PocketAnalyzerPCA 1.30 – Pocket-space Maps to Identify novel Binding-site Conformations in Proteins

PocketAnalyzerPCA 1.30

:: DESCRIPTION

PocketAnalyzer(PCA) combines a geometric algorithm for detecting pockets in proteins with Principal Component Analysis and clustering. This enables visualization and analysis of pocket conformational distributions of large sets of protein structures.

::DEVELOPER

the Gohlke Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  PocketAnalyzerPCA

:: MORE INFORMATION

Citation

J Chem Inf Model. 2011 Oct 24;51(10):2666-79. doi: 10.1021/ci200168b. Epub 2011 Sep 30.
Pocket-space maps to identify novel binding-site conformations in proteins.
Craig IR1, Pfleger C, Gohlke H, Essex JW, Spiegel K.

Fitmunk – Improving Protein Structures by accurate, automatic Modeling of Side-chain Conformations

Fitmunk

:: DESCRIPTION

Fitmunk provides a framework for fitting conformations on a fixed backbone into electron density.

::DEVELOPER

Minor Lab at University of Virginia

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Fitmunk: improving protein structures by accurate, automatic modeling of side-chain conformations.
Porebski PJ, Cymborowski M, Pasenkiewicz-Gierula M, Minor W.
Acta Crystallogr D Struct Biol. 2016 Feb;72(Pt 2):266-80. doi: 10.1107/S2059798315024730.

3PD – Primer design for Chromosome Conformation Capture Assays

3PD

:: DESCRIPTION

3PD is a bioinformatics solution  to support the experimentalist in detecting long-ranging intra or inter chromosomal contacts by Chromosome conformation capture (3C) assays.

::DEVELOPER

3PD team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Genomics. 2009 Dec 29;10:635. doi: 10.1186/1471-2164-10-635.
3PD: Rapid design of optimal primers for chromosome conformation capture assays.
Fröhler S, Dieterich C.

PREDDIMER – Prediction tool for an Ensemble of Transmembrane α-helical Dimer Conformations

PREDDIMER

:: DESCRIPTION

PREDDIMER reconstructs putative dimer conformations for given sequences of transmembrane protein fragments, which are considered as ideal α-helices.

::DEVELOPER

Laboratory of biomolecular modeling.

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Mar 15;30(6):889-90. doi: 10.1093/bioinformatics/btt645.
PREDDIMER: a web server for prediction of transmembrane helical dimers.
Polyansky AA1, Chugunov AO, Volynsky PE, Krylov NA, Nolde DE, Efremov RG.

Ribomaker 20140124 – Computational Design of Conformation-based Riboregulation

Ribomaker 20140124

:: DESCRIPTION

RiboMaker is a webserver for the computational design of conformation-based riboregulation.

::DEVELOPER

Jaramillo Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • G++

:: DOWNLOAD

 Ribomaker

:: MORE INFORMATION

Citation

Bioinformatics. 2014 May 14. pii: btu335. [Epub ahead of print]
RiboMaker: computational design of conformation-based riboregulation.
Rodrigo G1, Jaramillo A2.

Curves+ 2.6 – Analyzing the Conformation of Nucleic Acid Structures

Curves+ 2.6

:: DESCRIPTION

Curves+ is a revised version of the Curves software for analyzing the conformation of nucleic acid structures.

::DEVELOPER

Richard Lavery (r.lavery@ibcp.fr)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Fortran

:: DOWNLOAD

 Curves+

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W68-73. doi: 10.1093/nar/gkr316. Epub 2011 May 10.
CURVES+ web server for analyzing and visualizing the helical, backbone and groove parameters of nucleic acid structures.
Blanchet C1, Pasi M, Zakrzewska K, Lavery R.

SIDEpro 1.0 – Prediction of Protein side-chain Conformations

SIDEpro 1.0

:: DESCRIPTION

SIDEpro is a novel machine learning approach for the fast and accurate prediction of side-chain conformations.

::DEVELOPER

Institute for Genomics and Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 SIDEpro

:: MORE INFORMATION

Citation:

K. Nagata, A. Randall, & P. Baldi.
SIDEpro: a novel machine learning approach for the fast and accurate prediction of side-chain conformations.
Proteins. 2012 Jan;80(1):142-53. doi: 10.1002/prot.23170. Epub 2011 Nov 9.

IRECS 1.3 – Predict Conformation of Protein Side Chains

IRECS 1.3

:: DESCRIPTION

IRECS ( REduction of Conformational Space) can predict multiple conformations for all side chains of a target protein. Side-chain conformations are selected according to the flexibility of the respective side chain. IRECS is also able to mutate single side chains or read in alignments to create a homology model of the target protein on a template backbone.

::DEVELOPER

Joachim Büch ,

Max-Planck-Institut Informatik

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  •  Linux

:: DOWNLOAD

  IRECS

:: MORE INFORMATION

Citation:

Hartmann, C., Antes, I., Lengauer, T.
IRECS: A new algorithm for the selection of most probable ensembles of side-chain conformations in protein models.
Protein Sci. 2007 16: 1294-1307.

tCONCOORD 1.0 – Predict Protein Conformational Flexibility

tCONCOORD 1.0

:: DESCRIPTION

tCONCOORD predicts protein conformational flexibility based on geometrical considerations. In a first step, the protein structure is analyzed and turned into a set of constraints, mostly distance constraints but also angle, chiral and planarity constraints with upper and lower bounds. This set of constraints serves as a kind of construction plan for the protein.

::DEVELOPER

Daniel Seeliger

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  tCONCOORD

:: MORE INFORMATION

Citation

Daniel Seeliger and Bert L. de Groot.
tCONCOORD-GUI: Visually supported conformational sampling of bioactive molecules.
J. Comp. Chem. 30:1160-1166 (2009)

SCWRL 4.0 – Prediction of Protein Side-chain Conformation

SCWRL 4.0

:: DESCRIPTION

SCWRL is the  program for prediction of protein side-chain conformations. SCWRL is based on a new algorithm and new potential function that results in improved accuracy at reasonable speed. This has been achieved through: 1) a new backbone-dependent rotamer library based on kernel density estimates; 2) averaging over samples of conformations about the positions in the rotamer library; 3) a fast anisotropic hydrogen bonding function; 4) a short-range, soft van der Waals atom-atom interaction potential; 5) fast collision detection using k-discrete oriented polytopes; 6) a tree decomposition algorithm to solve the combinatorial problem; and 7) optimization of all parameters by determining the interaction graph within the crystal environment using symmetry operators of the crystallographic space group.

::DEVELOPER

Dunbrack Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Mac OsX /  Linux

:: DOWNLOAD

SCWRL

:: MORE INFORMATION

Citation

G. G. Krivov, M. V. Shapovalov, and R. L. Dunbrack, Jr.
Improved prediction of protein side-chain conformations with SCWRL4.
Proteins (2009).