AlignExIn 20130624 – Alignment Exon Intron Structure

AlignExIn 20130624

:: DESCRIPTION

AlignExIn ( Align Exon Intron) is a handy and useful utility built in order to display the alignment of exons. The program displays the exon painted in red and the alignments painted in blue by default, but it is possible to change the colors.All you have to do is select the input files (fasta and exon) and the program will do the rest.

::DEVELOPER

Institute of Bioinformatics WWU Muenster

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 alignexin

:: MORE INFORMATION

NOFOLD 1.0.1 – RNA Structure Clustering without Folding or Alignment

NOFOLD 1.0.1

:: DESCRIPTION

NoFold is an approach for characterizing and clustering RNA secondary structures without computational folding or alignment. It works by mapping each RNA sequence of interest to a structural feature space, where each coordinate within the space corresponds to the probabilistic similarity of the sequence to an empirically defined structure model (e.g. Rfam family covariance models).

::DEVELOPER

the Kim Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • R

:: DOWNLOAD

NOFOLD

:: MORE INFORMATION

Citation

Middleton SA, Kim J.
NoFold: RNA structure clustering without folding or alignment.
RNA. 2014 Nov;20(11):1671-83. doi: 10.1261/rna.041913.113. Epub 2014 Sep 18. PMID: 25234928; PMCID: PMC4201820.

ORTEP-III 1.03 /for Windows 2021.3 – Crystal Structure Illustration

ORTEP-III 1.03 /for Windows2021.3

:: DESCRIPTION

ORTEP-III is Oak Ridge Thermal Ellipsoid Plot Program for crystal structure illustrations.Ball-and-stick type illustrations of a quality suitable for publication are produced with either spheres or thermal-motion probability ellipsoids, derived from anisotropic temperature factor parameters, on the atomic sites. The program also produces stereoscopic pairs of illustrations which aid in the visualization of complex arrangements of atoms and their correlated thermal motion patterns.

Ortep-3 for Windows developed by Dr. Louis Farrugia is a MS-Windows version of the current release of ORTEP-III

::DEVELOPER

Michael N. Burnett and Carroll K. Johnson

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac /  Linux /
  • POV-Ray

:: DOWNLOAD

ORTEP-III ; Ortep-3 for Windows

:: MORE INFORMATION

Citation:

Michael N. Burnett and Carroll K. Johnson,
ORTEP-III: Oak Ridge Thermal Ellipsoid Plot Program for Crystal Structure Illustrations,
Oak Ridge National Laboratory Report ORNL-6895, 1996.

WinGX and ORTEP for Windows: an update
L. J. Farrugia,
J. Appl. Cryst (2012), 45, 849-854.

SMOG 2.4.2 / OpenSMOG 1.1 – Structure-based Models for Biomolecules

SMOG 2.4.2 / OpenSMOG 1.1

:: DESCRIPTION

SMOG is a versatile software package for generating structure-based models.SMOG 2 is a downloadable software package that reads user-designated structural information and user-defined energy definitions, in order to produce the files necessary to use SBMs with high performance molecular dynamics packages: GROMACS and NAMD.

OpenSMOG : Simulating SMOG models in OpenMM

::DEVELOPER

SMOG team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SMOG / OpenSMOG

:: MORE INFORMATION

Citation

de Oliveira AB Jr, Contessoto VG, Hassan A, Byju S, Wang A, Wang Y, Dodero-Rojas E, Mohanty U, Noel JK, Onuchic JN, Whitford PC.
SMOG 2 and OpenSMOG: Extending the limits of structure-based models.
Protein Sci. 2021 Oct 16. doi: 10.1002/pro.4209. Epub ahead of print. PMID: 34655449.

SMOG 2: A Versatile Software Package for Generating Structure-Based Models.
Noel JK, Levi M, Raghunathan M, Lammert H, Hayes RL, Onuchic JN, Whitford PC.
PLoS Comput Biol. 2016 Mar 10;12(3):e1004794. doi: 10.1371/journal.pcbi.1004794

SBAL 1.8 – Structure-based Amino Acid Sequence Alignments

SBAL 1.8

:: DESCRIPTION

SBAL is intended for multiple protein sequence alignments guided by secondary structure elements. The program provides automatic and semi-automatic alignment features, and also possesses manual editing capabilities.

::DEVELOPER

Hofmann Laboratory, Eskitis Institute

:: SCREENSHOTS

SBAL

:: REQUIREMENTS

  • linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 SBAL

 :: MORE INFORMATION

Citation

Wang, C.K., Broder, U., Weeratunga, S.K., Gasser, R.B., Loukas, A., Hofmann, A. (2012)
SBAL: a practical tool to generate and edit structure-based amino acid sequence alignments.
Bioinformatics 28, 1026-1027.

NASP 1.5 – Nucleic Acid Structures Predictor

NASP 1.5

:: DESCRIPTION

NASP is a computer program that will allow predict the most evolutionarily conserved secondary structures evident within a set of aligned nucleic acid sequences. It will progressively identify all of the most probable secondary structures that display some degree of sequence conservation between sequences in an analysed alignment.

::DEVELOPER

CBIO

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 NASP

 :: MORE INFORMATION

Citation

Bioinformatics. 2011 Sep 1;27(17):2443-5. doi: 10.1093/bioinformatics/btr417. Epub 2011 Jul 14.
NASP: a parallel program for identifying evolutionarily conserved nucleic acid secondary structures from nucleotide sequence alignments.
Semegni JY1, Wamalwa M, Gaujoux R, Harkins GW, Gray A, Martin DP.

LTR_STRUC – LTR Retrotransposon Structure program

LTR_STRUC

:: DESCRIPTION

LTR_STRUC is a new data-mining program that scans nucleotide sequence files for LTR retrotransposons and analyzes any resulting hits. Input files can be in fasta or NCBI flat file format.

::DEVELOPER

McDonald Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  Contact with Vinay Mittal ( vinaykmittal@gatech.edu )

:: MORE INFORMATION

Citation:

McCarthy, E.M., and J.F. McDonald. 2003.
LTR_STRUC: A novel search and identification program for LTR retrotransposons.
Bioinformatics 19: 362-367

DISCO 1.0 – Structure Determination of Protein Homo-oligomers

DISCO 1.0

:: DESCRIPTION

DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer.

::DEVELOPER

Donald Lab at Duke University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

DISCO

:: MORE INFORMATION

Citation

Jeffrey W. Martin, Anthony K. Yan, Chris Bailey-Kellogg, Pei Zhou, and Bruce R. Donald.
A graphical method for analyzing distance restraints using residual dipolar couplings for structure determination of symmetric protein homo-oligomers.
Protein Science, 20(6):970-985, 2011.

QRNAS – software tool for Refinement of Nucleic Acid structures

QRNAS

:: DESCRIPTION

QRNAS (Quick Refinement of Nucleic Acid Structures) is an extension of the AMBER simulation method with additional terms associated with explicit hydrogen bonds, co-planarity base pairs, backbone regularization, and custom restraints. QRNAS is capable of handling RNA, DNA, chimeras and hybrids thereof, and enables modeling of nucleic acids containing modified residues.

::DEVELOPER

Laboratory Of Bioinformatics And Protein Engineering

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

QRNAS

:: MORE INFORMATION

Citation

Stasiewicz J, Mukherjee S, Nithin C, Bujnicki JM.
QRNAS: software tool for refinement of nucleic acid structures.
BMC Struct Biol. 2019 Mar 21;19(1):5. doi: 10.1186/s12900-019-0103-1. PMID: 30898165; PMCID: PMC6429776.

POLYVIEW-2D / POLYVIEW-3D / POLYVIEW-MM – Protein Structure Annotation using Sequence Profiles / Structures / Motions

POLYVIEW-2D / POLYVIEW-3D / POLYVIEW-MM

:: DESCRIPTION

The POLYVIEW-2D protein structure visualization server can be used to generate amino acid sequence annotations, such as secondary structure, relative solvent accessibility, evolutionary conservation, and physico-chemical property profiles. It can also be used to identify residues involved in protein-protein interactions and highlight other important sites and motifs.

POLYVIEW-3D is a web-based tool for macromolecular structure visualization and analysis. In particular, it provides a wide array of options for automated structural and functional analysis of proteins and their complexes. This tutorial aims to describe and illustrate the available rendering options and annotation capabilities of POLYVIEW-3D.

POLYVIEW-MM (Molecular Motion) enables animation of trajectories generated by Molecular Dynamics and related simulation techniques, as well as visualization of alternative conformers, e.g., obtained as a result of protein structure prediction methods or small molecule docking, using an intuitive web-based interface.

:: SCREENSHOTS

N/A

::DEVELOPER

Meller Lab

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

POLYVIEW: a flexible visualization tool for structural and functional annotations of proteins.
Porollo AA, Adamczak R, Meller J.
Bioinformatics. 2004 Oct 12;20(15):2460-2. Epub 2004 Apr 8.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W662-6. doi: 10.1093/nar/gkq445. Epub 2010 May 26.
POLYVIEW-MM: web-based platform for animation and analysis of molecular simulations.
Porollo A, Meller J.