:: DESCRIPTION
LOCPRED is a tool for local structure prediction from protein sequence using a structural alphabet approach.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
In Silico Biol. 2004;4(3):381-6.
Local backbone structure prediction of proteins.
de Brevern AG1, Benros C, Gautier R, Valadié H, Hazout S, Etchebest C.
:: DESCRIPTION
COMPASS is used for protein backbone resonance assignment from unassigned triple resonance peak lists. Compared to most other software for the same purpose, COMPASS lets the user control the assignment process, enabling supreme accuracy. COMPASS is well suited for the assignment of larger deuterated proteins.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Fast and accurate resonance assignment of small-to-large proteins by combining automated and manual approaches.
Niklasson M, Ahlner A, Andresen C, Marsh JA, Lundström P.
PLoS Comput Biol. 2015 Jan 8;11(1):e1004022. doi: 10.1371/journal.pcbi.1004022.
:: DESCRIPTION
ANGLOR is a machine-learning based algorithm for ab initio prediction of protein backbone torsion angles. For a given amino acid sequence, the real-value backbone torsion angles (phi and psi) for each residue are predicted by the combination of the neural network training and the support vector machine
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: MORE INFORMATION
Citation
PLoS One. 2008;3(10):e3400. doi: 10.1371/journal.pone.0003400. Epub 2008 Oct 15.
ANGLOR: a composite machine-learning algorithm for protein backbone torsion angle prediction.
Wu S1, Zhang Y.
:: DESCRIPTION
BkTree is an utility capable of predicting all familites of RNA nucleotide interactions, including base-base, base-phosphate, base-ribose, and base-stacking interactions, from the input query sequence (along with predicted or known canonical Watson-Crick base pairs).
::DEVELOPER
The RNA-Informatics Research Lab
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Accurate Prediction of RNA Nucleotide Interactions with Backbone k-Tree Model.
Ding L, Xue X, LaMarca S, Mohebbi M, Samad A, Malmberg RL, Cai L.
Bioinformatics. 2015 Apr 16. pii: btv210.
:: DESCRIPTION
RNABC (RNA Backbone Correction) is designed for reducing the steric clashes in dinucleotides of existing RNA backbone structures. It first fixes the phosphate and base positions, which are the clearest parts in X-ray crystallography structure, and then reconstructs the remaining atoms of the dinucleotide using forward kinematics and conjugate gradient method. The input parameters, like bond lengths, bond angles, and sugar pucker types, are from canonical values or specified by users. The output results cluster the possible suite conformations (from base to base) without steric clashes.
::DEVELOPER
Xueyi Wang & Prof. Jack Snoeyink
Richardson Lab
:: SCREENSHOTS
Command Line
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
RNABC is described in X. Wang, G. Kapral, L. Murray, D. Richardson, J. Richardson & J. Snoeyink. “RNABC: forward kinematics to reduce all-atom steric clashes in RNA backbone”. Journal Mathematical Biology (published January 2008, doi: 10.1007/s00285-007-0082)
RNABC is free software available under the terms of its own BSD-style license.
