CoreAligner – Multiple Genome Alignment for Core Genome Structure Identification

CoreAligner

:: DESCRIPTION

CoreAligner is a software for identifying the core structure of related genomes, which is defined as a set of sufficiently long segments in which gene orders are conserved among multiple genomes so that they are likely to have been inherited mainly through vertical transfer. Using a dynamic programming based algorithm, CoreAligner finds the order of pre-identified orthologous groups (OGs) that retains to the greatest possible extent the conserved gene orders.

::DEVELOPER

Ikuo Uchiyama (uchiyama@nibb.ac.jp)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  •  Linux / Windows/ MacOsX
  • Perl

:: DOWNLOAD

 CoreAligner

:: MORE INFORMATION

Citation

I. Uchiyama (2008)
Multiple genome alignment for identifying the core structure among moderately related microbial genomes
BMC Genomics, 9:515.

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.

STRUCTURE HARVESTER 0.6.93 – Collating Results Generated by the program STRUCTURE

STRUCTURE HARVESTER 0.6.93

:: DESCRIPTION

STRUCTURE HARVESTER is a web-based program for collating results generated by the program STRUCTURE.The program provides a fast way to assess and visualize likelihood values across multiple values of K and hundreds of iterations for easier detection of the number of genetic groups that best fit the data. In addition, STRUCTURE HARVESTER will reformat data for use in downstream programs, such as CLUMPP.

::DEVELOPER

Dent Earl

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Python

:: DOWNLOAD

  STRUCTURE HARVESTER

:: MORE INFORMATION

Citation

Earl, Dent A. and vonHoldt, Bridgett M. (2012)
STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method.
Conservation Genetics Resources vol. 4 (2) pp. 359-361 doi: 10.1007/s12686-011-9548-7

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.