SSIA is a program for predicting the magnitude and orientation of a sterically induced alignment tensor from a solute's (protein or DNA/RNA) three-dimensional shape.
Steric calculates the steric size of molecules about a point in terms of their cone angles and solid angles, as well as their total volumes and projected areas.
Swiss-PdbViewer is an application that provides a user friendly interface allowing to analyse several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface.
Symmetry is a set of C codes for automatic molecular symmetry recognition. Nothing fancy, but can be of use as an analytical or educational tool.
Tessel2 is a 3D compiler to produce crystal and molecular models, parametric surfaces and several forms of sphere tesselations. The program produces output to be rendered with POV-Ray 2 or 3, Geomview (OFF format), or any Virtual Reality renderer (VRML V1.0 format).
Powerful and flexible software for all kinds of thermodynamic calculations in multicomponent systems. It is widely used to calculate phase diagrams, thermochemical data, solidification simulations and Pourbaix diagrams.
Tinker is a complete and general package for MM/MD, with some special features for polypeptides. TINKER has the ability to use any of several common parameter sets, such as AMBER, CHARMM, MM2, MM3, OPLS, and our own AMOEBA force field based upon polarizable atomic multipole electrostatics.
Triton is a graphical tool for modelling protein mutants (using the external program MODELLER) and assessment of their activities (using the external program MOPAC). Semi-quantitative predictions of mutants' activities can be achieved by evaluating the changes in energies of the system and partial atomic charges of the active site residues during the reaction.
TURBOMOLE is a program package for ab initio electronic structure calculations. Outstanding features of TURBOMOLE are: semi-direct algorithms with adjustable main memory and disk space requirements; full use of all point groups; efficient integral evaluation; stable and accurate grids for numerical integration.
Semiempirical program package containingthe MINDO3, MNDO, MNDOC, AM1 and PM3 Hamiltonian. It is capable of performing geometry optimisations as well as transition state searches and provides some extended multi center charge models (NAO-PC, HO-PC, LMO-PC); additionally, it may be used for some QM/MM calculations.