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.

MultiTypeTree 7.0.1 – Structured Population Inference for BEAST 2

MultiTypeTree 7.0.1

:: DESCRIPTION

MultiTypeTree is a BEAST 2 package for performing phylogenetic inference under models incorporating some form of population structure. It implements a “multi-type” tree object, representing a phylogenetic tree with every time on each edge associated with one of a finite number of discrete types. These types often represent locations, but can in principle represent any well-defined sub-population

::DEVELOPER

The University of Auckland Computational Evolution Group

:: SCREENSHOTS

 N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS
  • Java
  • BEAST 2

:: DOWNLOAD

 MultiTypeTree

 :: MORE INFORMATION

Citation:

Bioinformatics. 2014 Apr 20.
Efficient Bayesian inference under the structured coalescent.
Vaughan TG1, Kühnert D, Popinga A, Welch D, Drummond AJ.

RNAcompete / RNAcompete-S – Analysis of RNA Sequence/structure preferences for RNA binding proteins

RNAcompete / RNAcompete-S

:: DESCRIPTION

RNAcompete is a method for the systematic analysis of RNA binding specificities that uses a single binding reaction to determine the relative preferences of RBPs for short RNAs that contain a complete range of k-mers in structured and unstructured RNA contexts.

RNAcompete-S couples a single-step competitive binding reaction with an excess of random RNA 40-mers to a custom computational pipeline for interrogation of the bound RNA sequences and derivation of SSMs (Sequence and Structure Models).

rnascan is a (mostly) Python suite to scan RNA sequences and secondary structures with sequence and secondary structure PFMs. Secondary structure is represented as weights in different secondary structure contexts, similar to how a PFM represents weights of different nucleotides or amino acids.

::DEVELOPER

Morris Lab , Hughes lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R
  • Python

:: DOWNLOAD

RNAcompete , RNAcompete-S , rnascan

:: MORE INFORMATION

Citation:

Nat Biotechnol. 2009 Jul;27(7):667-70. doi: 10.1038/nbt.1550. Epub 2009 Jun 28.
Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins.
Ray D, Kazan H, Chan ET, Peña Castillo L, Chaudhry S, Talukder S, Blencowe BJ, Morris Q, Hughes TR.

Cook, K.B., Vembu, S., Ha, K.C.H., Zheng, H., Laverty, K.U., Hughes, T.R., Ray, D., Morris, Q.D., 2017.
RNAcompete-S: Combined RNA sequence/structure preferences for RNA binding proteins derived from a single-step in vitro selection.
Methods 126, 18–28.