Max-Planck-Institut für Informatik
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Software from the past years



FlexX is a computer program for predicting receptor-ligand interactions. For a given receptor and a ligand, FlexX predicts the geometry of the complex as well as the free energy of binding. FlexX is made for interactive work on receptor-ligand complexes as well as for screening a larger set of ligands in order to detect leads for drug design.
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FlexS is a software tool for superimposing flexible ligands. Either the structural alignment of two rigid molecules is possible within a few seconds, or a flexible molecule can be fitted on a rigid reference structure within a few minutes. The run time performance of FlexS enables interactive usage as well as screening through databases of nontrivial size.


FlexE is a computer program for predicting protein-ligand interactions. For a protein with known three-dimensional structure and a small ligand molecule, FlexE predicts the geometry of the protein-ligand complex and estimates the binding affinity.


FlexV is a general-purpose molecular viewer for UNIX System V workstations. It was originally developed to be the visualization front end for the protein-ligand docking program FlexX, but because it is a stand-alone tool with easy interfaces, it can be used in combination with any kind of molecular modeling software.


Feature Trees is a new kind of descriptor for molecular similarity and diversity analysis. Instead of a linear representation of a molecule like a bitstring or a vector, the molecule is described by a tree structure representing its major chemical building blocks and the way they are connected. In order to compare two molecules, highly efficient mapping algorithms are used to generate a matching between groups of molecule with similar steric and chemical properties.


HTSview is a graphical user interface (GUI) for the analysis of huge HTS data sets.


The focus of this project is the improvement of structure prediction methods and the development of computational approaches for the analysis of protein structure-function relationships.


ToPLign implements standard pairwise and multiple alignment methods with flexible parameter handling. The analysis of alignments is supported by offering different visualisations of alignments. In addition, ToPLign includes innovative approaches to the parametric alignment problem and the threading problem. Protein structure prediction methods via thrading have been extendend to EST assemblies to allow for EST translation and fold prediction in one integrated procedure.


ToPNet is a new tool for visualization and exploration of gene networks and expression data. ToPNet provides various ways of restricting, manipulating and combining biological networks according to annotation data (e.g. Gene Ontology terms) and presents results to the user by different visualization methods and hyperlinks to the underlying data sources.