Fit3D v005 – Small Structural Motif Screening in Proteins and further analyses

Fit3D v005

:: DESCRIPTION

Fit3D is a command line software tool to search for small structural motifs of amino acids in target proteins. It can also be used for batch-processing by applying to a large number of target structures.

::DEVELOPER

Fit3D team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX/Windows
  • Java

:: DOWNLOAD

 Fit3D

:: MORE INFORMATION

Citation:

Fit3D – A web application for highly accurate screening of spatial residue patterns in protein structure data.
Kaiser F, Eisold A, Bittrich S, Labudde D.
Bioinformatics. 2015 Oct 30. pii: btv637.

PharmaGist 1.0 – Multiple flexible alignment of small drug-like ligand molecules

PharmaGist 1.0

:: DESCRIPTION

PharmaGist is a freely available web server for pharmacophore detection. The employed method is ligand based. It does not require the structure of the target receptor. Instead, the input is a set of structures of drug-like molecules that are known to bind to the receptor. We compute candidate pharmacophores by multiple flexible alignments of the input ligands. The main innovation of this approach is that the flexibility of the input ligands is handled explicitly and in deterministic manner within the alignment process. The method is highly efficient, where a typical run with up to 32 drug-like molecules takes seconds to a few minutes on a stardard PC. Another important characteristic of the method is the capability of detecting pharmacophores shared by different subsets of input molecules.

::DEVELOPER

 the BioInfo3D group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 PharmaGist

:: MORE INFORMATION

Citation:

Schneidman-Duhovny D, Dror O, Inbar Y, Nussinov R, Wolfson HJ.
PharmaGist: a webserver for ligand-based pharmacophore detection.
Nucl. Acids Res. (2008) 36 (suppl 2): W223-W228.

 

PATHGROUPS – Rapid Small Phylogeny

PATHGROUPS

:: DESCRIPTION

The PATHGROUPS program optimizes the gene order at ancestral nodes of a given phylogeny, given the order in modern genomes.

::DEVELOPER

Sankoff Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 PATHGROUPS

:: MORE INFORMATION

Citaion

On the PATHGROUPS approach to rapid small phylogeny.
Zheng C, Sankoff D.
BMC Bioinformatics. 2011 Feb 15;12 Suppl 1:S4.