PDEXK – Server for Detection of new Protein Families from the PD-(D/E)XK Superfamily

PDEXK

:: DESCRIPTION

The PDEXK server is developed for detecting new protein families of the PD-(D/E)XK superfamily using Support Vector Machines trained on data derived from profile-profile alignments. Using a number of both superfamily-specific and general features, SVMs were trained to identify true positive alignments of PD-(D/E)XK representatives.

::DEVELOPER

VU Institute of Biotechnology

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Laganeckas M., Margelevičius M., Venclovas Č. (2010)
Identification of new homologs of PD-(D/E)XK nucleases by Support Vector Machines trained on data derived from profile-profile alignments.
Nucl. Acids Res. (2011) 39 (4): 1187-1196.

JPred 4 – Protein Secondary Structure Prediction Server

JPred 4

:: DESCRIPTION

JPred is a Protein Secondary Structure Prediction server. JPred incorporates the Jnet algorithm in order to make more accurate predictions. In addition to protein secondary structure JPred also makes predictions on Solvent Accessibility and Coiled-coil regions (Lupas method).

:: DEVELOPER

The Barton Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2015 Apr 16. pii: gkv332.
JPred4: a protein secondary structure prediction server.
Drozdetskiy A, Cole C, Procter J, Barton GJ.

Cyscon 20150927 – Disulfide Connectivity Prediction Server

Cyscon 20150927

:: DESCRIPTION

Cyscon is a new hierarchical order reduction protocol for disulfide-bonding prediction.

::DEVELOPER

Computational Systems Biology Group, Shanghai Jiao Tong University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Accurate disulfide-bonding network predictions improve ab initio structure prediction of cysteine-rich proteins.
Yang J, He BJ, Jang R, Zhang Y, Shen HB.
Bioinformatics. 2015 Aug 7. pii: btv459.

SWISS-MODEL – Protein Structure Homology-modelling Server

SWISS-MODEL

:: DESCRIPTION

SWISS-MODEL is a fully automated protein structure homology-modelling server, accessible via the ExPASy web server, or from the program DeepView (Swiss Pdb-Viewer).

::DEVELOPER

Protein Structure Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Biasini M, Bienert S, Waterhouse A, Arnold K, Studer G, Schmidt T, Kiefer F, Cassarino TG, Bertoni M, Bordoli L, Schwede T. Nucleic Acids Res. 2014 Jul;42(Web Server issue):W252-8. doi: 10.1093/nar/gku340. Epub 2014 Apr 29.

ModFOLD 6 – Model Quality Assessment Server

ModFOLD 6

:: DESCRIPTION

The ModFOLD server is the latest version of server for the estimation of both the global and local (per-residue) quality of 3D protein models.

::DEVELOPER

McGuffin Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 ModFOLD

:: MORE INFORMATION

Citation

Maghrabi, A.H.A. & McGuffin, L.J. (2017)
ModFOLD6: an accurate web server for the global and local quality estimation of 3D models of proteins,
Nucleic Acids Res. 2017 Jul 3;45(W1):W416-W421. doi: 10.1093/nar/gkx332.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W368-72. doi: 10.1093/nar/gkt294. Epub 2013 Apr 25.
The ModFOLD4 server for the quality assessment of 3D protein models.
McGuffin LJ1, Buenavista MT, Roche DB.

INFO-RNA 2.2.0 – A Server for Inverse Folding of RNA

INFO-RNA 2.2.0

:: DESCRIPTION

INFO-RNA is a server for the design of RNA sequences that fold into a given pseudo-knot free RNA secondary structure. Here, you can get an example of the settings and the results.

::DEVELOPER

Bioinformatics Group
Albert-Ludwigs-University Freiburg

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 INFO-RNA

:: MORE INFORMATION

Citation

Anke Busch, Rolf Backofen.
INFO-RNA – A Server for Fast Inverse RNA Folding Satisfying Sequence Constraints.
Nucleic Acid Res, 2007; 35(Web Server Issue):W310-3.

MARNA 100729 – Server for Multiple Alignment of RNAs

MARNA 100729

:: DESCRIPTION

MARNA (Multiple Alignment of RNAs) is a multiple alignment of RNAs taking into consideration both the primary sequence and the secondary structure. It is based on pairwise comparisons using costs of edit operations. The edit operations can be divided into edit operations on arcs and edit operations on bases. Additionally, MARNA predicts a consensus sequence as well as a consensus structure.

::DEVELOPER

Chair for Bioinformatics Freiburg

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 MARNA

:: MORE INFORMATION

Citation

Sven Siebert and Rolf Backofen,
MARNA: multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons“,
Bioinformatics 2005, Volume 21, Issue 16, 3352-3359

FALC-Loop – Protein Loop Modeling Server

FALC-Loop

:: DESCRIPTION

FALC(Fragment Assembly and Loop Closure) is an internet server for protein loop modeling.

::DEVELOPER

Lab of Computational Biology and Biomolecular Engineering,  Seoul National University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 FALC

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W210-4. doi: 10.1093/nar/gkr352. Epub 2011 May 16.
The FALC-Loop web server for protein loop modeling.
Ko J1, Lee D, Park H, Coutsias EA, Lee J, Seok C.

MP-T 201407 – Membrane Protein Sequence-structure Alignment

MP-T 201407

:: DESCRIPTION

MP-T is a sequence-structure alignment algorithm for membrane proteins. It produces accurate sequence alignments for use in homology modelling. The inputs are a fasta-formatted sequence and an annotated structure file from the iMembrane webserver.

::DEVELOPER

Oxford Protein Informatics Group (OPIG)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  MP-T

:: MORE INFORMATION

Citation

Jamie R. Hill and Charlotte M. Deane
MP-T: improving membrane protein alignment for structure prediction
Bioinformatics (2013) 29 (1): 54-61.

RCD+ 1.4 – Fast Loop Modeling Server

RCD+ 1.4

:: DESCRIPTION

RCD (Random Coordinate Descent) is a versatile loop closure tool to efficiently generate loop ensembles. The algorithm solves the loop closure problem by optimizing randomly selected bonds and updating loop conformations using spinor matrices (geometric algebra).

::DEVELOPER

The Structural Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

RCD+

:: MORE INFORMATION

Citation

RCD+: Fast loop modeling server.
López-Blanco JR, Canosa-Valls AJ, Li Y, Chacón P.
Nucleic Acids Res. 2016 Jul 8;44(W1):W395-400. doi: 10.1093/nar/gkw395