STAR3D 1.2 / WebSTAR3D / LocalSTAR3D v1 – Alignment of RNA 3D Structures

STAR3D 1.2 / WebSTAR3D / LocalSTAR3D v1

:: DESCRIPTION

STAR3D is a stack-based RNA 3D structural alignment tool.

WebSTAR3D is a web server for RNA 3D structure alignment

LocalSTAR3D is a program for the local alignment of RNA 3D structures.

::DEVELOPER

UCF Computational Biology and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

STAR3D / LocalSTAR3D

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2015 Nov 16;43(20):e137. doi: 10.1093/nar/gkv697. Epub 2015 Jul 15.
STAR3D: a stack-based RNA 3D structural alignment tool.
Ge P, Zhang S.

Bioinformatics. 2016 Dec 1;32(23):3673-3675. Epub 2016 Aug 6.
WebSTAR3D: a web server for RNA 3D structural alignment.
Holzhauser E, Ge P, Zhang S

RNAssess – Quality Assessment of RNA 3D Structures

RNAssess

:: DESCRIPTION

RNAssess is a computational server for comparison of RNA 3D models with the reference structure and for discrimination between the correct and incorrect models.

::DEVELOPER

The Bioinformatics Group, Poznan University of Technology.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

RNAssess-a web server for quality assessment of RNA 3D structures.
Lukasiak P, Antczak M, Ratajczak T, Szachniuk M, Popenda M, Adamiak RW, Blazewicz J.
Nucleic Acids Res. 2015 Jun 11. pii: gkv557.

i3Drefine / 3Drefine – Protein 3D Structure Refinement

i3Drefine / 3Drefine

:: DESCRIPTION

i3Drefine is a completely automated and computationally efficient protein 3D structure refinement method which based on an iterative and highly convergent energy minimization algorithm with a powerful all-atom composite physics and knowledge-based force fields and hydrogen bonding (HB) network optimization technique.

3Drefine: protein structure refinement server

::DEVELOPER

Dr. Jianlin Cheng’

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

i3Drefine

:: MORE INFORMATION

Citation

3Drefine: an interactive web server for efficient protein structure refinement.
Bhattacharya D, Nowotny J, Cao R, Cheng J.
Nucleic Acids Res. 2016 Apr 29. pii: gkw336

3Drefine: consistent protein structure refinement by optimizing hydrogen bonding network and atomic-level energy minimization.
Bhattacharya D, Cheng J.
Proteins. 2013 Jan;81(1):119-31. doi: 10.1002/prot.24167.

PLoS One. 2013 Jul 19;8(7):e69648. doi: 10.1371/journal.pone.0069648. Print 2013.
i3Drefine software for protein 3D structure refinement and its assessment in CASP10.
Bhattacharya D1, Cheng J.

ProFunc – Predicting Protein Function from 3D Structure

ProFunc

:: DESCRIPTION

ProFunc helps identify the likely biochemical function of a protein from its three-dimensional structure. It uses both sequence- and structure-based methods to try to provide clues as the the protein’s likely or possible function. Often, where one method fails to provide any functional insight another may be more helpful.

::DEVELOPER

Thornton group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

ProFunc: a server for predicting protein function from 3D structure.
Laskowski RA, Watson JD, Thornton JM.
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W89-93.

BARNACLE 0.21 – RNA 3D Structure Prediction

BARNACLE 0.21

:: DESCRIPTION

BARNACLE (BAyesian network model of RNA using Circular distributions and maximum Likelihood Estimation) is a Python library for RNA 3D structure prediction. It can be used for probabilistic sampling of RNA structures that are compatible with a given nucleotide sequence and that are RNA like on a local length scale.

::DEVELOPER

The Bioinformatics Centre , University of Copenhagen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ MacOsX/ Windows
Python

:: DOWNLOAD

BARNACLE

:: MORE INFORMATION

Citation:

Frellsen J, Moltke I, Thiim M, Mardia KV, Ferkinghoff-Borg J, HamelryckT (2009)
A Probabilistic Model of RNA Conformational Space.
PLoS Comput Biol 5(6): e1000406.

SwarmDock – Webservice for Generating 3D Structures of Protein-protein complexes

SwarmDock

:: DESCRIPTION

SwarmDock is a server for flexible protein-protein docking.

::DEVELOPER

Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute

:: SCREENSHOTS

N/A

::REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

SwarmDock: a server for flexible protein-protein docking.
Torchala M, Moal IH, Chaleil RA, Fernandez-Recio J, Bates PA.
Bioinformatics. 2013 Mar 15;29(6):807-9. doi: 10.1093/bioinformatics/btt038. Epub 2013 Jan 23.

Swiss-PdbViewer 4.1 – Analyze Several Proteins 3D Structure at the Same Time

Swiss-PdbViewer 4.1

:: DESCRIPTION

DeepView (Swiss-PdbViewer) is an application that provides a user friendly interface allowing to analyze several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface.

::DEVELOPER

the Swiss Institute of Bioinformatics (SIB) at the Structural Bioinformatics Group at the Biozentrum in Basel.

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Mac / Linux

:: DOWNLOAD

DeepView

:: MORE INFORMATION

Citation:

Guex, N. and Peitsch, M.C. (1997)
SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling.
Electrophoresis 18, 2714-2723.

DipoCoup 1.0 – 3D-structure Homology Comparison

DipoCoup 1.0

:: DESCRIPTION

DipoCoup is presented that allows to search the protein data bank for proteins which have a three dimensional fold that is at least partially homologous to a protein under investigation. The program offers a fast and comfortable tool analyzing and handling dipolar coupling data. Powder pattern can be visualized, theoretical dipolar couplings can be calculated for a given structure and alignment and experimental values can be fitted over one or even a set of structures in order to perform e. g. a 3D homology search for proteins. A well distributed database extracted from the PDB is available. Moreover restraint files for XPlor and CNS calculations can be written.

::DEVELOPER

Jens Meiler

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

DipoCoup

:: MORE INFORMATION

Citation

J Biomol NMR. 2000 Aug;17(4):283-94.
DipoCoup: A versatile program for 3D-structure homology comparison based on residual dipolar couplings and pseudocontact shifts.
Meiler J, Peti W, Griesinger C.

FT-COMAR – Fault Tolerance Reconstruction of 3D Structure from Protein Contact Maps

FT-COMAR

:: DESCRIPTION

FT-COMAR ( Fault Tolerant COntact MAp Reconstruction) implements a heuristic procedure for recovering a set of 3D coordinates from an incomplete contact map.

FT-COMAR Online Version

::DEVELOPER

Bioinformatics group, Department of Computer Science, University of Bologna

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / MacOsX

:: DOWNLOAD

FT-COMAR

:: MORE INFORMATION

Citation

FT-COMAR: fault tolerant three-dimensional structure reconstruction from protein contact maps.
Vassura M, Margara L, Di Lena P, Medri F, Fariselli P, Casadio R.
Bioinformatics. 2008 May 15;24(10):1313-5. Epub 2008 Apr 1.

CryoBayes beta – Bayesian method for Inferring 3D structure of Macromolecules

CryoBayes beta

:: DESCRIPTION

CryoBayes is a Bayesian method for inferring 3D structure of macromolecules imaged by Electron Cryo-Microscopy experiments. We encourage experimental Structural Biologists to download and try our code. We hope that our technique will be useful as a method of automatically generating intial models given only class average images.

::DEVELOPER

Lilien Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows

:: DOWNLOAD

CryoBayes

:: MORE INFORMATION

Citation:

Jaitly, N., Brubaker, M.A., Rubinstein, J.L. and Lilien, R.H.
A Bayesian Method for 3-D Macromolecular Structure Inference using Class Average Images from Single Particle Electron Microscopy,
Bioinformatics, 26(19):2406-15 (2010).