Tag: Protein Structure

xPyder 201208 – Analyze Coupled Residues and their networks in Protein Structures

xPyder 201208

:: DESCRIPTION

xPyder is a PyMOL plugin to analyze and visualize on the 3D structure dynamical cross-correlation matrices (DCCM), linear mutual information (LMI), communication propensities (CP), intra- and inter-molecular interactions (e.g. PSN), and more, to produce highly customizable publication-quality images.

::DEVELOPER

Papaleo Research Group

:: SCREENSHOTS

xPyder

:: REQUIREMENTS

  • Linux /Windows/ MacOsX
  • Python
  • PyMol

:: DOWNLOAD

 xPyder

:: MORE INFORMATION

Citation

xPyder: a PyMOL plugin to analyze coupled residues and their networks in protein structures.
Pasi M, Tiberti M, Arrigoni A, Papaleo E.
J Chem Inf Model. 2012 Jul 23;52(7):1865-74. doi: 10.1021/ci300213c

CABS-flex – Server for fast Simulation of Protein Structure Fluctuations

CABS-flex

:: DESCRIPTION

CABS-flex is an efficient procedure for the simulation of structure flexibility of folded globular proteins.

::DEVELOPER

Laboratory of Theory of Biopolymers,  University of Warsaw

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2014 May 2.
CABS-flex predictions of protein flexibility compared with NMR ensembles.
Jamroz M1, Kolinski A, Kmiecik S.

HDXanalyzer 1.0 – Statistical Analysis of Protein Structure Dynamics

HDXanalyzer 1.0

:: DESCRIPTION

HDXanalyzer is software package to enable the statistical analysis of HDX mass spectrometry data. The software will help the protein structure dynamics study tremendously.

::DEVELOPER

Joshua Yuan lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Python

:: DOWNLOAD

 HDXanalyzer

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2011 Feb 15;12 Suppl 1:S43. doi: 10.1186/1471-2105-12-S1-S43.
HDX-analyzer: a novel package for statistical analysis of protein structure dynamics.
Liu S, Liu L, Uzuner U, Zhou X, Gu M, Shi W, Zhang Y, Dai SY, Yuan JS.

ResProx – Comparing the overall Quality of NMR Protein Structures

ResProx

:: DESCRIPTION

ResProx (Resolution-by-proxy or Res(p)) is a web server that predicts the atomic resolution of NMR protein structures using only PDB coordinate data as input.

::DEVELOPER

Wishart Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • VMware

:: DOWNLOAD

  ResProx

:: MORE INFORMATION

Citation

Resolution-by-proxy: a simple measure for assessing and comparing the overall quality of NMR protein structures.
Berjanskii M, Zhou J, Liang Y, Lin G, Wishart DS.
J Biomol NMR. 2012 Jul;53(3):167-80. doi: 10.1007/s10858-012-9637-2

J3DPSV 1.0 – Java Three-dimensional (3D) Protein Structure Viewer

J3DPSV 1.0

:: DESCRIPTION

J3dPSV is a graphical application package for viewing and modeling of three dimensional structures of protein structure, including multiple chain sequence table and a three-dimensional (3D) protein structure viewer.

:: DEVELOPER

Hyun Seok Park

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/ Linux / MacOsX
  • JAVA

:: DOWNLOAD

 J3DPSV

:: MORE INFORMATION

Citation

Chun, Yoo Jin, Il Ham, Seong, Yang, San Duk, Rhie, Arang, Park, Hyun Seok
Refactoring the code for visualizing protein database information in a 3D viewer for software reusability
Genomics & Informatics, 6:50-53, MAR 31 2008

Concoord 2.1.2 – Protein Structure Generation from Distance Constraint

Concoord 2.1.2

:: DESCRIPTION

CONCOORD is a method to generate protein conformations around a known structure based on geometric restrictions. Principal component analyses of Molecular Dynamics (MD) simulations of proteins have indicated that collective degrees of freedom dominate protein conformational fluctuations. These large-scale collective motions have been shown essential to protein function in a number of cases. The notion that internal constraints and other configurational barriers restrict protein dynamics to a limited number of collective degrees of freedom has led to the design of the CONCOORD method to predict these modes without doing explicit, more CPU intensive, MD simulations.

::DEVELOPER

Bert de Groot

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Concoord

:: MORE INFORMATION

Citation

B.L. de Groot, D.M.F. van Aalten, R.M. Scheek, A. Amadei, G. Vriend and H.J.C. Berendsen;
“Prediction of protein conformational freedom from distance constraints“,
Proteins 29: 240-251 (1997)

QCS – Quality Control Score For Quality Assessment of Protein Structure Prediction

QCS

:: DESCRIPTION

QCS (Quality Control Score) is a new method to evaluate the quality of structure predictions, especially for template free structure prediction. It was developed to mimic visual inspction by human expert and it captures both global and local structural features, with emphasis on global topology.

::DEVELOPER

Grishin Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • GCC
  • Python

:: DOWNLOAD

 QCS

:: MORE INFORMATION

Citation

Cong Q, Kinch LN, Pei J, Shi S, Grishin VN, Li W, Grishin NV.
An automatic method for CASP9 free modeling structure prediction assessment.
Bioinformatics. 2011 Dec 15;27(24):3371-8. Epub 2011 Oct 12.

ExonVisualiser – Exon Identification & Visualization in Protein Structures

ExonVisualiser

:: DESCRIPTION

ExonVisualiser is dedicated to everyone (e.g computer scientists, biotechnologists, biologists) who is interested in visualization protein regions (2D and 3D structures) encoded by particular exons.

::DEVELOPER

Krzysztof Porembski  & dr Monika Piwowar (mpiwowar@cm-uj.krakow.pl)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformation. 2012;8(25):1280-2. doi: 10.6026/97320630081280. Epub 2012 Dec 19.
ExonVisualiser – application for visualization exon units in 2D and 3D protein structures.
Piwowar M, Krzysztof P, Piotr P.

Helix Packing Pair – Calculation of Helix Packing Angles in Protein Structures

Helix Packing Pair

:: DESCRIPTION

 Helix Packing Pair is a program that analyses the geometry and the packing of helicies.

::DEVELOPER

University of Leeds Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX

:: DOWNLOAD

 Helix Packing Pair

:: MORE INFORMATION

Citation

Dalton, J.A.R., Michalopoulos, I., and Westhead, D.R. (2003).
“Calculation of helix packing angles in protein structures“.
Bioinformatics 19, 1298-1299

Exit mobile version