GMA is a combined 2D/3D approach for the superposition of flexible chemical structures, which is based on recent progress in the efficient identification of common subgraphs and a gradient-based torsion space optimization algorithm. The simplicity of the approach is reflected in its generality and computational efficiency: the approach neither requires precalculated statistics on the conformations of the molecules nor does it make simplifying assumptions on the topology of the molecules being compared. Graph-based molecular alignment produces alignments that are consistent with the chemistry of the molecules as well as their general structure, as it depends on both the local connectivities between atoms and the overall topology of the molecules. Results from extensive evaluation suggest that, for most practical purposes, graph-based molecular alignment is a viable alternative to molecular field alignment with respect to structural superposition and leads to structures of comparable quality in a fraction of the time.
HomDock is a combination of the ligand based GMA molecular alignment tool and our receptor based docking tool GlamDock. This combined approach can be used to improve docking accuracy and efficiency in cases where a complex structure of a ligand with the target protein is known. The approach can be extended to cases where a known ligand exists, however the complex structure is unknown, so only the identity of a active molecule is needed to improve efficiency of docking.
Imaginary transition states are simple graphs that represent chemical reactions and to a certain extent their mechanism. We are developing methods for predicting them and for applying them to address a number of important questions in biochemistry and metabolomics
Fuzzee is an algorithm that describes molecules as reduced graphs of functional groups or fragments. Each node in the graph represents a fragment in the molecule. Edges between the nodes represent the connectivity of the corresponding fragments. Each node obtains a number of features describing the atoms that constitute the original fragment. Each feature has a weight and a value, which counts the occurrences of the feature in the fragment. The overall similarity between two molecules is the normalised sum of the similarities of mapped nodes. The algorithm is used for the identification of topological different molecules with simiilar physico-chemical features.
