Reconstruct 1.0 – Reconstructing 3D Structures from Contact Maps

Reconstruct 1.0

:: DESCRIPTION

RECONSTRUCT is a command line program for reconstruction of protein contact maps that uses the distgeom program of the TINKER package.

::DEVELOPER

Reconstruct team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java
  • Tinker

:: DOWNLOAD

 Reconstruct

:: MORE INFORMATION

Citation

Optimal contact definition for reconstruction of Contact Maps.
Jose M Duarte, Rajagopal Sathyapriya, Henning Stehr, Ioannis Filippis and Michael Lappe.
BMC Bioinformatics 2010, 11:283.

CMView 1.1.1 – Protein Contact Map Visualization and Analysis

CMView 1.1.1

:: DESCRIPTION

CMView is an intervative contact map visualization and analysis tool. The tool provides functions for contact map calculation from structure, basic editing, visualization in contact map and 3D space and structural comparison with different built-in alignment methods.

::DEVELOPER

CMView team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 CMView

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Jun 1;27(11):1573-4. Epub 2011 Apr 5.
CMView: interactive contact map visualization and analysis.
Vehlow C, Stehr H, Winkelmann M, Duarte JM, Petzold L, Dinse J, Lappe M.

PROTMAP2D 1.2.2 – Calculation, Visualization & Comparison of Contact Map

PROTMAP2D 1.2.2

:: DESCRIPTION

PROTMAP2D is a tool for calculation, visualization and comparison of contact maps. It can be used for quantitative and qualitative characterization of differences and similarities between alternative models of the same protein, e.g. members of the ensemble calculated from the results of the nuclear magnetic resonance (NMR) analysis, crystal structures solved under different conditions, theoretical models calculated with different programs, or series of conformations obtained in the course of  molecular dynamics (MD) simulations. PROTMAP2D allows analyzing multimeric proteins, and can be used to visualize intermolecular contacts in protein-protein complexes.

::DEVELOPER

Bujnicki Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX

:: DOWNLOAD

PROTMAP2D

:: MORE INFORMATION

Citation

Michal J. Pietal, Irina Tuszynska and Janusz M. Bujnicki
PROTMAP2D: visualization, comparison and analysis of 2D maps of protein structure
Bioinformatics (2007) 23 (11): 1429-1430.

NNcon 1.0 – Protein Contact Map Prediction Using Artificial Neural Networks

NNcon 1.0

:: DESCRIPTION

NNCon is one of the most effective protein contact map predictors. The software finds information about protein-protein residue contacts.

::DEVELOPER

Jianlin Jack Cheng

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 NNcon

:: MORE INFORMATION

Citation

Allison N. Tegge, Zheng Wang, Jesse Eickholt, and Jianlin Cheng.
NNcon: Improved Protein Contact Map Prediction Using 2D-Recursive Neural Networks.
Nucleic Acids Research, vol. 37, pp. w515-w518,2009

ConSole – Contact Map based Solenoid Detection

ConSole

:: DESCRIPTION

The ConSole algorithm provides a fast and accurate tool to recognize solenoid protein structures as a whole and to identify individual solenoid repeat units from a structure.

::DEVELOPER

Godzik Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Python
  • BioPython
:: DOWNLOAD

 ConSole

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2014 Apr 27;15:119. doi: 10.1186/1471-2105-15-119.
ConSole: using modularity of contact maps to locate solenoid domains in protein structures.
Hrabe T, Godzik A

SVMcon 1.0 – Protein Contact Map Prediction using Support Vector Machine

SVMcon 1.0

:: DESCRIPTION

SVMcon predicts medium- to long-range residue-residue contacts using Support Vector Machines. The contact predictions are in the CASP format (residue index 1, residue index 2, 0, 8, contact probability). The contact distance threshold is 8 angstrom. The sequence separation between two residues is at least 6 residues.

::DEVELOPER

Dr. Jianlin Cheng

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SVMcon

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2007 Apr 2;8:113.
Improved residue contact prediction using support vector machines and a large feature set.
Cheng J, Baldi P.

Al-Eigen – Contact Map Overlap by Alignment of Eigenvectors

Al-Eigen

:: DESCRIPTION

Al-Eigen (Alignment of Eigenvectors)  implements a heuristic procedure for computing a solution to the Contact Map Opverlap (CMO) problem. The algorithm uses the standard eigenvalue decomposition of symmetric matrices to obtain a set of principal eigenvectors weighted by the square root of corresponding eigenvalues. The overlap between the two maps is obtained by computing the optimal global alignment between the respective two sets of weighted eigenvectors.

::DEVELOPER

 Bioinformatics group, Department of Computer Science, University of Bologna

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX

:: DOWNLOAD

 Al-Eigen

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Sep 15;26(18):2250-8. Epub 2010 Jul 7.
Fast overlapping of protein contact maps by alignment of eigenvectors.
Di Lena P, Fariselli P, Margara L, Vassura M, Casadio R.

FT-COMAR – Fault Tolerance Reconstruction of 3D Structure from Protein Contact Maps

FT-COMAR

:: DESCRIPTION

FT-COMAR ( Fault Tolerant COntact MAp Reconstruction) implements a heuristic procedure for recovering a set of 3D coordinates from an incomplete contact map.

FT-COMAR Online Version

::DEVELOPER

 Bioinformatics group, Department of Computer Science, University of Bologna

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX

:: DOWNLOAD

  FT-COMAR

:: MORE INFORMATION

Citation

FT-COMAR: fault tolerant three-dimensional structure reconstruction from protein contact maps.
Vassura M, Margara L, Di Lena P, Medri F, Fariselli P, Casadio R.
Bioinformatics. 2008 May 15;24(10):1313-5. Epub 2008 Apr 1.

HMMSTR-CM – Protein Contact Map Prediction

HMMSTR-CM

:: DESCRIPTION

HMMSTR-CM is a software for protein contact map predictions. As above a sequence profile is the input. HMMSTR-CM gives you a JPEG image and text file showing the residues that are most likely to come into contact (distance < 8.0A) in the folded structure. This too is a bare-bones package. This script runs as part of the HMMSTR/Rosetta server.

::DEVELOPER

Chris Bystroff

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

HMMSTR-CM

:: MORE INFORMATION

Citaiton

Shao Y & Bystroff C. (2003a).
Predicting inter-residue contacts using templates and pathways.
Proteins, Structure, Function and Genetics 53 Suppl 6:497-502.