NetMHCpan 4.0 – Predicts Binding of Peptides to Known MHC Molecule

NetMHCpan 4.0

:: DESCRIPTION

NetMHCpan predicts binding of peptides to any known MHC molecule using artificial neural networks (ANNs). The method is trained on more than 115,000 quantitative binding data covering more than 120 different MHC molecules. Predictions can be made for HLA-A, B, C, E and G alleles, as well as for non-human primates, mouse, Cattle and pig. Further, the user can upload full length MHC protein sequences, and have the server predict MHC restricted peptides from any given protein of interest.

::DEVELOPER

DTU Health Tech

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

NetMHCpan

:: MORE INFORMATION

Citation

NetMHCpan – MHC class I binding prediction beyond humans
Ilka Hoof, Bjoern Peters, John Sidney, Lasse Eggers Pedersen, Ole Lund, Soren Buus, and Morten Nielsen
Immunogenetics. 2009 Jan;61(1):1-13. Epub 2008 Nov 12.

CPHmodels 3.2 – Protein Homology Modeling server

CPHmodels 3.2

:: DESCRIPTION

CPHmodels is a protein homology modeling server. The template recognition is based on profile-profile alignment guided by secondary structure and exposure predictions.

::DEVELOPER

DTU Health Tech

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Send inquiries by e-mail to software@cbs.dtu.dk.

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W576-81. doi: 10.1093/nar/gkq535. Epub 2010 Jun 11.
CPHmodels-3.0–remote homology modeling using structure-guided sequence profiles.
Nielsen M1, Lundegaard C, Lund O, Petersen TN.

seqr v0.3.0 – Web-based Analysis tool for Rare Disease Genomics

seqr v0.3.0

:: DESCRIPTION

seqr is a software tool for searching for causal variants in Mendelian disease families.

::DEVELOPER

MacArthur Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOs
  • python

:: DOWNLOAD

seqr

:: MORE INFORMATION

 

GibbsCluster 2.0 – Simultaneous Alignment and Clustering of Peptide data

GibbsCluster 2.0

:: DESCRIPTION

GibbsCluster is a web server for simultaneous alignment and clustering of peptide data

::DEVELOPER

DTU Health Tech

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GibbsCluster

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jan 1;29(1):8-14. doi: 10.1093/bioinformatics/bts621. Epub 2012 Oct 24.
Simultaneous alignment and clustering of peptide data using a Gibbs sampling approach.
Andreatta M1, Lund O, Nielsen M.

Cofactory v.1.0 – Identification of Rossmann folds and prediction of FAD, NAD and NADP specificity

Cofactory v.1.0

:: DESCRIPTION

Cofactory is a server that identifies Rossmann fold sequence domains and predicts their specificity for the cofactors FAD, NAD or NADP.

::DEVELOPER

DTU Health Tech

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Cofactory

:: MORE INFORMATION

Citation

Cofactory: sequence-based prediction of cofactor specificity of Rossmann folds.
Geertz-Hansen HM, Blom N, Feist AM, Brunak S, Petersen TN.
Proteins. 2014 Sep;82(9):1819-28. doi: 10.1002/prot.24536.

VisualCNA 1.0 – Constraint Network Analysis and Protein Engineering

VisualCNA 1.0

:: DESCRIPTION

VisualCNA is a PyMOL plug-in for interactive Constraint Network Analysis and protein engineering for improving thermostability

::DEVELOPER

the Gohlke Group

:: SCREENSHOTS

VisualCNA

:: REQUIREMENTS

  • Linux/ Windows/MacOsX
  • Python
  • PyMOL

:: DOWNLOAD

 VisualCNA

:: MORE INFORMATION

Citation

VisualCNA: A GUI for interactive Constraint Network Analysis and protein engineering for improving thermostability.
Rathi PC, Mulnaes D, Gohlke H.
Bioinformatics. 2015 Mar 12. pii: btv139.

PocketAnalyzerPCA 1.30 – Pocket-space Maps to Identify novel Binding-site Conformations in Proteins

PocketAnalyzerPCA 1.30

:: DESCRIPTION

PocketAnalyzer(PCA) combines a geometric algorithm for detecting pockets in proteins with Principal Component Analysis and clustering. This enables visualization and analysis of pocket conformational distributions of large sets of protein structures.

::DEVELOPER

the Gohlke Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  PocketAnalyzerPCA

:: MORE INFORMATION

Citation

J Chem Inf Model. 2011 Oct 24;51(10):2666-79. doi: 10.1021/ci200168b. Epub 2011 Sep 30.
Pocket-space maps to identify novel binding-site conformations in proteins.
Craig IR1, Pfleger C, Gohlke H, Essex JW, Spiegel K.

NMSim – Modeling Macromolecular Conformational Transitions

NMSim

:: DESCRIPTION

NMSim is a normal mode-based geometric simulation approach for exploring biologically relevant conformational transitions in proteins.

::DEVELOPER

the Gohlke Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W310-6. doi: 10.1093/nar/gks478. Epub 2012 Jun 4.
NMSim web server: integrated approach for normal mode-based geometric simulations of biologically relevant conformational transitions in proteins.
Krüger DM1, Ahmed A, Gohlke H.

SuperLink 1.3 – Genetic Linkage Analysis

SuperLink 1.3

:: DESCRIPTION

Superlink is a computer program that performs exact genetic linkage analysis with input-output relationships

::DEVELOPER

Ma’ayan Fishelson

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/WIndows

:: DOWNLOAD

 Superlink

:: MORE INFORMATION

Citation

Fishelson M, Geiger D.
Exact genetic linkage computations for general pedigrees.
Bioinformatics. 2002;18 Suppl 1:S189-98.