Available software
ASCONA is a fully automated command line tool for generating sequence alignments and superpositions of protein binding sites. It is geared to the alignment of alternative protein conformations and especially addresses the tasks of dealing with highly flexible backbone regions, detecting multiple occurrences of a binding site in oligomeric structures, and coping with arbitrary annotation inconsistencies and structural artifacts.
For more information click here.
Conformator is a novel conformer ensemble generator that stands out by its handling of macrocycles, high accuracy, as well as robustness with respect to input formats and molecular geometries. With an extended set of rules for sampling torsion angles, a novel algorithm for macrocycle conformer generation, and a new clustering algorithm for the assembly of conformer ensembles, Conformator generates high-quality conformation ensembles.i
Please find a full description of Conformator in a recent publication [“Conformator: A Novel Method for the Generation of Conformer Ensembles”]
For more information click here
The CSFPy is a Python module for the generation of the Connected Subgraph Fingerprint (CSFP).The user can load molecules by file or SMILES string, generate fingerprints and derive similarity measurements. A pdf file with a detailed description of the module is contained as well.
For more information click here.
The electron density score for individual atoms (EDIA) quantifies the electron density fit of each atom in a crystallographically resolved structure. Multiple EDIA values can be combined with the help of the power mean to compute EDIAm, the electron density score for multiple atoms to score a set of atoms such as a ligand, a residue, or an active site.
For more information click here.
fragment space exhaustive enumeration system (FSees) is an efficient method for exhaustively enumerating all molecules within a certain molecular subspace. This chemical space is described as a fragment space and constrained by a set of user-defined physicochemical properties. The FSees algorithm uses file-based data structures to overcome the limitation of computer main memory thus allowing to enumerate very large chemical spaces. The resulting chemical library can be used as a starting point for computational lead-finding technologies, like similarity searching, pharmacophore mapping, docking, or virtual screening.
For more information click here.
iRAISE is an inverse screening tool based on the RAISE (=RApid Index-based Screening Engine) technology. The triangle-descriptor abstraction of proteins and molecules allows fast non-sequential screening of thousands of target structures. Scoring measures applied for selectivity considering the reference ligand and coverages of the pocket and the ligand pose support inter-protein ranking.
For more information click here.
JamdaScorer applies the novel JAMDA scoring function as well as the LSL-BFGS optimization algorithm to protein-ligand poses. Note that JamdaScorer is not a docking program, therefore the ligand to be scored must be given with coordinates describing the binding pose relative to the protein.
Mona is an interactive tool that can be used to prepare and visualize large small-molecule datasets. A set centric workflow allows to intuitively handle hundred thousands of molecules. Building upon the robust framework Naomi common cheminformatics tasks such as analysis, filtering and converting of molecular files can be performed with high efficiency.
For more information click here.
mRAISE is a tool for ligand-based virtual screening based on the RAISE (=RApid Index-based Screening Engine) technology. The triangle-descriptor abstraction of small molecules allows fast non-sequential screening of millions of compounds. Calculated alignments are scored using a Gaussian-type scoring function which scores the general shape overlap as well as the compatibility of physicochemical features of aligned molecules.
For more information click here.
NAOMInext is a software tool supporting medicinal chemists during hit-to-lead optimization. Starting from a co-crystallized small fragment, synthetic feasible lead compounds are generated directly within the proteins binding site.
For further information click hereNAOMInova is a software tool enabling the geometrical and chemical analysis of atoms surrounding a user-defined structure of interest. Based on a user-selected set of protein structures, substructures can be searched and the distribution of partner points can be visualized.
For more information click here.
PELIKAN is a software tool enabling rapid searching of spatial interaction patterns in large collections of protein-ligand complexes. Data from protein-ligand complexes is stored in an SQLite database which can be subjected to different search processes.
For more information click here.
A command line tool for virtual screening with a pharmacophore model as query. Returns all molecules which can be mapped on the pharmacophore query together with a score based on their compatibility to the query model. The returned molecules are superposed on the query. The output file is empty when no input molecule could be mapped on the query. It contains the calculated score of the structure.
ReactionViewer is a command line tool for visualizing generic reaction patterns written as Reaction SMILES, Reaction SMARTS or in the SMIRKS language. Visualization of individual SMILES or SMARTS patterns is also possible. Images can be exported as .pdf, .png or .svg.
REMUS is a software tool for the efficient calculation of 3D shape-based similarity for small molecules. It uses a range of Gaussian functions, a step-limited BFGS optimization algorithm and random starting positions to calculate superimpositions. To address molecular flexibility, starting conformations are sampled using Conformator. REMUS allows the calculation of flexible alignments by adjusting the torsion angles during numerical alignment optimization.
SIENA is a software pipeline enabling the fully automated construction of protein structure ensembles from the PDB. Starting with a single query structure, all binding sites with high sequence similarity are extracted from the PDB, aligned, and protonated. SIENA is able to deal with complicated cases like binding sites at protein domain interfaces or within homo-multimeric proteins.
For more information click here.
The graphical SMARTScompareViewer and the accompanying SMARTScompare command line tool allow for in depth SMARTS pattern comparisons and analysis.
The SMARTSeditor is a graphic editing tool for generic chemical patterns. Based on the SMARTS language, chemical patterns can be created and edited interactively, similar to molecule editing in a chemical structure editor. The SMARTSeditor supports editing of given SMARTS or editing of chemical pattern without knowledge of the SMARTS language from scratch. It supports logic combinations as well as atom environment definitions. The generated pattern is converted into a SMARTS string which can be used in any application where the pattern is needed, e.g. for filtering of molecule databases.
For more information click here.
SpaceCompare has three modes of operation on ultra-large, non-enumerable combinatorial chemical spaces:
- calculate the exact overlap of two combinatorial chemical spaces and generate a CSV file containing all their shared products (only functionality in version 1.0)
- calculate physicochemical property distributions of all products of a combinatorial chemical space
- optimize the distribution of a specified property by removing fragments with high property values
You can use SpaceLight to generate custom topological fragment spaces or access the publicly-available KnowlegeSpace .
Please note that the current version of SpaceCompare cannot be run on commercial fragment spaces from BioSolveIT GmbH.
SpaceLight is a command line tool for similarity-based virtual screening in large combinatorial fragment spaces. It utilizes well-known fingerprints methods such as the Extended Connectivity Fingerprints (ECFP) and is able to search spaces containing billions or even trillions of compounds within seconds on a standard PC. In addition SpaceLight can be used for scaffold detection and custom fragment spaces generation. A pdf file with a detailed description of the module is contained as well.
Please note that SpaceLight as available from here cannot be used with commercial fragment spaces from BioSolveIT GmbH. If you are interested to do so, please contact BioSolveIT GmbH.
For more information click here.
SpaceMACS is a command line tool for maximum common connected substructure search and substructure search in general in large combinatorial fragment spaces. Therefore, the tool enables chemical structure search and topological similarity searching. SpaceMACS is able to screen Spaces containing billions or even trillions of compounds in seconds to minutes on a standard PC.
Please note that SpaceMACS as available from here cannot be used with commercial fragment spaces from BioSolveIT GmbH. If you are interested to do so, please contact BioSolveIT GmbH.
For more information click here.StructureProfiler assists in automatically profiling protein structures (PDB file format) ranging from model characteristics like R factor over active site features to ligand properties such as molecular geometry, electron density coverage and frequently seen torsion angles.
For more information click hereSynthesia is a command-line tool that uses an entire retrosynthetic route as a guide pathway to generate optimized structural analogues of a lead compound without compromising the synthesizability of the structure. The user has the ability to guide the structural modifications in a desired direction by specifying structural constraints.
For information on configuring Synthesia, see the README file that is part of the Synthesia package.
The TorsionAnalyzer is a commandline tool that classifies the torsion angles of rotatable bonds into relaxed, tolerable, and strained according to their likelihood in the CSD. The statistics are taken from the Torsion Library, a pregenerated collection of torsion angle statistics for a hierarchy of SMARTS.
Further information can be found in the most recent publication, as well as the preceding ones.
The TorsionPatternMiner is a commandline tool that mines torsion angles statistics from crystal conformations. It also checks the consistency of the Torsion Library SMARTS hierarchy with an extended SMARTScompare algorithm.
Further information about torsion libraries and their analysis can be found in the most recent publication, as well as the preceding ones.
UNICON is a command-line tool to cope with common cheminformatics tasks. The functionality of UNICON ranges from file conversion between standard formats SDF, MOL2, SMILES, and PDB via the generation of 2D structure coordinates and 3D structures to the enumeration of tautomeric forms, protonation states and conformer ensembles.
For more information click here.