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FTrees specifications


Unique identifier OMICS_20182
Name FTrees
Alternative name Feature Trees
Software type Application/Script
Interface Command line interface
Restrictions to use License purchase required
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Version 3.4
Stability Stable
Registration required Yes
Maintained Yes


  • FTrees-FS (Feature Trees – Fragment Space)




No version available



  • person_outline FTrees Team

Additional information

Department of Lead Discovery, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany; BioSolveIT, St. Augustin, Germany

Publications for Feature Trees

FTrees citations


A Role for Fragment Based Drug Design in Developing Novel Lead Compounds for Central Nervous System Targets

PMCID: 4566055
PMID: 26441817
DOI: 10.3389/fneur.2015.00197

[…] and the resulting structures are scored using the FlexX docking program. Filters can be applied to sort structures by size of fragment used or various geometic properties, such as torsion angles. The Feature Trees (FTrees) module explores chemical spaces with fragment hopping and using overlapping fragments to create a composite ligand structure (). The starting fragment is modified with linker fr […]


Building a virtual ligand screening pipeline using free software: a survey

Brief Bioinform
PMCID: 4793892
PMID: 26094053
DOI: 10.1093/bib/bbv037

[…] ral features, fragment counts and rule-based sub-structure representations known as SMILES/SMARTS []); 2D-descriptors (topological descriptors / graph invariants like connectivity indices, as well as feature trees [], see discussion below); 3D-descriptors (geometry, surface and volume descriptors like 3D-WHIM [] and 3D-MORSE []); and 4D-descriptors (stereoelectronic and stereodynamic descriptors, […]


Prospective performance evaluation of selected common virtual screening tools. Case study: Cyclooxygenase (COX) 1 and 2

Eur J Med Chem
PMCID: 4444576
PMID: 25916906
DOI: 10.1016/j.ejmech.2015.04.017

[…] -based methods still needs to be performed. Tresadern et al. also included a prospective part in their comparison, where they evaluated the performance of Extended-connectivity fingerprints (ECFP) 6, Ftrees, Topomers, Cresset FieldScreen, and ROCS OpenEye Shape Tanimoto (OEST), OpenEye ComboScore (OECS), and OpenEye electrostatics in identifying ligands for the corticotropin releasing factor 1 rec […]


A New Graph Based Molecular Descriptor Using the Canonical Representation of the Molecule

Sci World J
PMCID: 4130360
PMID: 25140330
DOI: 10.1155/2014/286974

[…] nerate a mapping or alignment between molecules. Maximum common subgraph method (MCS) is an example of the graph-based similarity methods. Another example of the graph-based similarity methods is the feature trees. The feature trees were introduced by Rarey and Dixon [], which are the most abstract way of representing a molecule by means of a graph. A feature tree represents hydrophobic fragments […]


Computational mass spectrometry for small molecules

J Cheminform
PMCID: 3648359
PMID: 23453222
DOI: 10.1186/1758-2946-5-12

[…] using the Tanimoto score (Jaccard index). This was applied for metabolite identification in [].Aligning fragmentation trees is similar in spirit to the feature tree comparison of Rarey and Dixon []. Feature trees were computed from the molecular structure of a known compound, and represent hydrophobic fragments and functional groups of the compound, and the way these groups are linked together. […]


Estimating Empirical Codon Hidden Markov Models

Mol Biol Evol
PMCID: 3563974
PMID: 23188590
DOI: 10.1093/molbev/mss266

[…] sitive selection are conservative. However, for standard tests M1a–M2a and M7–M8, we observed high proportions of false positives (), often above acceptable levels, especially with small phylogenetic ftrees (e.g., 26.9 and 28.0 for the Dmel–Dsim tree). In contrast to , we simulated with an ECM and therefore generated MNSs. These MNSs are not accounted for by classical models such as M1a–M2a or M7– […]


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