:: 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
JabberDock tackles the problem of protein-protein docking while accommodating for rearrangements upon binding including side chain reorientations and backbone flexibility.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Rudden LSP, Degiacomi MT.
Transmembrane Protein Docking with JabberDock.
J Chem Inf Model. 2021 Mar 22;61(3):1493-1499. doi: 10.1021/acs.jcim.0c01315. Epub 2021 Feb 26. PMID: 33635637; PMCID: PMC8041277.
:: DESCRIPTION
Biobox is a Python-based toolbox facilitating the implementation of biomolecular modelling methods.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Rudden LSP, Musson SC, Benesch JLP, Degiacomi MT.
Biobox: a toolbox for biomolecular modelling.
Bioinformatics. 2021 Nov 15:btab785. doi: 10.1093/bioinformatics/btab785. Epub ahead of print. PMID: 34791029.
:: DESCRIPTION
CNSsolve (Crystallography & NMR System or CNS) is an X-ray crystallography suite used for refinement, phasing, and molecular replacement
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
A.T. Brunger,
Version 1.2 of the Crystallography and NMR System,
Nature Protocols 2, 2728-2733 (2007).
:: DESCRIPTION
WHAT IF is a versatile protein structure analysis program that can be used for mutant prediction, structure verification, molecular graphics, etc.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
G.Vriend,
WHAT IF: A molecular modeling and drug design program.
J Mol Graph. 1990 Mar;8(1):52-6, 29.
:: DESCRIPTION
ModeRNA is a program for comparative modeling of RNA 3D structures. It requires a pairwise sequence alignment and a structural template to generate a 3D structural model of the target RNA sequence via either a fully automated or script-based approaches. ModeRNA is capable of handling 115 different nucleotide modifications and bridging gaps using fragments derived from an extensive fragment library.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Magdalena Rother, Kristian Rother, Tomasz Puton and Janusz M. Bujnicki
ModeRNA: a tool for comparative modeling of RNA 3D structure
Nucl. Acids Res.(2011)doi: 10.1093
:: DESCRIPTION
FiltRest3D is a software for scoring and ranking of models according to their agreement with user-defined restraints.Automatic methods for protein structure prediction (fold-recognition, de novo folding, and docking programs) produce large sets of alternative models. These large model sets often include many native-like structures, which are scored as high as false positives. Such native-like models can be more easily identified based on data from experimental analyses used as structural restraints (e.g. identification of nearby residues by crosslinking, chemical modification, site-directed mutagenesis, deuterium exchange coupled with mass spectrometry etc.)
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Michal J. Gajda,Irina Tuszynska1, Marta Kaczor, Anastasia Yu. Bakulina and Janusz M. Bujnicki
FILTREST3D: discrimination of structural models using restraints from experimental data
Bioinformatics (2010) 26 (23): 2986-2987
:: DESCRIPTION
Raster3D is a set of tools for generating high quality raster images of proteins or other molecules. The core program renders spheres, triangles, cylinders, and quadric surfaces with specular highlighting, Phong shading, and shadowing. It uses an efficient software Z-buffer algorithm which is independent of any graphics hardware. Ancillary programs process atomic coordinates from PDB files into rendering descriptions for pictures composed of ribbons, space-filling atoms, bonds, ball+stick, etc. Raster3D can also be used to render pictures composed in other programs such as Molscript in glorious 3D with highlights, shadowing, etc. Output is to pixel image files with 24 bits of color information per pixel.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Merritt, Ethan A. and Bacon, David J. (1997).
“Raster3D: Photorealistic Molecular Graphics”
Methods in Enzymology 277, 505-524.
:: DESCRIPTION
LIGPLOT is a program which plots schematic diagrams of protein-ligand interactions.
LigPlot+ is a graphical front-end to the LIGPLOT and DIMPLOT programs. The plots generated by these programs can be interactively edited on screen, superposed and printed.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Wallace A C, Laskowski R A, Thornton J M (1996).
LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions.
Protein Eng., 8, 127-134.
LigPlot+: multiple ligand-protein interaction diagrams for drug discovery.
Laskowski RA, Swindells MB.
J Chem Inf Model. 2011 Oct 24;51(10):2778-86. Epub 2011 Oct 5.
:: DESCRIPTION
Cn3D is a helper application for your web browser that allows you to view 3-dimensional structures from NCBI’s Entrez retrieval service. Cn3D simultaneously displays structure, sequence, and alignment, and now has powerful annotation and alignment editing features.
What sets Cn3D apart from other software is its ability to correlate structure and sequence information: for example, a scientist can quickly find the residues in a crystal structure that correspond to known disease mutations, or conserved active site residues from a family of sequence homologs. Cn3D displays structure-structure alignments along with their structure-based sequence alignments, to emphasize what regions of a group of related proteins are most conserved in structure and sequence.
Cn3D reads only data files from the MMDB database, not PDB formatted records.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Below is a complete list (with links into Entrez) of all literature cited in the preparation of this tutorial.
