:: DESCRIPTION
PESS (Protein Empirical Structure Space) is a software of sensitive protein fold recognition using an empirical structure space and 1NN.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Middleton SA, Illuminati J, Kim J.
Complete fold annotation of the human proteome using a novel structural feature space.
Sci Rep. 2017 Apr 13;7:46321. doi: 10.1038/srep46321. PMID: 28406174; PMCID: PMC5390313.
:: DESCRIPTION
selfAT-fold: protein fold recognition based on residue-based and motif-based self-attention networks
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Pang Y, Liu B.
SelfAT-Fold: protein fold recognition based on residue-based and motif-based self-attention networks.
IEEE/ACM Trans Comput Biol Bioinform. 2020 Oct 22;PP. doi: 10.1109/TCBB.2020.3031888. Epub ahead of print. PMID: 33090951.
:: DESCRIPTION
FoldHSphere is a method to learn a better fold embedding space through a two-stage training procedure.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: MORE INFORMATION
Citation
Villegas-Morcillo A, Sanchez V, Gomez AM.
FoldHSphere: deep hyperspherical embeddings for protein fold recognition.
BMC Bioinformatics. 2021 Oct 12;22(1):490. doi: 10.1186/s12859-021-04419-7. PMID: 34641786; PMCID: PMC8507389.
:: DESCRIPTION
COPRED is a web server for the concomitant prediction of fold, molecular function and functional sites at the domain level, based on a methodology for domain molecular function prediction and a resource of domain functional annotations previously developed and benchmarked.
::DEVELOPER
Computational Systems Biology Group (CNB-CSIC)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Bioinformatics. 2013 Jul 15;29(14):1811-2. doi: 10.1093/bioinformatics/btt283. Epub 2013 May 29.
COPRED: prediction of fold, GO molecular function and functional residues at the domain level.
López D1, Pazos F.
:: DESCRIPTION
ORION (Optimized fold RecognitION) is a new fold recognition method based on the pairwise comparison of hybrid profiles that contain evolutionary information from both protein sequence and structure.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Improving protein fold recognition with hybrid profiles combining sequence and structure evolution.
Ghouzam Y, Postic G, de Brevern AG, Gelly JC.
Bioinformatics. 2015 Aug 7. pii: btv462.
:: DESCRIPTION
LFC is a fundamentally different approach by directly modeling count ratios and reveal that bias also affects fold changes severely.
::DEVELOPER
Institut für Informatik, Ludwig-Maximilians-Universität München
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Count ratio model reveals bias affecting NGS fold changes.
Erhard F, Zimmer R.
Nucleic Acids Res. 2015 Jul 8. pii: gkv696.
:: DESCRIPTION
PFP-Pred is an ensemble classifier for protein fold pattern recognition
::DEVELOPER
Computational Systems Biology Group, Shanghai Jiao Tong University
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Hong-Bin Shen and Kuo-Chen Chou,
“Ensemble classifier for protein folding pattern recognition“.
Bioinformatics, 2006, 22: 1717-22.
:: DESCRIPTION
TIM-Finder (Tim-barrel Fold Recognition System) is a computational tool to predict if a query sequence belongs to TIM-barrel protein or not.
::DEVELOPER
Ziding Zhang’s Lab, China Agricultural University
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Struct Biol. 2009 Dec 14;9:73. doi: 10.1186/1472-6807-9-73.
TIM-Finder: a new method for identifying TIM-barrel proteins.
Si JN1, Yan RX, Wang C, Zhang Z, Su XD.
:: DESCRIPTION
RNAFold is a freeware stand-alone program that creates batch files for the FOLD module of the GCG program package. RNAFold allows easy sliding-window analyses of RNA secondary structure by creating batch files with repeated calls to the FOLD module. This program does not calculate RNA folding energies directly.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
