Triforce is a new approach to the calculation of solvent-accessible surface areas of molecules with potential application to surface area based methods for determination of solvation free energies. As in traditional analytical and statistical approaches, this new algorithm reports both component areas and derivatives as a function of the atomic coordinates and radii. Unique to TRIFORCE are the rapid and scalable approaches for the determination of sphere intersection points and numerical estimation of the surface areas, derivatives, and other properties that can be associated with the surface area facets. The algorithm performs a special tessellation and semianalytical integration that uses a precomputed look-up table. This provides a simple way to balance numerical accuracy and memory usage. TRIFORCE calculates derivatives in the same manner, enabling application in force-dependent activities such as molecular geometry minimization. TRIFORCE is available free of charge for academic purposes as both a C++ library, which can be directly interfaced to existing molecular simulation packages, and a web-accessible application.
Envisioned, developed and implemented by:
Nils J. D. Drechsel at the Computational Biochemistry and Biophysics Laboratory at Universitat Pompeu Fabra, the Laufer Center for Physical and Quantitative Biology at Stony Brook University and the Fennell Laboratory at Oklahoma State University
Christopher J. Fennell at the Laufer Center for Physical and Quantitative Biology at Stony Brook University and the Fennell Laboratory at Oklahoma State University
Ken A. Dill at the Laufer Center for Physical and Quantitative Biology
Jordi Villà Freixa at the Universitat de Vic
Integrator
This form can be used to upload a structure file and calculate semi-analytically solvent accessible surface areas.
TRIFORCE comes in 4 packages. triforce-lib contains the main library to calculate surface areas and solvations free energies. triforce-grids is comprised of integration tables which are vital for the calculations and default topologies in case there are none supplied by the user. triforce-dat contains scripts to generate the tables amongst other development stuff. Last but not least triforce-tool is a small command-line tool that interfaces with the library and produces the same output as displayed here on this website.
The supported way to install triforce is via the boost-build. Installation can be invoked by changing in the triforce directory and executing b2. There are 2 build variants that can be chosen: "b2 double" will build a library which expects atomic coordinate and force memory cells to be of double precision on the calling program side (triforce internally will use floats). "b2 float" will make triforce expect float precision memory cells. The default installation directories are /usr/local/lib for the library and /usr/local/include for the header files. If these directories do not suit you, you can simply change them in the jamroot file. If header and library files for boost armadillo etc. are located in non-standard folders, you might have to add their path to the searchpath in the jamroot.
For any enquiries, questions or comments, please send an email to nils [dot] drechsel [at] gmail [dot] com.
Topology
This is a topology file specified in gromacs format. It needs to have a .top file extension and specify sigma values for each atom type specified in the structure file.
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Structure
A structure file can be submitted in eiter .pdb, .gro, .xyzr or .tri format. .pdb is a file format used in the protein structure databank, .gro is a gromacs file format, xyzr specifies coordinates and radii for each atom and tri is a triforce file which is also the output of this integrator.
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Resolution
This specifies the resolution of the integration table. The higher the grid-size, the finer the interpolation points are set and the better the results will be.
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Numerical Detail
Optionally, a numerical detail can be set. In addition to the semi-analytical triforce calculations, a numerical integration scheme will be used and displayed at the end of the results. The detail corresponds quadratically to the number of discrete sampling points set on the sphere and should not be set higher than 100.
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Logistic Smoother
As described in the TRIFORCE main article, this option activates a logsitic smoother which closes a force gap between two spheres that do not touch (force is a 0-vector) and spheres that just touch each other (force is a non-zero vector).
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Force Balance
Extreme geometries, e.g. when two spheres are directly on top of each other, can lead to very large forces that are able to catapult partaking spheres into nirvana. If force balance is activated, abnormallyu large force are scaled down to the force median which will prevent such explosions. This should never occur anyways in a proper molecular dynamics simulation (in which atoms are strongly repelled before they are on top of each other), but might occur in non-physical scenarios.
