FoldX 3.0 – Force Field for Energy Calculations and Protein Design

FoldX 3.0

:: DESCRIPTION

FoldX conduct rapid evaluation of the effect of mutations on the stability, folding and dynamics of proteins and nucleic acids.

The FoldX/Yasara ( FoldX plugin for YASARA) is a software package to access and run FoldX commands in YASARA.

::DEVELOPER

Serrano’s laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 FoldX

:: MORE INFORMATION

Citation

The FoldX web server: an online force field.
Schymkowitz J, Borg J, Stricher F, Nys R, Rousseau F, Serrano L.
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W382-8.

IRF 3.07 – Inverted Repeats Finder

IRF 3.07

:: DESCRIPTION

IRF(Inverted Repeats Finder) investigate inverted repeat structure of the Human Genome

::DEVELOPER

Laboratory for Biocomputing and Informatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX

:: DOWNLOAD

 IRF

:: MORE INFORMATION

Citation:

P. E. Warburton, J. Giordano, F. Cheung, Y. Gelfand and G. Benson.
“Inverted Repeat Structure of the Human Genome: The X-Chromosome Contains a Preponderance of Large, Highly Homologous Inverted Repeats That Contain Testes Genes” ,
Genome Research, 14:1861-1869, 2004.

Pro-origami – Protein Structure Cartoons

Pro-origami

:: DESCRIPTION

Pro-origami is a system for automatically generating protein structure cartoons. The cartoons are intended to make protein structure easy to interpret by laying out the secondary and super-secondary structure in two dimensions in a manner that makes the structure clear.

::DEVELOPER

IALab: Immersive Analytics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX / Windows
  • Python
  • BioPython
  • Dunnart

:: DOWNLOAD

Pro-origami

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Dec 1;27(23):3315-6. doi: 10.1093/bioinformatics/btr575.
Automatic generation of protein structure cartoons with Pro-origami.
Stivala A1, Wybrow M, Wirth A, Whisstock JC, Stuckey PJ.

QUANTO 1.2.4 – Computes Sample Size or Power for Association Studies

QUANTO 1.2.4

:: DESCRIPTION

Quanto is a program that computes sample size or power for association studies of genes, environmental factors, gene-environment interaction, or gene-gene interaction. Available study designs for a disease (binary) outcome include the unmatched case-control, matched case-control, case-sibling, case-parent, and case-only designs. Study designs for a quantitative tra it include independent individuals and case parent designs.

::DEVELOPER

The Division of Biostatistics @ usc.edu

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 QUANTO

:: MORE INFORMATION

Citation

Gauderman (2002),
“Sample size requirements for matched case-control studies of gene-environment interaction“,
Statistics in Medicine, 21:35-50.

METASOFT 2.0.1 – Meta-analysis Tool

METASOFT 2.0.1

:: DESCRIPTION

METASOFT is a meta-analysis software tool for genome-wide association studies that provides the following methods

Fixed Effects model (FE): Fixed effects model based on inverse-variance-weighted effect size.
Random Effects model (RE): Conventional random effects model based on inverse-variance-weighted effect size. Heterogeneity is estimated using DerSimonian-Laird method.
Han and Eskin’s Random Effects model (RE2): Random effects model that increases power under heterogeneity.
Binary Effects model (BE): Random effects model assuming that the effects either exist or not in the studies.

::DEVELOPER

ZarLab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX / Windows
  • Java  

:: DOWNLOAD

 METASOFT

:: MORE INFORMATION

Citation

Buhm Han and Eleazar Eskin,
“Random-Effects Model Aimed at Discovering Associations in Meta-Analysis of Genome-wide Association Studies”,
The American Journal of Human Genetics (2011) 88, 586-598.

Panache v1.0.0 – PANgenome Analyzer with CHromosomal Exploration

Panache v1.0.0

:: DESCRIPTION

Panache is a web-based interface designed for the visualization of linearized pangenomes. It can be used to show presence/absence information of pangenomic blocks of sequence or genes in a browser-like display.

::DEVELOPER

Panache team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser
:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Durant É, Sabot F, Conte M, Rouard M.
Panache: a Web Browser-Based Viewer for Linearized Pangenomes.
Bioinformatics. 2021 Oct 2:btab688. doi: 10.1093/bioinformatics/btab688. Epub ahead of print. PMID: 34601567.

iDNA-ABT – Detecting DNA Methylation with Adaptive Features and Transductive Information Maximization

iDNA-ABT

:: DESCRIPTION

iDNA-ABT is an advanced deep learning model that utilizes adaptive embedding based on bidirectional transformers for language understanding (BERT) together with a novel transductive information maximization (TIM) loss.

::DEVELOPER

iDNA-ABT team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
:: DOWNLOAD

iDNA-ABT

:: MORE INFORMATION

Citation

Yu Y, He W, Jin J, Cui L, Zeng R, Wei L.
iDNA-ABT : advanced deep learning model for detecting DNA methylation with adaptive features and transductive information maximization.
Bioinformatics. 2021 Oct 2:btab677. doi: 10.1093/bioinformatics/btab677. Epub ahead of print. PMID: 34601568.

JChem for Office 21.15.603 – Chemical Structure Handling & Visualizing within Microsoft Office

JChem for Office 21.15.603

:: DESCRIPTION

JChem for Office integrates structure handling and visualizing capabilities within a Microsoft Office environment. The bundle includes JChem for Excel which is our long-standing Excel integration. With JChem for Office, chemistry is made live in your Office application and structures are fully supported within spreadsheets, documents, slides and e-mails. Implementation is robust with fast loading/scrolling of many thousands of structure rows and copy-paste throughout the Microsoft Office suite. More advanced functionality includes: structure based calculations, R-group decomposition and library enumeration.

::DEVELOPER

ChemAxon Ltd.

:: SCREENSHOTS

:: REQUIREMENTS

  • Microsoft Office®

:: DOWNLOAD

 JChem for Office

:: MORE INFORMATION

TopPIC 1.6 – TOP-Down Mass Spectrometry Based Proteoform Identification and Characterization

TopPIC 1.6

:: DESCRIPTION

TopPIC is a software tool for identification and characterization of proteoforms at the whole proteome level by top-down tandem mass spectra using database search.

::DEVELOPER

TopPIC team

:: REQUIREMENTS

  • Linux/windows

:: DOWNLOAD

 TopPIC

:: MORE INFORMATION

Citation:

TopPIC: A software tool for top-down mass spectrometry-based proteoform identification and characterization.
Kou Q, Xun L, Liu X.
Bioinformatics. 2016 Jul 16. pii: btw398.

Protein identification using top-down spectra.
Liu X, Sirotkin Y, Shen Y, Anderson G, Tsai YS, Ting YS, Goodlett DR, Smith RD, Bafna V, Pevzner PA.
Mol Cell Proteomics. 2012 Jun;11(6):M111.008524. doi: 10.1074/mcp.M111.008524.

CSS-Palm 4.0 – Palmitoylation Site Prediction with a Clustering and Scoring Strategy

CSS-Palm 4.0

:: DESCRIPTION

CSS-Palm is a computer program for palmitoylation site prediction, Clustering and Scoring Strategy for Palmitoylation Sites Prediction.The program’s prediction performance is encouraging with highly positive Jack-Knife validation results (sensitivity 82.16% and specificity 83.17% for cut-off score 2.6).

::DEVELOPER

The CUCKOO Workgroup

:: SCREENSHOTS

:: REQUIREMENTS

  • WIndows / Linux / MacOsX
  • Java

:: DOWNLOAD

 CSS-Palm

:: MORE INFORMATION

Citation

CSS-Palm 2.0: an updated software for palmitoylation sites prediction
Jian Ren, Longping Wen, Xinjiao Gao, Changjiang Jin, Yu Xue and Xuebiao Yao.
Protein Engineering, Design and Selection.2008 21(11):639-644