:: DESCRIPTION
Surface Diver allows describing, comparing, and classifying proteins according to their physicochemical properties without the need of prior 3D structural alignment.
::DEVELOPER
Biomolecular Machines Laboratory
:: SCREENSHOTS
n/a
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Maciej Dlugosz, Joanna Trylska
Electrostatic similarity of proteins: Application of 3D spherical harmonic decomposition,
J. Chem. Phys., 129:015103, 2008
:: 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
ProtRe-CN is a novel ranking method for protein remote homology detection by combining classification methods and network methods via Learning to Rank.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Shao J, Chen J, Liu B.
ProtRe-CN: Protein Remote Homology Detection by Combining Classification Methods and Network Methods via Learning to Rank.
IEEE/ACM Trans Comput Biol Bioinform. 2021 Aug 30;PP. doi: 10.1109/TCBB.2021.3108168. Epub ahead of print. PMID: 34460380.
:: DESCRIPTION
DeepIDP-2L is a web server for protein intrinsically disordered region prediction by combining convolutional attention network and hierarchical attention network
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Tang YJ, Pang YH, Liu B.
DeepIDP-2L: protein intrinsically disordered region prediction by combining convolutional attention network and hierarchical attention network.
Bioinformatics. 2021 Dec 2:btab810. doi: 10.1093/bioinformatics/btab810. Epub ahead of print. PMID: 34864847.
:: DESCRIPTION
PClust is a scalable parallel software for detecting dense subgraphs.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
C. Wu, A. Kalyanaraman.
An efficient parallel approach for identifying protein families in large-scale metagenomic data sets.
Proc. ACM/IEEE Supercomputing Conference (SC’08), Austin, TX, November 15-21. pp. 1-10. 2008
:: 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
NucImport is a protein sequence and interaction prediction service designed to determine the nuclear transport of proteins in mouse and yeast. NucImport uses Bayesian networks, recognizes NLSs, links interactions to localization signals and incorporates sequence similarity. NucImport accepts amino acid sequences from user, presented in the FASTA format, and determines the probability of nuclear import as well as the location of nuclear localization signal in the query protein.
::DEVELOPER
Institute for Molecular Bioscience, The University of Queensland
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2011 May 1;27(9):1239-46. Epub 2011 Mar 3.
A probabilistic model of nuclear import of proteins.
Mehdi AM, Sehgal MS, Kobe B, Bailey TL, Bodén M.
:: DESCRIPTION
STRAP, the Software Tool for Rapid Annotation of Proteins, saves you time by automatically annotating a protein list with information that helps you meaningfully interpret your mass spectrometry data.
::DEVELOPER
Cardiovascular Proteomics Center ，BU School of Medicine
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bhatia VN, Perlman DH, Costello CE, McComb ME.
Software tool for researching annotations of proteins: open-source protein annotation software with data visualization.
Analytical Chemistry 2009, 81 (23), 9819-23.
:: DESCRIPTION
Cytoprophet is a project developed by the Laboratory for Computational Life Sciences at the Computer Science Department of the University of Notre Dame. It is a tool to help researchers to infer new potential protein (PPI) and domain (DDI) interactions. It is implemented as a Cytoscape plugin, where users input a set of proteins and retrieve a network of plausible protein and domain interactions with a score. Three algorithms are used for the estimation of PPI/DDI: Maximum Specificity Set Cover (MSSC) Approach, Maximum Likelihood Estimation (MLE) and the Sum-Product Algorithm (SPA) for protein networks.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Chengbang Huang , Faruck Morcos, Simon P. Kanaan, Stefan Wuchty, Danny Z. Chen, and Jesús A. Izaguirre
Predicting Protein-Protein Interactions from Protein Domains Using a Set Cover Approach.
IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol 4 pp. 78-87. Jan-March 2007
:: DESCRIPTION
PSAAM (Protein Sequence Analysis And Modelling) includes many useful features for analysis of structural information from sequence data, cartoons for graphical representation of secondary structures, prediction programs, and prediction aids, a ribosome function for generation of coordinates sets in PDB format (including Header information) for viewing by molecular graphics packages (examples, see also PDVWIN), and a SeqPlot function for plotting secondary structural models (helical cylinders and wheels, coils, etc., with each residue indicated by a circle, color-coded (or coded by line thickness) according to the current physico-chemical index.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
