Tag: Server

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

AntiMPmod – Modified Antimicrobial Peptides Prediction Server

AntiMPmod

:: DESCRIPTION

AntiMPmod is an in silico method, which is developed to predict efficient modified antimicrobial peptides (ModAMP).

::DEVELOPER

AntiMPmod team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Prediction of Antimicrobial Potential of a Chemically Modified Peptide From Its Tertiary Structure.
Agrawal P, Raghava GPS.
Front Microbiol. 2018 Oct 26;9:2551. doi: 10.3389/fmicb.2018.02551.

PROCLASS – Protein Structure Classification Server

PROCLASS

:: DESCRIPTION

 PROCLASS allows to predict the class of protein from its amino acid sequence. It predict weather protein belong to class Alpha or Beta or Alpha+Beta or Alpha/Beta.

::DEVELOPER

Dr. G P S Raghava,

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Raghava, G P S (1999)
Proclass: A computer program for predicting the protein structural classes.
J. Biosciences 24, 176.

APSSP2 – Advanced Protein Secondary Structure Prediction Server

APSSP2

:: DESCRIPTION

APSSP2 allows to predict the secondary structure of protein’s from their amino acid sequence.

::DEVELOPER

Dr. G P S Raghava

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Raghava, G. P. S. (2002)
APSSP2 : A combination method for protein secondary structure prediction based on neural network and example based learning.
CASP5. A-132.