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

 NO

:: 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

 NO

:: 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

 NO

:: 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

RW 1.0 – Protein Structure Modeling and Structure Decoy Recognition

RW 1.0

:: DESCRIPTION

RW (Random-Walk) is distance-dependent atomic potential for protein structure modeling and structure decoy recognition. It was derived from 1,383 high-resolution PDB structures using an ideal random-walk chain as the reference state. The RW potential has been extensively optimized and tested on a variety of protein structure decoy sets and demonstrates a significant power in protein structure recognition and a strong correlation with the RMSD of decoys to the native structures

::DEVELOPER

Yang Zhang’s Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
:: DOWNLOAD

 calRW

:: MORE INFORMATION

Citation

Zhang J, Zhang Y (2010)
A Novel Side-Chain Orientation Dependent Potential Derived from Random-Walk Reference State for Protein Fold Selection and Structure Prediction.
PLoS ONE 5(10): e15386.

ModRefiner 20111024 – High-resolution Protein Structure Refinement

ModRefiner 20111024

:: DESCRIPTION

ModRefiner is an algorithm for atomic-level, high-resolution protein structure refinement, which can start from either C-alpha trace, main-chain model or full-atomic model. Both side-chain and backbone atoms are completely flexible during structure refinement simulations, where conformational search is guided by a composite of physics- and knowledge-based force field. ModRefiner has an option to allow for the assignment of a second structure which will be used as a reference to which the refinement simulations are driven. One aim of ModRefiner is to draw the initial starting models closer to their native state, in terms of hydrogen bonds, backbone topology and side-chain positioning. It also generates significant improvement in physical quality of local structures. The standalone program also supports ab initio full-atomic relaxation, where the refined model is not restrainted by the initial model or the reference model.

::DEVELOPER

Yang Zhang’s Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows
:: DOWNLOAD

  ModRefiner

:: MORE INFORMATION

Citation

Dong Xu and Yang Zhang.
Improving Physical Realism and Structural Accuracy of Protein Models by a Two-step Atomic-level Energy Minimization
(in preparation).

(PS)2 v3 – Protein Structure Prediction server

(PS)2 v3

:: DESCRIPTION

(PS)2 is an automated homology modeling server. The method uses an effective consensus strategy by combining PSI-BLAST, IMPALA, and T-Coffee in both template selection and target-template alignment. The final three dimensional structure is built using the modeling package MODELLER.

::DEVELOPER

(PS)2 team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

(PS)2: protein structure prediction server version 3.0.
Huang TT, Hwang JK, Chen CH, Chu CS, Lee CW, Chen CC.
Nucleic Acids Res. 2015 May 5. pii: gkv454.

Chen CC, Hwang JK, Yang JM.
(PS)2: protein structure prediction server.
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W152-7.

Chen CC, Hwang JK, Yang JM:
(PS)2-v2: template-based protein structure prediction server.
BMC Bioinformatics 2009, 10:366

Pcons – Protein Structure Prediction Meta Server

Pcons

:: DESCRIPTION

The Pcons.net Meta Server provides improved automated tools for protein structure prediction and analysis using consensus. It essentially implements all the steps necessary to produce a high quality model of a protein.

::DEVELOPER

Stockholm University, Stockholm Bioinformatics Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Pcons

:: MORE INFORMATION

Citation

Identification of correct regions in protein models using structural, alignment and consensus information.
Wallner B and Elofsson A. (2006).
Protein Sci., 15(4):900-913.

Pcons.net: protein structure prediction meta server.
Wallner B, Larsson P, Elofsson A.
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W369-74. Epub 2007 Jun 21.