TM-score 20190822 – Calculate Similarity of Topologies of two Protein Structures

TM-score 20190822

:: DESCRIPTION

TM-score is an algorithm to calculate the similarity of topologies of two protein structures. It can be exploited to quantitatively access the quality of protein structure predictions relative to native. Because TM-score weights the close matches stronger than the distant matches, TM-score is more sensitive than root-mean-square deviation (RMSD)

::DEVELOPER

Yang Zhang’s Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
:: DOWNLOAD

 TM-score

:: MORE INFORMATION

Citation

J. Xu, Y. Zhang,
How significant is a protein structure similarity with TM-score=0.5?
Bioinformatics, 2010 26, 889-895

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.

lDDT – Comparing Protein Structures and Models using Distance Difference Tests

lDDT

:: DESCRIPTION

The lDDT (local Distance Difference Test) is a superposition-free score which evaluates local distance differences in a model compared to a reference structure.

::DEVELOPER 

lDDT team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Bioinformatics. 2013 Nov 1;29(21):2722-8. doi: 10.1093/bioinformatics/btt473. Epub 2013 Aug 27.
lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests.
Mariani V1, Biasini M, Barbato A, Schwede T.

M4T 3.0 – Comparative Protein Structure Modeling

M4T 3.0

:: DESCRIPTION

M4T, Multiple Mapping Method with Multiple Templates, is a fully automated comparative protein structure modeling server. The novelty of M4T resides in two of its major modules, Multiple Templates (MT) and Multiple Mapping Method (MMM).

::DEVELOPER

Bioinformatics Lab :: IBERS :: Aberystwyth University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Server

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

J Struct Funct Genomics. 2009 Mar;10(1):95-9. doi: 10.1007/s10969-008-9044-9. Epub 2008 Nov 5.
Improved scoring function for comparative modeling using the M4T method.
Rykunov D1, Steinberger E, Madrid-Aliste CJ, Fiser A.

Bioinformatics. 2007 Oct 1;23(19):2558-65. Epub 2007 Sep 6.
Comparative protein structure modeling by combining multiple templates and optimizing sequence-to-structure alignments.
Fernandez-Fuentes N1, Rai BK, Madrid-Aliste CJ, Fajardo JE, Fiser A.

CPSP Tools 4.8.0 – Constraint-based Protein Structure Prediction

CPSP Tools 4.8.0

:: DESCRIPTION

CPSP-tools package provides programs to solve exactly and completely the problems typical of studies using 3D lattice protein models. Among the tasks addressed are the prediction of globally optimal and/or suboptimal structures as well as sequence design and neutral network exploration.

::DEVELOPER

Bioinformatics Group
Albert-Ludwigs-University Freiburg

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 CPSP Tools

:: MORE INFORMATION

Citation

Martin Mann, Sebastian Will, and Rolf Backofen.
CPSP-tools – Exact and Complete Algorithms for High-throughput 3D Lattice Protein Studies.
BMC Bioinformatics, 9, 230, 2008.

RBRDetector – Prediction of Binding Residues on RNA-binding Protein Structures

RBRDetector

:: DESCRIPTION

RBRDetector is a novel structure-based algorithm to identify RNA-binding residues by combining feature- and template-based prediction strategies.

::DEVELOPER

Rong Liu’s Lab of Protein Bioinformatics at Huazhong Agriculture University!

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Web Browser
:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Proteins. 2014 Oct;82(10):2455-71. doi: 10.1002/prot.24610. Epub 2014 Jun 9.
RBRDetector: Improved prediction of binding residues on RNA-binding protein structures using complementary feature- and template-based strategies.
Yang XX1, Deng ZL, Liu R.

SUBWAI 1.0 – Protein Structure Prediction program

SUBWAI 1.0

:: DESCRIPTION

SUBWAI (SUBoptimal Weighted AlIgnment) is the protein structure prediction program based on threading strategy with SPAD.

::DEVELOPER

Kihara Bioinformatics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SUBWAI

:: MORE INFORMATION

Citation

Proteins. 2008 May 15;71(3):1255-74.
Estimating quality of template-based protein models by alignment stability.
Chen H1, Kihara D.

PSVS 1.5 – Protein Structure Validation Software Suite

PSVS 1.5

:: DESCRIPTION

PSVS systematically evaluates the quality of protein structures. PSVS integrates analyses from several widely-used structure quality evaluation tools, including RPF , PROCHECK, MolProbity , Verify3D  Prosa II , the PDB validation software, and various structure-validation tools.PSVS provides standard constraint analyses, statistics on the PDB validation goodness-of-fit between structures and experimental data, and knowledge-based structure quality scores in standardized format suitable for database integration. Global quality measures are reported as Z scores, based on calibration with a set of high-resolution X-ray crystal structures.

::DEVELOPER

CABM Structural Bioinformatics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web BRowser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Proteins. 2007 Mar 1;66(4):778-95.
Evaluating protein structures determined by structural genomics consortia.
Bhattacharya A, Tejero R, Montelione GT.

Concavity 0.1 – Ligand Binding Site Prediction from Protein Sequence and Structure

Concavity 0.1

:: DESCRIPTION

Concavity predicts ligand-binding sites from structure.

::DEVELOPER

John A. Capra , Thomas Funkhouser , Mona Singh

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX

:: DOWNLOAD

 Concavity

:: MORE INFORMATION

Citation

PLoS Comput Biol. 2009 Dec;5(12):e1000585. doi: 10.1371/journal.pcbi.1000585. Epub 2009 Dec 4.
Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure.
Capra JA1, Laskowski RA, Thornton JM, Singh M, Funkhouser TA.

SAINT2 – Cotranslational Protein Structure prediction

SAINT2

:: DESCRIPTION

SAINT2 is a fragment-based de novo protein structure prediction software. It is based on the notion that some proteins fold as they are being synthesised, which is known as the cotranslational protein folding hypothesis.

::DEVELOPER

the Oxford Protein Informatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOs/ Linux

:: DOWNLOAD

SAINT2

:: MORE INFORMATION

Citation

Bioinformatics. 2018 Apr 1;34(7):1132-1140. doi: 10.1093/bioinformatics/btx722.
Sequential search leads to faster, more efficient fragment-based de novo protein structure prediction.
de Oliveira SHP, Law EC, Shi J, Deane CM.