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.

Vienna+P – Modeling the interplay of Single-stranded Binding Proteins and Nucleic Acid Secondary Structure

Vienna+P

:: DESCRIPTION

Vienna+P is a tool for predicting nucleic acid secondary structure in the presence of single-stranded binding proteins, and implement it as an extension of the Vienna RNA Package.

::DEVELOPER

Ralf Bundschuh’s Statistical Physics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Vienna+P

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Jan 1;26(1):61-7. doi: 10.1093/bioinformatics/btp627. Epub 2009 Nov 4.
Modeling the interplay of single-stranded binding proteins and nucleic acid secondary structure.
Forties RA1, Bundschuh R.

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

Prof. Ron Shamir’s Computational Genomics Group at Tel Aviv University.

:: 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

PyRy3D 4.2.0 – Modeling of large Macromolecular Complexes

PyRy3D 4.2.0

:: DESCRIPTION

PyRy3D is a software tool for modeling of structures for large macromolecular complexes. It uses Monte Carlo simulation in order to sample conformational space and to identify the best fit complex components structures into a density map of a whole complex with the use of distance restraints derived from experiments.The components (proteins, nucleic acids and any other type of physical objects including e.g. solid surfaces) can be represented as rigid bodies (e.g. based on atomic coordinates of structures determined experimentally or modeled computationally) or as flexible shapes (e.g. for parts, whose structure is dynamic or unknown). The model building procedure applies a Monte Carlo approach to sample the space of solutions. Spatial restraints are used to define components interacting with each other, and a a simple scoring function is applied to pack them tightly into contours of the entire complex (e.g. cryoEM density maps). This approach enables the construction of low-resolution models even for very large macromolecular complexes with components of unknown 3D structure, such as human mitochondrial RNA polymerase gamma.

::DEVELOPER

Bujnicki lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python
  • BioPython
  • Numpy

:: DOWNLOAD

 PyRy3D

:: MORE INFORMATION

EPISIM 1.5.2 – Multi-Scale Modeling and Simulation Platform

EPISIM 1.5.2

:: DESCRIPTION

The EPISIM Platform provides the two ready-to-use and easy-to-install software systems EPISIM Modeller and EPISIM Simulator. EPISIM Modeller enables graphical multi-scale modeling of cellular behaviour in a multicellular context using process diagrams. The graphical cell behavioral models are automatically translated into executable code. This code can be loaded with EPISIM Simulator to conduct either a 2D or a 3D tissue simulation.

::DEVELOPER

The TIGA Center (TISSUE IMAGING AND ANALYSIS CENTER)

:: SCREENSHOTS

EPISIM

:: REQUIREMENTS

  •  Linux /Windows/MacOsX

:: DOWNLOAD

 EPISIM

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jan 15;29(2):223-9. doi: 10.1093/bioinformatics/bts659. Epub 2012 Nov 18.
Bridging the scales: semantic integration of quantitative SBML in graphical multi-cellular models and simulations with EPISIM and COPASI.
Sütterlin T1, Kolb C, Dickhaus H, Jäger D, Grabe N.