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.

FTG – Fast Fourier Transform based GENE Prediction Server

FTG

:: DESCRIPTION

FTG is aweb server for locating probable protein coding region in nucleotide sequence using fourier tranform approach

::DEVELOPER

FTG Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Issac, B., Singh, H., Kaur, H. and Raghava, G.P.S. (2002)
Locating probable genes using fourier transform approach.
Bioinformatics 18:196

ProtMod – Protein Modeling Server

ProtMod

:: DESCRIPTION

ProtMod is a protein modeling server. Its task is to predicts 3-dimensional structures of proteins based on their sequences. Instead of generating only one model for a given protein, ProtMod produces a list of protein models and orders them by different model evaluation scores.

::DEVELOPER

Godzik Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser
:: DOWNLOAD

 NO

:: MORE INFORMATION

AIDA – Ab Initio Domain Assembly Server

AIDA

:: DESCRIPTION

AIDA is a tool that can identify domains in multi-domain proteins and then predict their 3D structures and relative spatial arrangements.

::DEVELOPER

Godzik Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
:: DOWNLOAD

 AIDA

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W308-13. doi: 10.1093/nar/gku369. Epub 2014 May 15.
AIDA: ab initio domain assembly server.
Xu D, Jaroszewski L, Li Z, Godzik A

bSiteFinder – Protein-binding Sites Prediction Server

bSiteFinder

:: DESCRIPTION

bSiteFinder is a web server for indentifying protein-binding sites.

::DEVELOPER

bSiteFinder team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation:

bSiteFinder, an improved protein-binding sites prediction server based on structural alignment: more accurate and less time-consuming.
Gao J, Zhang Q, Liu M, Zhu L, Wu D, Cao Z, Zhu R.
J Cheminform. 2016 Jul 11;8:38. doi: 10.1186/s13321-016-0149-z.

FALCON@home – High-throughput Protein Structure Prediction server

FALCON@home

:: DESCRIPTION

The design of FALCON@home is based on the observation that a structural template, especially for remote homologous proteins, consists of conserved regions interweaved with highly-variable regions.

::DEVELOPER

Bioinformatics Lab, Institute of Computing Technology Chinese Academy of Sciences

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

FALCON@home: a high-throughput protein structure prediction server based on remote homologue recognition.
Wang C, Zhang H, Zheng WM, Xu D, Zhu J, Wang B, Ning K, Sun S, Li SC, Bu D.
Bioinformatics. 2015 Oct 10. pii: btv581.