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

:: 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.

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

:: 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

:: 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

:: 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

Linux
Gecode

:: 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

:: 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.