Tag: Loop

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

 NO

:: 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.

CTCF-MP – Predicting CTCF-mediated Chromatin Loops

CTCF-MP

:: DESCRIPTION

CTCF-MP predicts if a convergent CTCF motif pair is able to form a chromatin loop using sequence-level features.

::DEVELOPER

Ma Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Python

:: DOWNLOAD

CTCF-MP

:: MORE INFORMATION

Citation

Bioinformatics. 2018 Jul 1;34(13):i133-i141. doi: 10.1093/bioinformatics/bty248.
Predicting CTCF-mediated chromatin loops using CTCF-MP.
Zhang R, Wang Y, Yang Y, Zhang Y, Ma J.

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.

LoopTK 2.0.1 – Protein Loop Kinematic Toolkit

LoopTK 2.0.1

:: DESCRIPTION

LoopTK (Protein Loop Kinematic Toolkit)is a C++ based object-oriented toolkit which models the kinematics of a protein chain and provides methods to explore its motion space. In LoopTK, a protein chain is modeled as a robot manipulator with bonds acting as arms and the dihedral degree of freedoms acting as joints. LoopTK is designed specifically to model the kinematics of protein loops, but it can be used to analyze the motion of any part of the protein chain. LoopTK provides methods for sampling the conformation space of protein loops as well as the self motion space of a loop. Example applications for LoopTK include x-ray crystallography, homology modeling, and drug design.

::DEVELOPER

LoopTK Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 LoopTK

:: MORE INFORMATION

Citation

P. Yao, A. Dhanik, N. Marz, R. Propper, C. Kou, G. Liu, H. van den Bedem, J.C. Latombe, I. Halperin-Landsberg, R.B. Altman.
“Efficient Algorithms to Explore Conformation Spaces of Flexible Protein Loops“,
IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 5, pp. 534-545, 2008. (2008)