipulated by interactive rotation about individual dihedral angles. Special efforts were made to allow for appropriate display and analysis of sets of (typically 20–40) conformers that are conventionally used to represent the result of an NMR structure determination, using functions for superimposing sets of conformers, calculation of root-mean-square-distance (r.m.s.d.) values, identification of hydrogen bonds, checking and displaying violations of NMR constraints, and identification and listing of short distances between pairs of hydrogen atoms.

Location: http://www.mol.biol.ethz.ch/wuthrich/software/molmol/ . Operating systems: UNIX, IRIX, AIX, OSF1 and LINUX. Type: source code and binary. Distribution: free.

O (Jones et al., 1991) is a general-purpose macromolecular-modelling package. The program is aimed at scientists with a need to model, build and display macromolecules. Unlike other molecular-modelling programs, such as FRODO (Section 25.1.7.10), O is a graphical display program built on top of a versatile database system. All molecular data are kept in this database, in a predefined data structure. However, any data can be stored in the database. Data produced by associated stand-alone programs can be stored very easily in the database and used by the program, for example for colouring of atoms. The powerful macro facility of O enables the user to customize the use of the program to satisfy his or her specific needs. The current version of O is mainly aimed at the field of protein crystallography, bringing into use several new tools which ease the building of models into electron density, allowing it to be done faster and more correctly. Notably, some new auto-build options greatly enhance the speed of building and rebuilding molecular models. See Chapter 17.1 for a detailed description.

Locations: http://xray.bmc.uu.se/~alwyn/ ; ftp://xray.bmc.uu.se/ . Operating systems: UNIX and ESV. Type: binary. Distribution: free academic.

QUANTA is an extensive library of crystallographic software programs that streamline and accelerate protein structure solution. QUANTA provides a powerful and comprehensive modelling environment for 2D and 3D modelling, simulation and analysis of macromolecules and small organic compounds.

Location: http://www.msi.com/life/products/quanta/index.html . Operating system: SGI. Type: binary. Distribution: commercial.

SYBYL is a comprehensive computational tool kit for molecular design and analysis, with a special focus on the creation of new chemical entities. SYBYL provides essential construction and analysis tools for both organic and inorganic molecular structures. It is especially useful in building the structures of ligands, substrates and inhibitors.

Location: http://www.tripos.com/ . Operating system: UNIX. Type: binary. Distribution: commercial.

FRODO (Jones, 1978) is a general-purpose molecular-modelling program which can be used to model de novo macromolecules, polypeptides and nucleic acids from experimental 3D data obtained from X-ray crystallography and NMR, and to display the resulting models using various representations including van der Waals and Connolly molecular dot surfaces, as well as spline surfaces. Turbo FRODO is designed for ligand fitting and protein stacking. The user can interactively mutate a protein or chemically modify it, and evaluate the resulting conformational changes. There are several versions of FRODO around the scientific community. For LINUX and HPUX use the Turbo FRODO X version.

Location: http://afmb.cnrs-mrs.fr/TURBO_FRODO/turbo.html . Operating systems: HPUX, IRIX and LINUX. Type: binary. Distribution: commercial.