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.

ModView 0.903 – Visualization of Multiple Protein Sequences & Structures

ModView 0.903

:: DESCRIPTION

ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments. As a Netscape plug-in , it can be embed into Web pages and controlled by JavaScript objects on the page. It has wide range of tools to manipulate and analyze sequences and structures by interactive control.

::DEVELOPER

Andrej Sali

:: SCREENSHOTS

:: REQUIREMENTS

  • Netscape 4.xx

:: DOWNLOAD

ModView

:: MORE INFORMATION

Citation:

Bioinformatics. 2003 Jan;19(1):165-6.
ModView, visualization of multiple protein sequences and structures.
Ilyin VA, Pieper U, Stuart AC, Marti-Renom MA, McMahan L, Sali A.

GMOL 2 – 3D Genome Structure Visualization

GMOL 2

:: DESCRIPTION

GMOL is an application designed to visualize genome structure in 3D. It allows users to view the genome structure at multiple scales, including: global, chromosome, loci, fiber, nucleosome, and nucleotide.

::DEVELOPER

Dr. Jianlin Cheng

:: SCREENSHOTS

GMOL

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 GMOL

:: MORE INFORMATION

MMB 2.19 – Model the Structure and Dynamics of Macromolecules

MMB 2.19

:: DESCRIPTION

MMB (a contraction of MacroMolecule Builder) was previously known as RNABuilder. The latter is available up to revision 2.2. We renamed the software since even some longtime users were unaware that the package now handles protein as well as RNA. Aside from the renaming, MMB 2.3 differs from RNABuilder 2.2 in two important ways. Release 2.3 has fully overhauled guts. It uses the BiopolymerClassContainer, a much cleaner programming construct which will make future upgrades and extensions more efficient. As of release 2.3.4, we link against new Molmodel binaries which have more efficient tracking of atoms in rigid regions. This yields a two-fold speed improvement and four-fold lower memory requirement for many problems. Also in this release, some rarely used features have been removed, but these were never in the tutorial literature so their absence should go largely unnoticed. The default input file name is now commands.dat rather than contacts.dat. A couple of somewhat obscure bugs were fixed. The error messages are more informative, and more aggressively prevent the user from risky or incorrect construction of the input file.

::DEVELOPER

MMB Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX
  • VMD

:: DOWNLOAD

 MMB

:: MORE INFORMATION

Citation:

Samuel Coulbourn Flores, Russ B. Altman.
Structural insights into Pre-Translocation Ribosome Motions.
In Proceedings of Pacific Symposium on Biocomputing’2011. pp.205~216 (2011)

Samuel Flores and Russ Altman,
Turning limited experimental information into 3D models of RNA,
RNA 16(9):1769-78 (2010).

KegDraw 0.1.15 beta – Draw Compound & Glycan Structures

KegDraw 0.1.15 beta

:: DESCRIPTION

KegDraw is a java application for drawing compound and glycan structures with capabilities to search against the KEGG databases.

::DEVELOPER

Kanehisa Laboratories

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac /  Linux
  • Java

:: DOWNLOAD

KegDraw

:: MORE INFORMATION

Citation

Glycobiology. 2006 May;16(5):63R-70R. Epub 2005 Jul 13.
KEGG as a glycome informatics resource.
Hashimoto K, Goto S, Kawano S, Aoki-Kinoshita KF, Ueda N, Hamajima M, Kawasaki T, Kanehisa M.

DireX 0.71 – Low-resolution Structure Refinement

DireX 0.71

:: DESCRIPTION

DireX is a software to generate ensembles of protein structures that are in agreement with low resolution or sparse experimental data.

::DEVELOPER

Gunnar Schröder

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX

:: DOWNLOAD

  DireX

:: MORE INFORMATION

Citation:

G.F.Schröder, A.T.Brunger, and M.Levitt
Combining Efficient Conformational Sampling with a Deformable Elastic Network Model Facilitates Structure Refinement at Low Resolution
Structure, Vol 15, 1630-1641 (2007)

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

Struct2Net

:: 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

  • WebServer

:: DOWNLOAD

 NO

:: 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

FOLDALIGN 2.5.2 / FOLDALIGNM 1.0.2 – RNA Structure and Sequence Alignment

FOLDALIGN 2.5.2 / FOLDALIGNM 1.0.2

:: DESCRIPTION

FOLDALIGN: Pairwise local and global structural alignment of RNA sequences.

FOLDALIGNM: Multiple glo-bal struc-tu-ral a-lign-ment of RNA se-quences

::DEVELOPER

Center for non-coding RNA in Technology and Health (RTH)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 FOLDALIGNFOLDALIGNM

:: MORE INFORMATION

Citation:

Foldalign 2.5: multithreaded implementation for pairwise structural RNA alignment.
Sundfeld D, Havgaard JH, de Melo AC, Gorodkin J.
Bioinformatics. 2015 Dec 24. pii: btv748.

Fast Pairwise Structural RNA Alignments by Pruning of the Dynamical Programming Matrix,
Havgaard JH, Torarinsson E, Gorodkin J. PLOS computational biology. 3:e193, 2007

Multiple structural alignment and clustering of RNA sequences,
Torarinsson E, Havgaard JH, Gorodkin J. Bioinformatics. 23:926-32, 2007

InfMod3DGen – Inferential Modeling of 3D Chromatin Structure

InfMod3DGen

:: DESCRIPTION

InfMod3DGen is a new Bayesian framework to derive the 3D architecture of a chromosome from 3C-based data.

::DEVELOPER

InfMod3DGen team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • MatLab

:: DOWNLOAD

 InfMod3DGen

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2015 Apr 30;43(8):e54. doi: 10.1093/nar/gkv100.
Inferential modeling of 3D chromatin structure.
Wang S, Xu J, Zeng J.

SMOG 2.2 – Structure-based Models for Biomolecules

SMOG 2.2

:: 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.

::DEVELOPER

SMOG team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SMOG

:: MORE INFORMATION

Citation

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