GOAP – Protein Structure Prediction

GOAP

:: DESCRIPTION

GOAP is a generalized orientation-dependent, all-atom statistical potential for protein structure prediction. It was benchmarked against other state-the-art similar potentials and was shown to be significantly better for discriminating native structures from decoys

::DEVELOPER

Center for the Study of Systems Biology

:: REQUIREMENTS

Linux

:: DOWNLOAD

GOAP

:: MORE INFORMATION

Citation

H. Zhou and J. Skolnick:
GOAP: A generalized orientation-dependent, all-atom statistical potential for protein structure prediction,
Biophysical Journal, 101(8):2043-2052, 2011

TASSER-Lite 1.0 – Protein Structure Modeling tool

TASSER-Lite 1.0

:: DESCRIPTION

TASSER-Lite is a protein structure comparative modeling tool. It is limited to protein target-template pairs whose pairwise sequence identity is >25% to the best threading template. It is optimized to model single domain proteins whose lengths range from 41-200 residues.

::DEVELOPER

Center for the Study of Systems Biology

:: REQUIREMENTS

Linux

:: DOWNLOAD

TASSER-Lite

:: MORE INFORMATION

Citation

Pandit, S B, Zhang Y, Skolnick J. 2006.
TASSER-Lite: an automated tool for protein comparative modeling.
Biophysical journal. 91(11):4180-90.

ProSTRIP – Find Similar Structural Repeats in Three-dimensional Protein Structures

ProSTRIP

:: DESCRIPTION

ProSTRIP is a web server to find the similar structural repeats in a three-dimensional protein structure.

::DEVELOPER

ProSTRIP team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Comput Biol Chem. 2010 Apr;34(2):126-30. doi: 10.1016/j.compbiolchem.2010.03.006. Epub 2010 Apr 3.
ProSTRIP: A method to find similar structural repeats in three-dimensional protein structures.
Sabarinathan R1, Basu R, Sekar K.

RaptorX Property 1.02 – Protein Structure Property Prediction

RaptorX Property 1.02

:: DESCRIPTION

RaptorX Property is a web server predicting structure property of a protein sequence without using any template information.

::DEVELOPER

Xu group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

PRaptorX Property

:: MORE INFORMATION

Citation:

RaptorX-Property: a web server for protein structure property prediction.
Wang S, Li W, Liu S, Xu J.
Nucleic Acids Res. 2016 Apr 25. pii: gkw306.

fastSCOP – Protein Structure Evolutionary Classifications

fastSCOP

:: DESCRIPTION

The fastSCOP is a web server that rapidly identifies the structural domains and determines the evolutionary superfamilies of a query protein structure.

::DEVELOPER

BioXGEM Lab.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W438-43.
fastSCOP: a fast web server for recognizing protein structural domains and SCOP superfamilies.
Tung CH, Yang JM.

3D-BLAST beta 1.02 – Protein Structure Search

3D-BLAST beta 1.02

:: DESCRIPTION

3D-BLAST is a very fast and accurate method for discovering the homologous proteins and evolutionary classifications of a newly determined protein structure.

::DEVELOPER

BioXGEM Lab.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/MacOsX

:: DOWNLOAD

3D-BLAST

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2006 Aug 2;34(13):3646-59.
Protein structure database search and evolutionary classification.
Yang JM, Tung CH.

Genome Biol. 2007;8(3):R31.
Kappa-alpha plot derived structural alphabet and BLOSUM-like substitution matrix for rapid search of protein structure database.
Tung CH, Huang JW, Yang JM.

PUDGE – Protein Structure Prediction Pipeline

PUDGE

:: DESCRIPTION

PUDGE is protein structure prediction server which provides a convenient means of integrating tools that may be used at different stages of the structural prediction process.

::DEVELOPER

Barry Honig’s group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W550-4. doi: 10.1093/nar/gkq475.
PUDGE: a flexible, interactive server for protein structure prediction.
Norel R, Petrey D, Honig B.

MarkUs – Assessment of the Biochemical Function for a given Protein Structure

MarkUs

:: DESCRIPTION

MarkUs is a web server for analysis and comparison of the structural and functional properties of proteins.

::DEVELOPER

Barry Honig’s group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

MarkUs: a server to navigate sequence-structure-function space.
Fischer M, Zhang QC, Dey F, Chen BY, Honig B, Petrey D.
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W357-61. doi: 10.1093/nar/gkr468.

SPICKER 2.0 – Cluster Protein Structures for Near-native Model Selection

SPICKER 2.0

:: DESCRIPTION

SPICKER is a clustering algorithm to identify the near-native models from a pool of protein structure decoys.

:DEVELOPER

Yang Zhang’s Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

SPICKER

:: MORE INFORMATION

Citation

Y. Zhang, J. Skolnick,
SPICKER: Approach to clustering protein structures for near-native model selection,
Journal of Computational Chemistry, 2004 25: 865-871.

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