3PD is a bioinformatics solution to support the experimentalist in detecting long-ranging intra or inter chromosomal contacts by Chromosome conformation capture (3C) assays.
SCWRL is the program for prediction of protein side-chain conformations. SCWRL is based on a new algorithm and new potential function that results in improved accuracy at reasonable speed. This has been achieved through: 1) a new backbone-dependent rotamer library based on kernel density estimates; 2) averaging over samples of conformations about the positions in the rotamer library; 3) a fast anisotropic hydrogen bonding function; 4) a short-range, soft van der Waals atom-atom interaction potential; 5) fast collision detection using k-discrete oriented polytopes; 6) a tree decomposition algorithm to solve the combinatorial problem; and 7) optimization of all parameters by determining the interaction graph within the crystal environment using symmetry operators of the crystallographic space group.
tCONCOORD predicts protein conformational flexibility based on geometrical considerations. In a first step, the protein structure is analyzed and turned into a set of constraints, mostly distance constraints but also angle, chiral and planarity constraints with upper and lower bounds. This set of constraints serves as a kind of construction plan for the protein.
PocketAnalyzer(PCA) combines a geometric algorithm for detecting pockets in proteins with Principal Component Analysis and clustering. This enables visualization and analysis of pocket conformational distributions of large sets of protein structures.
IRECS ( REduction of Conformational Space) can predict multiple conformations for all side chains of a target protein. Side-chain conformations are selected according to the flexibility of the respective side chain. IRECS is also able to mutate single side chains or read in alignments to create a homology model of the target protein on a template backbone.
