Tag: SURFace

ROCS 1.3 – Receiver Operating Characteristic Surface

ROCS 1.3

:: DESCRIPTION

Plots the ROCS for high-throughput class-skewed data, calculates the Volume under the Surface (VUS) and the FDR-Controlled Area Under the Curve (FCAUC), and conducts tests to compare two ROC surfaces. Computes eROC curve and the corresponding AUC for imperfect reference standard.

::DEVELOPER

Tianwei Yu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R

:: DOWNLOAD

ROCS

:: MORE INFORMATION

Citation

PLoS One. 2012;7(7):e40598. doi: 10.1371/journal.pone.0040598.
ROCS: receiver operating characteristic surface for class-skewed high-throughput data.
Yu T

HotSPRing – Hot Spot at Protein-RNA interacing surface

HotSPRing

:: DESCRIPTION

HotSPRing is a web server to predict the host spots in RNA binding proteins (RBPs)

::DEVELOPER

Computational Structural Biology Lab , Indian Institute of Technology Kharagpur

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Probing binding hot spots at protein-RNA recognition sites.
Barik A, Nithin C, Karampudi NB, Mukherjee S, Bahadur RP.
Nucleic Acids Res. 2016 Jan 29;44(2):e9. doi: 10.1093/nar/gkv876.

jsPISA 2.0.3 – Protein Interfaces, Surfaces and Assemblies

jsPISA 2.0.3

:: DESCRIPTION

jsPISA is an interactive web tool for the calculation of macromolecular surfaces and interfaces, assessment of their properties and inference on probable macromolecular assemblies (complexes) from coordinate data, typically delivered by crystallographic X-ray experiment.

:: DEVELOPER

Eugene Krissinel ( eugene.krissinel@stfc.ac.uk.)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2015 Apr 23. pii: gkv314.
Stock-based detection of protein oligomeric states in jsPISA.
Krissinel E

PSTP-finder 0.4.3.1 – Protein Surface Transient Pocket Finder

PSTP-finder 0.4.3.1

:: DESCRIPTION

PSTP-finder is a software developed in order to analyse a molecular dynamic of a protein structure and highlight time ranges in which a transient pocket could be found around certain aminoacid residues on the protein surface.

::DEVELOPER

SBL (Stuctural Biology Laboratory), University of Siena

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 PSTP-finder

:: MORE INFORMATION

Volarea – VMD Plug-in to Measure the Surface and calculate the Volume of Proteins

Volarea

:: DESCRIPTION

Volarea is a plug-in of the widely spread molecular graphics software Visual Molecular Dynamics (VMD), which allows the calculation of the volume as well as the surface area of any chemical structure. The surface area can be used also to map or calculate the exposed area of the structure to the solvent or to another chemical structure.

::DEVELOPER

Volarea team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows / MacOsX
  • VMD
  • Tclsh8.5
  • tcl-Thread

:: DOWNLOAD

 Volarea

 :: MORE INFORMATION

Citation:

Chem Biol Drug Des. 2013 Dec;82(6):743-55. doi: 10.1111/cbdd.12197. Epub 2013 Oct 25.
Volarea – a bioinformatics tool to calculate the surface area and the volume of molecular systems.
Ribeiro JV1, Tamames JA, Cerqueira NM, Fernandes PA, Ramos MJ.

SURFace – Calculate Solvent accessible surface area

SURFace

:: DESCRIPTION

SURFace is a programs that calculate solvent accessible surface area and curvature corrected solvent accessible surface area. The accessible surface output is calculated for the whole molecule, per residue, and per atom.

::DEVELOPER

Barry Honig’s group 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SURFace

:: MORE INFORMATION

Citation

  • Nicholls, A., Sharp, K. and Honig, B. Proteins (1991), 11:281
  • Sridharan, S., Nicholls, A., Honig, B. Biophys. J. (1992), 61:A174