FlexS 2.1.3 – Predict Ligand Superpositions

FlexS 2.1.3

:: DESCRIPTION

FlexS is a computer program for predicting ligand superpositions. For a given pair of ligands, FlexS predicts the conformation and orientation of one of the ligands relative to the other one. In FlexS the reference-ligand is assumed to be rigid, thus, it should be given in a conformation which is similar to the bound state. The superposition algorithm in FlexS requires only little manual intervention. Nevertheless, in some cases additional information about the ligands or even the superposition is known. You can integrate this knowledge into the computations with FlexS by carrying out single steps manually. Thus, FlexS is designed for interactive work on ligand pairs as well as for ligand-based virtual screening.

::DEVELOPER

BioSolveIT GmbH 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/SGI Irix

:: DOWNLOAD

 FlexS

:: MORE INFORMATION

Citation

C. Lemmen, T. Lengauer, and G. Klebe.
FLEXS: A method for fast flexible ligand superposition.
Journal of Medicinal Chemistry, 41:4502–4520, 1998.

LPIcom – Analysis, Comparison and Prediction of Protein Ligand Binding Sites

LPIcom

:: DESCRIPTION

LPIcom is a web server developed for understanding protein-ligand interaction for almost all ligands available in Protein Data Bank.

::DEVELOPER

LPIcom team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

A web server for analysis, comparison and prediction of protein ligand binding sites.
Singh H, Srivastava HK, Raghava GP.
Biol Direct. 2016 Mar 25;11(1):14. doi: 10.1186/s13062-016-0118-5.

USR-VS – Ligand-based Virtual Screening powered by Ultrafast Shape Recognition Techniques

USR-VS

:: DESCRIPTION

USR-VS is the first webserver for large-scale prospective virtual screening using USR and USRCAT, two ultrafast ligand-based 3D molecular similarity methods that have been retrospectively validated(a number of successful prospective virtual screening applications have also been reported for USR ).

::DEVELOPER

USR-VS team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

USR-VS: a web server for large-scale prospective virtual screening using ultrafast shape recognition techniques.
Li H, Leung KS, Wong MH, Ballester PJ.
Nucleic Acids Res. 2016 Apr 22. pii: gkw320.

SMAP 2.0 – Software for Ligand Binding Site Comparison

SMAP 2.0

:: DESCRIPTION

SMAP software package is designed for the comparison and the similarity search of protein three-dimensional motifs independent on the sequence order.

::DEVELOPER

Lei Xie

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows
  • Perl

:: DOWNLOAD

 SMAP

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W441-4. doi: 10.1093/nar/gkq400. Epub 2010 May 19.
SMAP-WS: a parallel web service for structural proteome-wide ligand-binding site comparison.
Ren J1, Xie L, Li WW, Bourne PE.

Twilight – A tool for Ligand Density Validation

Twilight

:: DESCRIPTION

Twilight is a standalone script for analysis, visualization, and annotation of a pre-filtered set of protein/ligand complexes deposited with the PDB with ligand RSCC values that are below a threshold of 0.6.

::DEVELOPER

Twilight team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Python

:: DOWNLOAD

 Twilight

:: MORE INFORMATION

Citation:

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2013 Feb 1;69(Pt 2):195-200. doi: 10.1107/S1744309112044387.
Visualizing ligand molecules in Twilight electron density.
Weichenberger CX1, Pozharski E, Rupp B.

eMatchSite 1.0 – Sequence Order-independent Ligand Binding Site Alignment

eMatchSite 1.0

:: DESCRIPTION

eMatchSite is a sequence order-independent algorithm for ligand binding site alignment and matching. It accurately identifies pairs of pockets that bind similar compounds even in proteins with different global structures. Furthermore, it tolerates structural distortions in protein models, thus experimentally solved structures are not required.

::DEVELOPER

Computational Systems Biology Group, Louisiana State University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 eMatchSite

:: MORE INFORMATION

Citation

eMatchSite: sequence order-independent structure alignments of ligand binding pockets in protein models.
Brylinski M.
PLoS Comput Biol. 2014 Sep 18;10(9):e1003829. doi: 10.1371/journal.pcbi.1003829.

LigMerge 1 – Generate models of novel potential Ligands from sets of known Binders

LigMerge 1

:: DESCRIPTION

LigMerge is a novel drug-design algorithm which combines structures of known binders to generate similar but structurally distinct compounds that can be tested for binding.

::DEVELOPER

Jacob Durrant, @ the lab of Rommie E. Amaro

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python

:: DOWNLOAD

LigMerge

:: MORE INFORMATION

Citation

Chem Biol Drug Des. 2012 Sep;80(3):358-65. doi: 10.1111/j.1747-0285.2012.01414.x. Epub 2012 Jun 27.
LigMerge: a fast algorithm to generate models of novel potential ligands from sets of known binders.
Lindert S, Durrant JD, McCammon JA.

OpenGrowth 0.43 – Construct de novo Ligands for Protein

OpenGrowth 0.43

:: DESCRIPTION

OpenGrowth is a research program which grows new ligands in proteins by connecting small organic fragments.

::DEVELOPER

The Shakhnovich Biophysics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX / Linux

:: DOWNLOAD

 OpenGrowth

:: MORE INFORMATION

Citation

OpenGrowth: An Automated and Rational Algorithm for Finding New Protein Ligands.
Chéron N, Jasty N, Shakhnovich EI.
J Med Chem. 2015 Sep 23

LIBRA v1 – Ligand Binding site Recognition Application

LIBRA v1

:: DESCRIPTION

LIBRA is based on a graph theory approach to find the largest subset of similar residues between an input protein and a collection of known functional sites.

::DEVELOPER

the Theoretical Biology and Bioinformatics Laboratory

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Windows/Linux
  • JRE

:: DOWNLOAD

 LIBRA

:: MORE INFORMATION

Citation

LIBRA: LIgand Binding site Recognition Application.
Viet Hung L, Caprari S, Bizai M, Toti D, Polticelli F.
Bioinformatics. 2015 Aug 26. pii: btv489.

MotiveValidator 1.1.15.5.12 – Validate Ligand and Residue Structure in Biomolecular Complexes

MotiveValidator 1.1.15.5.12

:: DESCRIPTION

MotiveValidator is a platform for a set of applications designed to help you determine whether a residue or a ligand in a biomolecule or biomolecular complex is structurally complete and correctly annotated according to its models stored in the wwPDB Chemical Component Dictionary (wwPDB CCD).

::DEVELOPER

MotiveValidator team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

MotiveValidator

:: MORE INFORMATION

Citation

MotiveValidator: interactive web-based validation of ligand and residue structure in biomolecular complexes.
Vařeková RS, Jaiswal D, Sehnal D, Ionescu CM, Geidl S, Pravda L, Horský V, Wimmerová M, Koča J.
Nucleic Acids Res. 2014 Jul;42(Web Server issue):W227-33. doi: 10.1093/nar/gku426.