RFPR-IDP – Reduce the False Positive Rates for intrinsically Disordered Protein

RFPR-IDP

:: DESCRIPTION

RFPR-IDP is a new method which trained with data containing ordered proteins. The predictor is constructed based on the combination of Convolution Neural Network (CNN) and Bidirectional Long Short-Term Memory (BiLSTM), in which CNN can capture the local information or motifs of proteins and BiLSTM can learn the long-term dependence information in both directions of proteins. Experimental results show that RFPR-IDP can effectively reduce the false positive rates and accurately predict IDPs from ordered proteins for real world applications.

::DEVELOPER

Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Liu Y, Wang X, Liu B.
RFPR-IDP: reduce the false positive rates for intrinsically disordered protein and region prediction by incorporating both fully ordered proteins and disordered proteins.
Brief Bioinform. 2021 Mar 22;22(2):2000-2011. doi: 10.1093/bib/bbaa018. PMID: 32112084; PMCID: PMC7986600.

IDP-Seq2Seq – Identification of Intrinsically Disordered Proteins and Regions based on Sequence to Sequence Learning

IDP-Seq2Seq

:: DESCRIPTION

IDP-Seq2Seq applied the Sequence to Sequence Learning (Seq2Seq) derived from natural language processing (NLP) to map protein sequences to “semantic space” to reflect the structure patterns with the help of predicted Residue-Residue Contacts (CCMs) and other sequence-based features. Furthermore, the Attention mechanism was employed to capture the global associations between all residue pairs in the proteins.

::DEVELOPER

Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Tang YJ, Pang YH, Liu B.
IDP-Seq2Seq: identification of intrinsically disordered regions based on sequence to sequence learning.
Bioinformatics. 2021 Jan 29;36(21):5177-5186. doi: 10.1093/bioinformatics/btaa667. PMID: 32702119.

KMAD 1.15 – Knowledge Based Multiple Sequence Alignment for Intrinsically Disordered Proteins

KMAD 1.15

:: DESCRIPTION

KMAD was designed to align intrinsically disordered (aka natively unfolded) proteins for the HOPE mutation analysis server.

::DEVELOPER

KAMD Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

KMAD

:: MORE INFORMATION

Citation

KMAD: Knowledge based multiple sequence alignment for intrinsically disordered proteins.
Lange J, Wyrwicz LS, Vriend G.
Bioinformatics. 2015 Nov 14. pii: btv663.