Pipasic 20140121 – Protein Abundance Correction in Metaproteomic Data

Pipasic 20140121

:: DESCRIPTION

Pipasic (peptide intensity-weighted proteome abundance similarity correction) is a tool which corrects identification and spectral counting based quantification results using peptide similarity estimation and expression level weighting within a non-negative lasso framework.

::DEVELOPER

Bernhard Y. Renard

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/ MacOsX
  • Python
  • BioPython

:: DOWNLOAD

 Pipasic

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Jun 15;30(12):i149-i156. doi: 10.1093/bioinformatics/btu267.
Pipasic: similarity and expression correction for strain-level identification and quantification in metaproteomics.
Penzlin A, Lindner MS, Doellinger J, Dabrowski PW, Nitsche A, Renard BY

NASCA 20110516 – Side-chain Resonance Assignment & NOE Assignment

NASCA 20110516

:: DESCRIPTION

NASCA (NOE Assignment and Side-Chain Assignment) is an automated program for side-chain resonance assignment and nuclear Overhauser effect (NOE) assignment from NOESY data. It does not require data from TOCSY experiments.NASCA casts the assignment problem into a Markov Random Field (MRF), and extends and applies combinatorial protein design algorithms to compute optimal assignments that best interpret the NMR data. The complexity of the combinatorial search is reduced by using a dead-end elimination (DEE) algorithm, which prunes side-chain resonance assignments that are provably not part of the optimal solution. Then an A* search algorithm is employed to find a set of optimal side-chain resonance assignments that best fit the NMR data. These side-chain resonance assignments are then used to resolve the NOE assignment ambiguity.

::DEVELOPER

Donald Lab at Duke University

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

NASCA

:: MORE INFORMATION

Citation

Jianyang Zeng, Pei Zhou, Bruce R. Donald.
Protein Side-Chain Resonance Assignment and NOE Assignment Using RDC-Defined Backbones without TOCSY Data.
J Biomol NMR. 2011 Aug;50(4):371-95. doi: 10.1007/s10858-011-9522-4.

OSPREY 3.2.289 / gOSPREY – Computational Structure-based Protein Design / for GPU

OSPREY 3.2.289 / gOSPREY

:: DESCRIPTION

OSPREY (Open Source Protein REdesign for You)is a suite of programs for computational structure-based protein design.OSPREY is specifically designed to identify protein mutants that possess desired target properties (e.g., improved stability, switch of substrate specificity, etc.). OSPREY can also be used for predicting small-molecule inhibitors. With certain limitations, the current version of OSPREY can also model protein-protein and protein-peptide interactions.

gOSPREY is the abbreviation for Open Source Protein REdesign for You on a GPU. It enables the user to utilize a GPU to accelerate the procedure of protein design in a massive parallel fashion.

::DEVELOPER

Donald Lab at Duke University , Machine Learning and Computational Biology Group at Tsinghua University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

OSPREY , gOSPREY

:: MORE INFORMATION

Citation

An efficient parallel algorithm for accelerating computational protein design.
Zhou Y, Xu W, Donald BR, Zeng J.
Bioinformatics. 2014 Jun 15;30(12):i255-i263. doi: 10.1093/bioinformatics/btu264.

Frey KM, Georgiev I, Donald BR, Anderson AC.
Predicting resistance mutations using protein design algorithms.
Proc Natl Acad Sci U S A. 2010 Aug 3;107(31):13707-12. Epub 2010 Jul 19. PMID: 20643959

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

SUMOsp 2.0.4 / GPS-SUMO 1.0 – SUMOylation sites Prediction

SUMOsp 2.0.4 / GPS-SUMO 1.0

:: DESCRIPTION

SUMOsp  based on a manually curated dataset, integrating the results of two methods, GPS and MotifX, which were originally designed for phosphorylation site prediction. SUMOsp offers at least as good prediction performance as the only available method, SUMOplot, on a very large test set. We expect that the prediction results of SUMOsp combined with experimental verifications will propel our understanding of sumoylation mechanisms to a new level.

GPS-SUMO is a tool for the prediction of sumoylation sites and SUMO-interaction motifs.

::DEVELOPER

The CUCKOO Workgroup

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / WIndows / MacOsX
  • Java

:: DOWNLOAD

 SUMOsp , GPS-SUMO

:: MORE INFORMATION

Citation

GPS-SUMO: a tool for the prediction of sumoylation sites and SUMO-interaction motifs.
Zhao Q, Xie Y, Zheng Y, Jiang S, Liu W, Mu W, Liu Z, Zhao Y, Xue Y, Ren J.
Nucleic Acids Res. 2014 May 31. pii: gku383

Systematic study of protein sumoylation: Development of a site-specific predictor of SUMOsp 2.0.
Jian Ren, Xinjiao Gao, Changjiang Jin, Mei Zhu, Xiwei Wang, Andrew Shaw, Longping Wen, Xuebiao Yao and Yu Xue.
Proteomics.2009; 9:3409-3412

HEA-PSP – Ab-initio Protein Structure Prediction

HEA-PSP

:: DESCRIPTION

HEA-PSP is a hybrid evolutionary search framework with various crossover implementations for Ab-initio protein structre prediction

::DEVELOPER

Computational Biology lab, George Mason University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  HEA-PSP

:: MORE INFORMATION

Citation

Brian Olson, Kenneth A. De Jong, and Amarda Shehu.
Off-Lattice Protein Structure Prediction with Homologous Crossover.
GECCO 2013, pages 287-294, Amsterdam,

SEPPA 3.0 – Server for Conformational B-cell Epitope Prediction

SEPPA 3.0

:: DESCRIPTION

SEPPA (Spatial Epitope Prediction of Protein Antigens) is spatial epitope prediction for protein antigens, particularly for N-linked glycoproteinsmeu ip

::DEVELOPER

Dr. Zhiwei Cao

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Winodows / Linux
  • Python
:: DOWNLOAD
:: MORE INFORMATION
Citation
Zhou C, Chen Z, Zhang L, Yan D, Mao T, Tang K, Qiu T, Cao Z.
SEPPA 3.0-enhanced spatial epitope prediction enabling glycoprotein antigens.
Nucleic Acids Res. 2019 Jul 2;47(W1):W388-W394. doi: 10.1093/nar/gkz413. PMID: 31114919; PMCID: PMC6602482.
SEPPA 2.0-more refined server to predict spatial epitope considering species of immune host and subcellular localization of protein antigen.
Qi T, Qiu T, Zhang Q, Tang K, Fan Y, Qiu J, Wu D, Zhang W, Chen Y, Gao J, Zhu R, Cao Z.
Nucleic Acids Res. 2014 May 16. pii: gku395

MemPype – Pipeline for Predicting the Topology and the Localization of Membrane Proteins

MemPype

:: DESCRIPTION

MemPype is a Python-based pipeline that integrates several tools the prediction of topology and subcellular localization of Eukaryotic membrane proteins.

::DEVELOPER

Bologna Biocomputing Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 No. Only Web Service

:: MORE INFORMATION

Citation

Pierleoni A, Indio V, Savojardo C, Fariselli P, Martelli PL, Casadio R.
MemPype: a pipeline for the annotation of eukaryotic membrane proteins.
Nucl. Acids Res. (2011) 39 (suppl 2): W375-W380.

BetAware – Beta-Barrel Detection and Topology Prediction

BetAware

:: DESCRIPTION

BETAWARE is a software package designed for the analysis of trans-membrane beta-barrel proteins.

::DEVELOPER

Castrense Savojardo

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX
  • Python
  • python argparse library
  • python numpy

:: DOWNLOAD

  BetAware

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Feb 15;29(4):504-5. doi: 10.1093/bioinformatics/bts728. Epub 2013 Jan 6.
BETAWARE: a machine-learning tool to detect and predict transmembrane beta-barrel proteins in prokaryotes.
Savojardo C, Fariselli P, Casadio R.