RNAmountAlign – RNA Sequence/Structure Alignment

RNAmountAlign

:: DESCRIPTION

RNAmountAlign is a novel algorithm for RNA sequence/structure pairwise alignment, that runs in O(n3) time and O(n2) space; moreover, our software returns a p-value (transformable to expect value E) based on Karlin-Altschul statistics as well as parameter fitting.

::DEVELOPER

Clote Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

RNAmountAlign

:: MORE INFORMATION

Citation:

PLoS One, 15 (1), e0227177 2020 Jan 24 eCollection 2020
RNAmountAlign: Efficient Software for Local, Global, Semiglobal Pairwise and Multiple RNA Sequence/Structure Alignment
Amir H Bayegan , Peter Clote

Struct2Net 1.0 – Structure-based Computational Predictions of Protein-protein interactions

Struct2Net 1.0

:: DESCRIPTION

The Struct2Net program predicts protein-protein interactions (PPI) by integrating structure-based information with other functional annotations, e.g. GO, co-expression and co-localization etc. The structure-based protein interaction prediction is conducted using a protein threading server RAPTOR plus logistic regression.

::DEVELOPER

Berger Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Struct2Net

:: MORE INFORMATION

Citation:

Struct2Net: a web service to predict protein-protein interactions using a structure-based approach.
Singh R, Park D, Xu J, Hosur R, Berger B.
Nucleic Acids Res. 2010 Jul;38(Web Server issue):W508-15. doi: 10.1093/nar/gkq481

SCALOP – Sequence-based antibody CAnonical LOoP structure annotation

SCALOP

:: DESCRIPTION

SCALOP is a sequence-based canonical form predictor for five of the six complementarity-determining regions (H1, H2, L1, L2 and L3) on an antibody.

::DEVELOPER

the Oxford Protein Informatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOs/ Linux

:: DOWNLOAD

SCALOP

:: MORE INFORMATION

Citation

SCALOP: sequence-based antibody canonical loop structure annotation.
Wong WK, Georges G, Ros F, Kelm S, Lewis AP, Taddese B, Leem J, Deane CM.
Bioinformatics. 2019 May 15;35(10):1774-1776. doi: 10.1093/bioinformatics/bty877.

TCRBuilder – Multi-state T-cell Receptor Structure prediction

TCRBuilder

:: DESCRIPTION

TCRBuilder is a TCR structure prediction algorithm.

::DEVELOPER

the Oxford Protein Informatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Front Immunol. 2019 Oct 15;10:2454. doi: 10.3389/fimmu.2019.02454. eCollection 2019.
Comparative Analysis of the CDR Loops of Antigen Receptors.
Wong WK, Leem J, Deane CM.

MP-T 201407 – Membrane Protein Sequence-structure Alignment

MP-T 201407

:: DESCRIPTION

MP-T is a sequence-structure alignment algorithm for membrane proteins. It produces accurate sequence alignments for use in homology modelling. The inputs are a fasta-formatted sequence and an annotated structure file from the iMembrane webserver.

::DEVELOPER

Oxford Protein Informatics Group (OPIG)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  MP-T

:: MORE INFORMATION

Citation

Jamie R. Hill and Charlotte M. Deane
MP-T: improving membrane protein alignment for structure prediction
Bioinformatics (2013) 29 (1): 54-61.

PROPOSAL – PROtein Comparison through Probabilistic Optimal Structure local ALignment

PROPOSAL

:: DESCRIPTION

PROPOSAL is a Gibbs sampling algorithm for multiple local alignment of 3D protein structures. PROPOSAL can produce biologically significant alignments in reasonable running time, even for large input instances.

::DEVELOPER

Giovanni Micale

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Java

:: DOWNLOAD

  PROPOSAL

:: MORE INFORMATION

Citation:

Proteins comparison through probabilistic optimal structure local alignment.
Micale G, Pulvirenti A, Giugno R, Ferro A.
Front Genet. 2014 Sep 2;5:302. doi: 10.3389/fgene.2014.00302.

Situs 3.1r2 – Integration of Multi-Resolution Structures

Situs 3.1r2

:: DESCRIPTION

Situs is a program package for the modeling of atomic resolution structures into low-resolution density maps e.g. from electron microscopy, tomography, or small angle X-ray scattering.

::DEVELOPER

Willy Wriggers

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Situs

:: MORE INFORMATION

Citation

Willy Wriggers.
Using Situs for the Integration of Multi-Resolution Structures.
Biophysical Reviews, 2010, Vol. 2, pp. 21-27.

Scaffold Hunter 2.6.3 – Analysis of Structure-related Biochemical data

Scaffold Hunter 2.6.3

:: DESCRIPTION

Scaffold Hunter is a tool for the visual analysis of data from the life sciences, aiming at intuitive access to large and complex data sets that offers a variety of views and analysis methods. It originates from drug discovery and has evolved into a reusable open source platform for a wider range of applications.

::DEVELOPER

Scaffold Hunter team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux/  MacOSX
  • Java

:: DOWNLOAD

Scaffold Hunter

:: MORE INFORMATION

Citation

Scaffold Hunter: a comprehensive visual analytics framework for drug discovery.
Schäfer T, Kriege N, Humbeck L, Klein K, Koch O, Mutzel P.
J Cheminform. 2017 May 11;9(1):28. doi: 10.1186/s13321-017-0213-3.

RNAConSLOpt 1.2 – Predicting Consensus stable local optimal Structures for Aligned RNA Sequences

RNAConSLOpt 1.2

:: DESCRIPTION

RNAConSLOpt is a program for predicting consensus stable local optimal structures (represented by stack configurations) for aligned RNA sequences. RNAConSLOpt can be used to predict consensus alternate structures for riboswitches.

::DEVELOPER

UCF Computational Biology and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 RNAConSLOpt

:: MORE INFORMATION

Citation

Int J Bioinform Res Appl. 2014;10(4):498-518. doi: 10.1504/IJBRA.2014.062997.
Finding consensus stable local optimal structures for aligned RNA sequences and its application to discovering riboswitch elements.
Li Y, Zhong C, Zhang S.