:: DESCRIPTION
PSTP-finder is a software developed in order to analyse a molecular dynamic of a protein structure and highlight time ranges in which a transient pocket could be found around certain aminoacid residues on the protein surface.
::DEVELOPER
SBL (Stuctural Biology Laboratory), University of Siena
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
jsPISA is an interactive web tool for the calculation of macromolecular surfaces and interfaces, assessment of their properties and inference on probable macromolecular assemblies (complexes) from coordinate data, typically delivered by crystallographic X-ray experiment.
:: DEVELOPER
Eugene Krissinel ( eugene.krissinel@stfc.ac.uk.)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation:
Nucleic Acids Res. 2015 Apr 23. pii: gkv314.
Stock-based detection of protein oligomeric states in jsPISA.
Krissinel E
:: DESCRIPTION
ProtPOS is a self-contained, lightweight, and easy-to-use software package for predicting the preferred orientation of protein on a given surface upon initial adsorption.
::DEVELOPER
Computational Biology and Bioinformatics Lab (CBBio)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Ngai JC, Mak PI, Siu SW.
ProtPOS: a python package for the prediction of protein preferred orientation on a surface.
Bioinformatics. 2016 Aug 15;32(16):2537-8. doi: 10.1093/bioinformatics/btw182. Epub 2016 Apr 10. PMID: 27153619; PMCID: PMC4978930.
:: DESCRIPTION
Volarea is a plug-in of the widely spread molecular graphics software Visual Molecular Dynamics (VMD), which allows the calculation of the volume as well as the surface area of any chemical structure. The surface area can be used also to map or calculate the exposed area of the structure to the solvent or to another chemical structure.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Chem Biol Drug Des. 2013 Dec;82(6):743-55. doi: 10.1111/cbdd.12197. Epub 2013 Oct 25.
Volarea – a bioinformatics tool to calculate the surface area and the volume of molecular systems.
Ribeiro JV1, Tamames JA, Cerqueira NM, Fernandes PA, Ramos MJ.
:: DESCRIPTION
CITE-sort conducts auto-gating with CITE-seq ADT data using recursive Gaussian Mixture Model. It is robust against artificial cell types that stem from multiplets. CITE-sort also provides concrete explanations of its internal decision process by constructing a biologically meaningful sort tree.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: MORE INFORMATION
Citation
Lian Q, Xin H, Ma J, Konnikova L, Chen W, Gu J, Chen K.
Artificial-cell-type aware cell-type classification in CITE-seq.
Bioinformatics. 2020 Jul 1;36(Suppl_1):i542-i550. doi: 10.1093/bioinformatics/btaa467. PMID: 32657383; PMCID: PMC7355304.
:: DESCRIPTION
HotSPRing is a web server to predict the host spots in RNA binding proteins (RBPs)
::DEVELOPER
Computational Structural Biology Lab , Indian Institute of Technology Kharagpur
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Probing binding hot spots at protein-RNA recognition sites.
Barik A, Nithin C, Karampudi NB, Mukherjee S, Bahadur RP.
Nucleic Acids Res. 2016 Jan 29;44(2):e9. doi: 10.1093/nar/gkv876.
:: DESCRIPTION
Plots the ROCS for high-throughput class-skewed data, calculates the Volume under the Surface (VUS) and the FDR-Controlled Area Under the Curve (FCAUC), and conducts tests to compare two ROC surfaces. Computes eROC curve and the corresponding AUC for imperfect reference standard.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
PLoS One. 2012;7(7):e40598. doi: 10.1371/journal.pone.0040598.
ROCS: receiver operating characteristic surface for class-skewed high-throughput data.
Yu T
:: DESCRIPTION
SURFace is a programs that calculate solvent accessible surface area and curvature corrected solvent accessible surface area. The accessible surface output is calculated for the whole molecule, per residue, and per atom.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation