M4T 3.0 – Comparative Protein Structure Modeling

M4T 3.0

:: DESCRIPTION

M4T, Multiple Mapping Method with Multiple Templates, is a fully automated comparative protein structure modeling server. The novelty of M4T resides in two of its major modules, Multiple Templates (MT) and Multiple Mapping Method (MMM).

::DEVELOPER

Bioinformatics Lab :: IBERS :: Aberystwyth University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Server

:: DOWNLOAD

:: MORE INFORMATION

Citation

J Struct Funct Genomics. 2009 Mar;10(1):95-9. doi: 10.1007/s10969-008-9044-9. Epub 2008 Nov 5.
Improved scoring function for comparative modeling using the M4T method.
Rykunov D1, Steinberger E, Madrid-Aliste CJ, Fiser A.

Bioinformatics. 2007 Oct 1;23(19):2558-65. Epub 2007 Sep 6.
Comparative protein structure modeling by combining multiple templates and optimizing sequence-to-structure alignments.
Fernandez-Fuentes N1, Rai BK, Madrid-Aliste CJ, Fajardo JE, Fiser A.

RLooM – RNA Loop Modeling

RLooM

:: DESCRIPTION

RLooM is a web application for homology-based modeling of RNA loops utilizing template structures extracted from the PDB. RLooM allows the insertion and replacement of loop structures of a desired sequence into an existing RNA structure. Furthermore, a comprehensive database of loops in RNA structures can be accessed through the web interface.

::DEVELOPER

Max Planck Institute for Molecular Plant Physiology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Modeling RNA loops using sequence homology and geometric constraints.
Schudoma C, May P, Walther D.
Bioinformatics. 2010 Jul 1;26(13):1671-2. Epub 2010 Apr 28.

BioNet Reasoning – Modeling Biological Systems

BioNet Reasoning

:: DESCRIPTION

BioNet Reasoning is a command line application for modeling biological systems. It allows to reason, i.e. predict, explain, and plan, about biological systems that are described in the action language C_TAID.

::DEVELOPER

Max Planck Institute for Molecular Plant Physiology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / MacOsX
Java

:: DOWNLOAD

BioNet Reasoning

:: MORE INFORMATION

Repertoire Builder – High-throughput structural modeling for B-cell and T-cell receptors

Repertoire Builder

:: DESCRIPTION

Repertoire Builder (earlier Kotai Antibody Builder) is a method for generating atomic-resolution, three-dimensional models of B cell receptors (BCRs) or T cell receptors (TCRs) from their amino acid sequences.

::DEVELOPER

Department of Genome Informatics; Research Institute for Microbial Diseases; Osaka University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Schritt, et al.;
Repertoire Builder: high-throughput structural modeling of B and T cell receptors
Molecular Systems Design & Engineering; 2019

Kotai Antibody Builder: Automated, high-resolution structural modeling of antibodies.
Yamashita K, Ikeda K, Amada K, Liang S, Tsuchiya Y, Nakamura H, Shirai H, Standley DM.
Bioinformatics. 2014 Jul 26. pii: btu510.

XSTREAM – Variable Sequence Tandem Repeats Extraction and Architecture Modeling

XSTREAM

:: DESCRIPTION

XSTREAM is a rapid and powerful algorithm for identifying perfect and degenerate tandem repeat motifs in protein (and nucleotide) sequence data. XSTREAM also effectively models the architecture of repetitive domains in tandem repeat proteins and eliminates motif redundancy to identify “fundamental” tandem repeat patterns.

::DEVELOPER

Newman Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2007 Oct 11;8:382.
XSTREAM: a practical algorithm for identification and architecture modeling of tandem repeats in protein sequences.
Newman AM, Cooper JB.

SignalSpider – Probabilistic Modeling and Pattern Discovery on Multiple Normalized ChIP-Seq Signal Profile

SignalSpider

:: DESCRIPTION

SignalSpider is a probabilistic model for deciphering the combinatorial binding of DNA-binding proteins. The model (SignalSpider) aims at modeling and extracting patterns from multiple ChIP-Seq profiles.

::DEVELOPER

Ka-Chun Wong

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX / Windows
MCR (Matlab Compiler Runtime)

:: DOWNLOAD

SignalSpider

:: MORE INFORMATION

Citation

SignalSpider: Probabilistic Pattern Discovery on Multiple Normalized ChIP-Seq Signal Profiles.
Wong KC, Li Y, Peng C, Zhang Z.
Bioinformatics. 2014 Sep 5. pii: btu604.

GraphProt 1.1.4 – Modeling Binding preferences of RNA-binding Proteins

GraphProt 1.1.4

:: DESCRIPTION

GraphProt can be used for modeling binding preferences of RNA-binding proteins from high-throughput experiments such as CLIP-seq and RNAcompete.

::DEVELOPER

Chair for Bioinformatics Freiburg

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Perl

:: DOWNLOAD

GraphProt

:: MORE INFORMATION

Citation

Genome Biol. 2014 Jan 22;15(1):R17. [Epub ahead of print]
GraphProt: modeling binding preferences of RNA-binding proteins.
Maticzka D, Lange SJ, Costa F, Backofen R.

AutoChrom3D v1 – Modeling and Visualization the 3D Structure of Human or Mouse Chromatin

AutoChrom3D v1

:: DESCRIPTION

AutoChrom3D was built for modeling and visualization the 3D structure of human or mouse chromatin. The 3D structure of chromatin is calculated and generated based on HiC data.

::DEVELOPER

PENG Cheng (email: pengcheng@mail.hzau.edu.cn).

:: SCREENSHOTS

n/a

:: REQUIREMENTS

Linux
Perl

:: DOWNLOAD

AutoChrom3D

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2013 Oct;41(19):e183. doi: 10.1093/nar/gkt745. Epub 2013 Aug 21.
The sequencing bias relaxed characteristics of Hi-C derived data and implications for chromatin 3D modeling.
Peng C1, Fu LY, Dong PF, Deng ZL, Li JX, Wang XT, Zhang HY.

LipidWrapper 1.15 – Lipid Bilayer Modeling

LipidWrapper 1.15

:: DESCRIPTION

LipidWrapper is capable of creating curved membrane models with geometries derived from various possible sources, both experimental and theoretical. We are hopeful that this utility will be a useful tool for the computational-biology community.

::DEVELOPER

Durrant Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows/ MacOsX
Python

:: DOWNLOAD

LipidWrapper

:: MORE INFORMATION

Citation

PLoS Comput Biol, 10 (7), e1003720 2014 Jul 17 eCollection Jul 2014
LipidWrapper: An Algorithm for Generating Large-Scale Membrane Models of Arbitrary Geometry
Jacob D Durrant , Rommie E Amaro

FALC-Loop – Protein Loop Modeling Server

FALC-Loop

:: DESCRIPTION

FALC(Fragment Assembly and Loop Closure) is an internet server for protein loop modeling.

::DEVELOPER

Lab of Computational Biology and Biomolecular Engineering, Seoul National University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

FALC

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W210-4. doi: 10.1093/nar/gkr352. Epub 2011 May 16.
The FALC-Loop web server for protein loop modeling.
Ko J1, Lee D, Park H, Coutsias EA, Lee J, Seok C.