mCross – Modeling RBP Binding Specificity by registering protein-RNA Crosslink Sites

mCross

:: DESCRIPTION

mCrossBase is a database of RNA-binding protein (RBP) binding motifs and crosslink sites defined jointly from CLIP data using a novel algorithm mCross

::DEVELOPER

Zhang Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Feng et al. (2019),
Modeling the in vivo specificity of RNA-binding proteins by precisely registering protein-RNA crosslink sites.
Mol Cell. 74:1189-1204.E6.

RCD+ 1.4 – Fast Loop Modeling Server

RCD+ 1.4

:: DESCRIPTION

RCD (Random Coordinate Descent) is a versatile loop closure tool to efficiently generate loop ensembles. The algorithm solves the loop closure problem by optimizing randomly selected bonds and updating loop conformations using spinor matrices (geometric algebra).

::DEVELOPER

The Structural Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

RCD+

:: MORE INFORMATION

Citation

RCD+: Fast loop modeling server.
López-Blanco JR, Canosa-Valls AJ, Li Y, Chacón P.
Nucleic Acids Res. 2016 Jul 8;44(W1):W395-400. doi: 10.1093/nar/gkw395

KORP v1 – knowledge-based 6D potential for Protein and Loop Modeling

KORP v1

:: DESCRIPTION

KORP (Knowledge-base ORientational Potential) utilizes a 6D joint probability and a minimalist representation to outperform state-of-the-art statistical potentials for protein and loop modeling.

::DEVELOPER

The Structural Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

KORP

:: MORE INFORMATION

Citation

Bioinformatics. 2019 Sep 1;35(17):3013-3019. doi: 10.1093/bioinformatics/btz026.
KORP: knowledge-based 6D potential for fast protein and loop modeling.
López-Blanco JR, Chacón P.

MetaReg – Graphical Interface for Modeling and Evaluation of Biological Systems

MetaReg.

:: DESCRIPTION

MetaReg is a Java application aimed to provide the biologist with an intuitive graphical interface for both definition and analysis of system models. The application makes it possible to navigate the model network and compare its predicted and observed behavior.

::DEVELOPER

Ron Shamir’s lab

:: SCREENSHOTS

::REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 MetaReg

:: MORE INFORMATION

Citation

I. Gat-Viks and R. Shamir.
MetaReg application: a graphical interface for modeling and evaluation of biological systems.
Genome Biology (2008) Vol. 9 No. R1

MIL – Multiple Instance Learning for Protein-DNA Interaction Modeling

MIL

:: DESCRIPTION

MIL(multiple-instance learning) is a novel algorithm, which breaks each DNA sequence into multiple overlapping subsequences and models each subsequence separately, therefore implicitly takes into consideration binding site locations, resulting in both higher accuracy and better interpretability of the models.

::DEVELOPER

Jianhua Ruan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  •  MatLab

:: DOWNLOAD

MIL

:: MORE INFORMATION

Citation

Computational modeling of in vivo and in vitro protein-DNA interactions by multiple instance learning.
Gao Z, Ruan J.
Bioinformatics. 2017 Jul 15;33(14):2097-2105. doi: 10.1093/bioinformatics/btx115.

BDTree 1.01 – Modeling of Gene Expression Regulation

BDTree 1.01

:: DESCRIPTION

BDTree is a Bi-dimensional Regression Tree approach for modeling transcriptional regulation

::DEVELOPER

Jianhua Ruan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  •  Java

:: DOWNLOAD

  BDTree

:: MORE INFORMATION

Citation

Bioinformatics. 2006 Feb 1;22(3):332-40. Epub 2005 Nov 22.
A bi-dimensional regression tree approach to the modeling of gene expression regulation.
Ruan J, Zhang W.

ProtMod – Protein Modeling Server

ProtMod

:: DESCRIPTION

ProtMod is a protein modeling server. Its task is to predicts 3-dimensional structures of proteins based on their sequences. Instead of generating only one model for a given protein, ProtMod produces a list of protein models and orders them by different model evaluation scores.

::DEVELOPER

Godzik Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser
:: DOWNLOAD

 NO

:: MORE INFORMATION

Fitmunk – Improving Protein Structures by accurate, automatic Modeling of Side-chain Conformations

Fitmunk

:: DESCRIPTION

Fitmunk provides a framework for fitting conformations on a fixed backbone into electron density.

::DEVELOPER

Minor Lab at University of Virginia

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Fitmunk: improving protein structures by accurate, automatic modeling of side-chain conformations.
Porebski PJ, Cymborowski M, Pasenkiewicz-Gierula M, Minor W.
Acta Crystallogr D Struct Biol. 2016 Feb;72(Pt 2):266-80. doi: 10.1107/S2059798315024730.

MODELLER 9.23 – Comparative Protein Structure Modeling

MODELLER 9.23

:: DESCRIPTION

MODELLER is used for homology or comparative modeling of protein three-dimensional structures. The user provides an alignment of a sequence to be modeled with known related structures and MODELLER automatically calculates a model containing all non-hydrogen atoms. MODELLER implements comparative protein structure modeling by satisfaction of spatial restraints, and can perform many additional tasks, including de novo modeling of loops in protein structures, optimization of various models of protein structure with respect to a flexibly defined objective function, multiple alignment of protein sequences and/or structures, clustering, searching of sequence databases, comparison of protein structures, etc

::DEVELOPER

Andrej Sali Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX

:: DOWNLOAD

  MODELLER

:: MORE INFORMATION

Citation

Methods Mol Biol. 2014;1137:1-15. doi: 10.1007/978-1-4939-0366-5_1.
Protein structure modeling with MODELLER.
Webb B1, Sali A.

N. Eswar, M. A. Marti-Renom, B. Webb, M. S. Madhusudhan, D. Eramian, M. Shen, U. Pieper, A. Sali.
Comparative Protein Structure Modeling With MODELLER.
Current Protocols in Bioinformatics, John Wiley & Sons, Inc., Supplement 15, 5.6.1-5.6.30, 2006.

Flux Simulator 1.2.1 – Modeling RNA-Seq Experiments

Flux Simulator 1.2.1

:: DESCRIPTION

The Flux Simulator aims at modeling RNA-Seq experiments in silico: sequencing reads are produced from a reference genome according annotated transcripts.

::DEVELOPER

Micha Sammeth

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 Flux Simulator

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2012 Nov 1;40(20):10073-83. doi: 10.1093/nar/gks666. Epub 2012 Sep 7.
Modelling and simulating generic RNA-Seq experiments with the flux simulator.
Griebel T, Zacher B, Ribeca P, Raineri E, Lacroix V, Guigó R, Sammeth M.