Emap2sec – Protein secondary structure detection in intermediate-resolution cryo-EM maps

Emap2sec

:: DESCRIPTION

Emap2sec is a deep learning-based tool for detecting protein secondary structures from intermediate resolution cryo-EM maps.

::DEVELOPER

Kihara Bioinformatics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

Emap2sec

:: MORE INFORMATION

Citation

Nat Methods. 2019 Sep;16(9):911-917. doi: 10.1038/s41592-019-0500-1. Epub 2019 Jul 29.
Protein secondary structure detection in intermediate-resolution cryo-EM maps using deep learning.
Maddhuri Venkata Subramaniya SR, Terashi G, Kihara D.

CROSS / CROSSalign / CROSSalive – Recognition of RNA Secondary Structure

CROSS / CROSSalign / CROSSalive

:: DESCRIPTION

CROSS predicts the secondary structure propensity profile of an RNA molecule at single-nucleotide resolution. CROSS produces a table with the propensity scores and a graphical representation of the profile.

CROSSalign computes the similarity of RNA secondary structure

CROSSalive computes the structure of RNA molecules in vivo. Changes of structure upon N6-Methyladenosine methylation can be predicted.

::DEVELOPER

Tartaglia Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

CROSSalive: a web server for predicting the in vivo structure of RNA molecules.
Delli Ponti R, Armaos A, Vandelli A, Tartaglia GG.
Bioinformatics. 2019 Aug 28. pii: btz666. doi: 10.1093/bioinformatics/btz666.

Front Mol Biosci. 2018 Dec 3;5:111. doi: 10.3389/fmolb.2018.00111. eCollection 2018.
A Method for RNA Structure Prediction Shows Evidence for Structure in lncRNAs.
Delli Ponti R, Armaos A, Marti S, Tartaglia GG

A high-throughput approach to profile RNA structure.
Delli Ponti R, Marti S, Armaos A, Tartaglia GG.
Nucleic Acids Res. 2017 Mar 17;45(5):e35. doi: 10.1093/nar/gkw1094.

comRNA 1.80 – Common RNA Secondary Structure Predictor

comRNA 1.80

:: DESCRIPTION

comRNA is a new program that predicts common RNA secondary structure motifs in a group of related sequences.The algorithm applies graph-theoretical approaches to automatically detect common RNA secondary structure motifs in a group of functionally or evolutionarily related RNA sequences.

::DEVELOPER

Stormo Lab in Department of Genetics, Washington University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

comRNA

:: MORE INFORMATION

Citation:

Yongmei Ji, Xing Xu and Gary D. Stormo,
A graph theoretical approach for predicting common RNA secondary structure motifs including pseudoknots in unaligned sequences
, Bioinformatics, 2004 Jul 10; 20(10):1591-1602.”

AlphaPred – Prediction of Alpha-turns in Proteins using Multiple Alignment and Secondary Structure Information

AlphaPred

:: DESCRIPTION

The AlphaPred server predicts the alpha turn residues in the given protein sequence. The method is based on the neural network training on PSI-BLAST generated position specific matrices and PSIPRED predicted secondary structure.

::DEVELOPER

Dr. G P S Raghava

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Kaur H & Raghava GP. (2004).
Prediction of alpha-turns in proteins using PSI-BLAST profiles and secondary structure information.
Proteins. 55: 83-90

GammaPred – Prediction of Gamma-turns in Proteins using Multiple Alignment and Secondary Structure Information

GammaPred

:: DESCRIPTION

The GammaPred server predicts the gamma turn residues in the given protein sequence. The method is based on the neural network training on PSI-BLAST generated position specific matrices and PSIPRED predicted secondary structure. Two neural networks with a single hidden layer have been used where the first sequence-to-structure network is trained on PSI-BLAST obtained position specific matrices. The filtering has been done by second structure-to-structure network trained on output of first net and PSIPRED predicted secondary structure. The training has been carried out using error backpropagation with a sum of square error function(SSE).

::DEVELOPER

Dr. G P S Raghava

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Kaur, H. and Raghava, G.P.S. (2003)
A neural network based method for prediction of gamma-turns in proteins from multiple sequence alignment.
Protein Science 12: 923-929.

APSSP2 – Advanced Protein Secondary Structure Prediction Server

APSSP2

:: DESCRIPTION

APSSP2 allows to predict the secondary structure of protein’s from their amino acid sequence.

::DEVELOPER

Dr. G P S Raghava

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Raghava, G. P. S. (2002)
APSSP2 : A combination method for protein secondary structure prediction based on neural network and example based learning.
CASP5. A-132.

assp 1.2 – Assess Protein Secondary Structure Prediction Accuracy

assp 1.2

:: DESCRIPTION

assp (Assess  Secondary Structure Prediction) takes a multiple protein sequence alignmentand estimates the range in accuracy that one can expect for a “perfect” secondary structure prediction made using the alignment.

::DEVELOPER

The Barton Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

assp

:: MORE INFORMATION

Citation:

Russell, R. B. and Barton, G. J. (1993),
J. Mol. Biol., 234, 951-957,
The Limits of Protein Structure Prediction Accuracy From Multiple Sequence Alignment

RNApdbee 2.0 – RNA Secondary Structures Extraction from PDB Files

RNApdbee 2.0

:: DESCRIPTION

RNApdbee is a webserver to derive secondary structures from pdb files of knotted and unknotted RNAs.

::DEVELOPER

The Bioinformatics Group, Poznan University of Technology.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2014 Apr 25. [Epub ahead of print]
RNApdbee–a webserver to derive secondary structures from pdb files of knotted and unknotted RNAs.
Antczak M1, Zok T, Popenda M, Lukasiak P, Adamiak RW, Blazewicz J, Szachniuk M.

rPredictor – Prediction of Ribosomal RNA Secondary Structure

rPredictor

:: DESCRIPTION

rPredictor is a bioinformatic infrastructure for prediction, analysis and storage of secondary structures of ribosomal RNAs.

::DEVELOPER

SIRET Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Josef Pánek, Jan Hajič jr., David Hoksza (2014)
Template-Based Prediction of Ribosomal RNA Secondary Structure,
IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Belfast, UK, pp.: 18-20, IEEE

RNAmutants 2.0 – Analysis of RNA Mutational Landscapes

RNAmutants 2.0

:: DESCRIPTION

RNAmutants is a web server to perform mutational analysis for a given RNA sequence. Previous methods relied on exhaustively enumerating k-point mutant sequences and subsequently applying mfold or RNAfold, a procedure with run time exponential in k. In contrast, RNAmutants computes the minimum free energy structure and Boltzmann partition function for all k-point mutants, for 0 ≤ k ≤ K, with run time O(K2n3).

::DEVELOPER

Clote Lab ,  Computer Science and Biology at McGill

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Mac OsX

:: DOWNLOAD

 RNAmutants 

:: MORE INFORMATION

Citation:

J Comput Biol. 2011 Nov;18(11):1465-79. doi: 10.1089/cmb.2011.0181. Epub 2011 Oct 28.
An unbiased adaptive sampling algorithm for the exploration of RNA mutational landscapes under evolutionary pressure.
Waldispühl J1, Ponty Y.

Jerome Waldispühl, Srinivas Devadas, Bonnie Berger, Peter Clote.
Efficient algorithms for probing the RNA mutation landscape.
PLoS Comput Biol. 2008 Aug 8;4(8):e1000124.