NAOMI ChemBio Suite - List of Tools

Mona An easy-to-use cheminformatics plattform

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.

iRAISE Inverse screening and structure-based target prediction

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.

SMARTSeditor Interactive and semi-automatic creation of molecular patterns

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.

SMARTScompareViewer Compare and analyze molecular patterns

The graphical SMARTScompareViewer and the accompanying SMARTScompare command line tool allow for in depth SMARTS pattern comparisons and analysis.

UNICON A universal converter, tautomer and conformer generator

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.

ASCONA Sequence-driven binding site alignment for multimeric proteins

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.

SIENA A fully-automated protein binding site ensemble generator

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.

mRAISE Ligand-based virtual screening

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.

FSees A fragment space exhaustive enumeration system

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.

PELIKAN Searching for spatial interaction patterns in sets of protein-ligand complexes

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.

TorsionAnalyzer Knowledge-based analysis of small molecule conformations

TorsionAnalyer is a graphical tool for the conformational analysis of small molecule conformations. After loading a 3D structure, all bonds are mapped to torsion patterns associated with histograms derived from CSD data. The package also contains the command line tool TorsionChecker. TorsionAnalyzer, TorsionChecker, and the TorsionLibrary were jointly developed with Roche, Basel.

For more information click here.

The TorsionLibrary can also be downloaded from here.

NAOMInova Geometrical and chemical analysis of atoms surrounding a user-defined structure

NAOMInova 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.

EDIAScorer Quantifying the electron density fit within structural models

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.

StructureProfiler Automatically profile protein structures in PDB format

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 here

NAOMInext Forward synthesis planning integrated into high throughput docking

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 here

Conformator A novel conformer ensemble generator

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

CSFPy Fingerprint generation considering all structural features

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.

REMUS Alignment-Driven Virtual Screening

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.

Torsionpatternminer generates statistical information about the pattern matching behavior of a torsion library with respect to a set of compounds.

The Torsiopatternminer describes the pattern matching behavior of a torsion library with respect to a set of compounds. Besides analyzing which patterns can match which molecules, it also generates a variety of statistical information such as: frequency with which patterns are matched, how often matches involving a pattern lead to a poorly scored torsion and which patterns are never matched in the given compound set. This can be used to characterize the torsion library, the matching behavior and the compound set.

Further information about torsion libraries and their analysis can be found in the most recent publication, as well as the preceding ones.

SpaceLight Topological similarity search in large combinatorial fragment spaces

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.

For more information click here.

JamdaScorer Scoring and numerical optimization of protein-ligand poses

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.