EDTSurf is a open source program to construct triangulated surfaces for macromolecules. It generates three major macromolecular surfaces: van der Waals surface, solvent-accessible surface and molecular surface (solvent-excluded surface). EDTsurf also identifies cavities which are inside of macromolecules.
FG-MD is a molecular dynamics (MD) based algorithm for atomic-level protein structure refinement. Given an initial protein structure, FG-MD first identifies analogous fragments from the PDB by the structural alignment program TM-align. Spatial restraints extracted from the fragments are then used to to re-shape the funnel of the MD energy landscape and guide the MD conformational sampling. FG-MD aims to refine the initial models closer to the native structure. It can also improve the local geometry of the structures by removing the steric clashes and improving the torsion angle and the hydrogen-binding networks.
REMO is a multifunctional program for constructing full-atom protein models from C-alpha traces by optimizing the backbone hydrogen-bonding networks. It gives options to choose models which are close to a given template or have more hydrogen-bonds. It has also options to build hydrogen atoms and side chain heavy atoms. The bond length and bond angle parameters are taken from CHARMM22.
SAXSTER is a new algorithm to combine small-angle x-ray scattering (SAXS) data and threading for high-resolution protein structure determination. Given a query sequence, SAXSTER first generates a list of template alignments using the MUSTER threading program from the PDB library. The SAXS data will then be used to prioritize the best template alignments based on the SAXS profile match, which are finally used for full-length atomic protein structure construction
ModRefiner is an algorithm for atomic-level, high-resolution protein structure refinement, which can start from either C-alpha trace, main-chain model or full-atomic model. Both side-chain and backbone atoms are completely flexible during structure refinement simulations, where conformational search is guided by a composite of physics- and knowledge-based force field. ModRefiner has an option to allow for the assignment of a second structure which will be used as a reference to which the refinement simulations are driven. One aim of ModRefiner is to draw the initial starting models closer to their native state, in terms of hydrogen bonds, backbone topology and side-chain positioning. It also generates significant improvement in physical quality of local structures. The standalone program also supports ab initio full-atomic relaxation, where the refined model is not restrainted by the initial model or the reference model.