PSpro 2.0 – Predict Secondary Structure, Solvent Accessibility, and Residue-residue Contacts

PSpro 2.0

:: DESCRIPTION

PSpro is a software to predict secondary structure, solvent accessibility, and residue-residue contacts . It is essentially a bundle of three tools including SSpro 4.1, ACCpro 4.1 and NNcon 1.0.

::DEVELOPER

Dr. Jianlin Cheng’s Bioinformatics and Systems Biology Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 PSpro 

:: MORE INFORMATION

SSpro / ACCpro 5.2 – Protein Secondary Structure /Solvent Accessibility Prediction with Homology Analysis

SSpro / ACCpro 5.2

:: DESCRIPTION

SSpro/ACCpro is the first hybrid approach of combining neural network (ab initio) and homology analysis to improve the prediction of secondary structure and solvent accessibility.

::DEVELOPER

Institute for Genomics and Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 SSpro / ACCpro

:: MORE INFORMATION

Citation:

Bioinformatics. 2014 May 24. pii: btu352. [Epub ahead of print]
SSpro/ACCpro 5: Almost Perfect Prediction of Protein Secondary Structure and Relative Solvent Accessibility Using Profiles, Machine Learning, and Structural Similarity.
Magnan CN1, Baldi P2.

J. Cheng, A. Randall, M. Sweredoski, & P. Baldi.
SCRATCH: a Protein Structure and Structural Feature Prediction Server.
Nucleic Acids Research, vol. 33 (web server issue), w72-76, (2005)

Sann – Solvent Accessibility Prediction by Nearest Neighbor Method

Sann

:: DESCRIPTION

Sann is a web server for prediction of protein solvent accessibility by nearest neighbor method.

::DEVELOPER

Korea Institute for Advanced Study

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Proteins. 2012 Jul;80(7):1791-7. doi: 10.1002/prot.24074. Epub 2012 May 8.
Sann: solvent accessibility prediction of proteins by nearest neighbor method.
Joo K1, Lee SJ, Lee J.

RSARF – Prediction of Solvent Accessibility from Protein Sequence using Random Forest Method

RSARF

:: DESCRIPTION

RSARF is a random forest method to predict residue accessible surface area from protein sequence information.

::DEVELOPER

RSARF team

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Windows/ Linux
  • R

:: DOWNLOAD

 RSARF

:: MORE INFORMATION

Citation

Protein Pept Lett. 2012 Jan;19(1):50-6.
RSARF: prediction of residue solvent accessibility from protein sequence using random forest method.
Pugalenthi G1, Kandaswamy KK, Chou KC, Vivekanandan S, Kolatkar P.

SPPIDER – Solvent accessibility based Protein-Protein Interface iDEntification and Recognition

SPPIDER

:: DESCRIPTION

The SPPIDER protein interface recognition server can be used to: (1) predict residues to be at the putative protein interface(s) by considering single protein chain with resolved 3D structure; (2) analyse protein-protein complex with given 3D structural information and identify residues that are being in interchain contact.

::DEVELOPER

Meller Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Proteins. 2007 Feb 15;66(3):630-45.
Prediction-based fingerprints of protein-protein interactions.
Porollo A1, Meller J.

Porter, PaleAle 4.0 – Prediction of Protein Secondary Structure and relative Solvent Accessibility

Porter, PaleAle 4.0

:: DESCRIPTION

Porter is a server for protein secondary structure prediction based on an ensemble of 25 BRNNs (bidirectional recurrent neural networks)

PaleAle is a server for the prediction of protein relative solvent accessibility.

::DEVELOPER

Gianluca Pollastri group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Aug 15;29(16):2056-8. doi: 10.1093/bioinformatics/btt344. Epub 2013 Jun 14.
Porter, PaleAle 4.0: high-accuracy prediction of protein secondary structure and relative solvent accessibility.
Mirabello C1, Pollastri G.

NETASA – Prediction of Solvent Accessibility using Neural Networks

NETASA

:: DESCRIPTION

NETASA ,a server, for predicting solvent accessibility of amino acids using our newly optimized neural network algorithm. Several new features in the neural network architecture and training method have been introduced, and the network learns faster to provide accuracy values, which are comparable or better than other methods of ASA prediction.

::DEVELOPER

Shandar Ahmad

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Server

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

NETASA: neural network based prediction of solvent accessibility.
Ahmad S, Gromiha MM.
Bioinformatics. 2002 Jun;18(6):819-24.

RVP-NET 2.0 – Real Value Prediction of Solvent Accessibility

RVP-NET 2.0

:: DESCRIPTION

RVP-net is an online program for the prediction of real valued solvent accessibility. All previous methods of accessible surface area (ASA) predictions classify amino acid residues into exposure states and named them buried or exposed based on different thresholds. Real values in some cases were generated by taking the mid points of these state thresholds. This is the first method, which provides a direct prediction of ASA without making exposure categories and achieves results better than 19% mean absolute error.

::DEVELOPER

Shandar Ahmad

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Server

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2003 Sep 22;19(14):1849-51.
RVP-net: online prediction of real valued accessible surface area of proteins from single sequences.
Ahmad S, Gromiha MM, Sarai A.

ASAView – Solvent Accessibility Graphics for Proteins

ASAView

:: DESCRIPTION

ASAView is an algorithm, an application and a database of schematic representations of solvent accessibility of amino acid residues within proteins. A characteristic two-dimensional spiral plot of solvent accessibility provides a convenient graphical view of residues in terms of their exposed surface areas. In addition, sequential plots in the form of bar charts are also provided. Online plots of the proteins included in the entire Protein Data Bank (PDB), are provided for the entire protein as well as their chains separately.

::DEVELOPER

Shandar Ahmad

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Server

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2004 May 1;5:51.
ASAView: database and tool for solvent accessibility representation in proteins.
Ahmad S, Gromiha M, Fawareh H, Sarai A.

WESA – Weighted Ensemble Solvent Accessibility

WESA

:: DESCRIPTION

WESA is a meta-predictor, based on a Weighted Ensemble of five methods, for Solvent Accessibility of residues, using the protein sequence as input. It has an expected accuracy of 80%. The prediction can be used for structure prediction.

::DEVELOPER

Zhou Biophysics Group at FSU

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 WESA

:: MORE INFORMATION

Citation:

Chen, H-L and Zhou, H-X.
Prediction of solvent accessibility and sites of deleterious mutations from protein sequence.
Nucl. Acids Res. 33, 3193-3199 (2005).