Tag: Determination

DISCO 1.0 – Structure Determination of Protein Homo-oligomers

DISCO 1.0

:: DESCRIPTION

DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer.

::DEVELOPER

Donald Lab at Duke University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

DISCO

:: MORE INFORMATION

Citation

Jeffrey W. Martin, Anthony K. Yan, Chris Bailey-Kellogg, Pei Zhou, and Bruce R. Donald.
A graphical method for analyzing distance restraints using residual dipolar couplings for structure determination of symmetric protein homo-oligomers.
Protein Science, 20(6):970-985, 2011.

RDC-PANDA 1.0 – NMR NOE Assignment & Protein Structure Determination

RDC-PANDA 1.0

:: DESCRIPTION

RDC-PANDA (RDC-based SSE PAcking with NOEs for Structure Determination and NOE Assignment) is a suite of programs for nuclear Overhauser effect (NOE) assignment and high-resolution structure determination starting with a global fold calculated from exact solutions to the residual dipolar coupling (RDC) equations. RDC-PANDA is specifically designed for automated NMR NOE assignment and protein structure determination.

::DEVELOPER

Donald Lab at Duke University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

RDC-PANDA

:: MORE INFORMATION

Citation

Jianyang Zeng, Jeffrey Boyles, Chittaranjan Tripathy, Lincong Wang, Anthony Yan, Pei Zhou, and Bruce Randall Donald.
High-resolution protein structure determination starting with a global fold calculated from exact solutions to the RDC equations.
Journal of Biomolecular NMR, 45(3):265-281, 2009

PCaAnalyser – 2D-Image Analysis Based Module for Effective Determination of Prostate Cancer Progression in 3D Culture

PCaAnalyser

:: DESCRIPTION

PCaAnalyser uses novel algorithms that allow accurate and rapid quantitation of protein expression in 3D cell culture.

::DEVELOPER

Hoque’s Lab, University of New Orleans

:: SCREENSHOTS

PCaAnalyser

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java

:: DOWNLOAD

 PCaAnalyser

:: MORE INFORMATION

Citation

PLoS One. 2013 Nov 20;8(11):e79865. doi: 10.1371/journal.pone.0079865. eCollection 2013.
PCaAnalyser: a 2D-image analysis based module for effective determination of prostate cancer progression in 3D culture.
Hoque MT1, Windus LC, Lovitt CJ, Avery VM.

PONDEROSA-C/S 20181026 – Automated Protein 3D structure Determination

PONDEROSA-C/S 20181026

:: DESCRIPTION

PONDEROSA-C/S  is a successor of the PONDEROSA (Peak picking Of NOE Data Enabled by Restriction Of Shift Assignments) program, which utilizes information from prior assignments to automatically pick NOE peaks from 3D-NOESY (13C-edited and 15N-edited) spectra and uses the results as input for a series of AUDANA (Automated Database-Assisted NOE Assignment) or CYANA structure calculations with the goal of achieving a publishable quality solution structure.

::DEVELOPER

The National Magnetic Resonance Facility at Madison (NMRFAM)

:: SCREENSHOTS

Ponderosa

:: REQUIREMENTS

  • Windows/Linux/MacOsX

:: DOWNLOAD

PONDEROSA-C/S

:: MORE INFORMATION

Citation

Lee W, Stark JL, Markley JL. (2014)
PONDEROSA-C/S: Client-server based software package for automated protein 3D structure determination.
Journal of Biomolecular NMR 60(2-3):73-5

PONDEROSA, an automated 3D-NOESY peak picking program, enables automated protein structure determination.
Lee W, Kim JH, Westler WM, Markley JL.
Bioinformatics. 2011 Jun 15;27(12):1727-8. doi: 10.1093/bioinformatics/btr200.

BCL 3.6.1 – Protein Structure Determination from sparse Experimental data

BCL 3.6.1

:: DESCRIPTION

The BCL (Bio Chemical Library) is a software package that provides unique tools for biological research, such as protein structure determination from sparse experimental data.The BCL contains the widely used secondary structure prediction program JUFO, a folding algorithm that assembles secondary structure elements, and loop construction tools that complete protein backbones. With this series of protocols the BCL allows construction of backbone models for large and membrane proteins from the primary sequence. Among its unique strengths are the incorporation of sparse and low resolution data into folding simulations.Additionally, the BCL contains a suite of cheminformatics tools that allow construction of quantitative structure-activity-relation (QSAR) models for virtual screening, pharmacophore mapping, and drug design.

::DEVELOPER

Jens Meiler

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX

:: DOWNLOAD

 BCL

:: MORE INFORMATION

Citation

BCL::Fold – De Novo Prediction of Complex and Large Protein Topologies by Assembly of Secondary Structure Elements.
Karakaş M, Woetzel N, Staritzbichler R, Alexander N, Weiner BE, Meiler J.
PLoS One. 2012;7(11):e49240. doi: 10.1371/journal.pone.0049240. Epub 2012 Nov 16.

DNABindProt – Server for Determination of Potential DNA Binding Sites of Proteins

DNABindProt

:: DESCRIPTION

DNABindProt is designed to predict DNA-binding residues, based on the fluctuations of residues in high-frequency modes by the Gaussian network model.

::DEVELOPER

Polymer Research Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser
:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W417-23. doi: 10.1093/nar/gkq396. Epub 2010 May 16.
DNABINDPROT: fluctuation-based predictor of DNA-binding residues within a network of interacting residues.
Ozbek P, Soner S, Erman B, Haliloglu T.

TWIN – Twin Zygosity Determination

TWIN

:: DESCRIPTION

TWIN is a software for twin zygosity determination

::DEVELOPER

Jing Hua Zhao

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • DOS

:: DOWNLOAD

 TWIN

:: MORE INFORMATION

Citation

Zhao, J. H., and Sham, P. C. (1998).
“A method for calculating probability convolution using ternary numbers with application in the determination of twin zygosity“.
Computional Statistics and Data Analysis, 28, 225-232.

Numbat 0.99 – Automatic Δχ-tensor Determination

Numbat 0.99

:: DESCRIPTION

Numbat is a user friendly software that fits Δχ-tensor to a set of PCS measurements and a structure from a PDB file. It has also been designed to assist in the semi automatic process of PCS assignment.

::DEVELOPER

Christophe Schmitz

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / MacOsX / Windows

:: DOWNLOAD

 Numbat

:: MORE INFORMATION

Citation

Christophe Schmitz, Mitchell J. Stanton-Cook, Xun-Cheng Su, Gottfried Otting, and Thomas Huber (2008).
Numbat: an interactive software tool for fitting Δχ-tensors to molecular coordinates using pseudocontact shifts.
Journal of Biomolecular NMR. 41:179-189.

BnP 1.02 – Protein Structure-determination package

BnP 1.02

:: DESCRIPTION

BnP is the Buffalo’s Pittsburgh Interface for complete protein phasing suite includes SnB and Phases.

::DEVELOPER

William Furey  , Charles Weeks 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 BnP

:: MORE INFORMATION

Citation:

Weeks, C. M., Blessing, R. H., Miller, R., Mungee, R., Potter, S. A., Rappleye, J., Smith, G. D., Xu, H. & Furey, W.
Towards automated protein structure determination: BnP, the SnB-PHASES interface,
Z. Kristallogr. 217, 686-693 (2002).

creto 1.0 – Determination of Cis-Regulatory Element Turn-Over rates

creto 1.0

:: DESCRIPTION

creto (Cis-Regulatory Element Turn-Over) is a program for the determination of the evolutionary origination and decay rates of transcription factor binding sites. Given a phylogenetic tree and the binding site numbers of the species at the tips, creto uses a maximum likelihood model that permits variable turnover rates in different parts of the species tree. This model can be used to detect changes in turnover rate as a proxy for differences in the selective pressures acting on TFBS in different clades.

::DEVELOPER

Wolfgang Otto

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 creto

:: MORE INFORMATION

Citation

Otto W, Stadler PF, Lopez-Gialdez F, Townsend JP, Lynch VJ, Wagner GP
Measuring Transcription Factor Binding Site Turnover: A Maximum Likelihood Approach using Phylogenies.
Genome Biol Evol. 2009 May 25;1:85-98.