SelfAT-Fold – Protein Fold Recognition

SelfAT-Fold

:: DESCRIPTION

selfAT-fold: protein fold recognition based on residue-based and motif-based self-attention networks

::DEVELOPER

Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

SelfAT-Fold

:: 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.

FoldHSphere – Deep Hyperspherical Embeddings for Protein Fold Recognition

FoldHSphere

:: DESCRIPTION

FoldHSphere is a method to learn a better fold embedding space through a two-stage training procedure.

::DEVELOPER

Amelia Villegas-Morcillo

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
:: DOWNLOAD

FoldHSphere

:: 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.

JabberDock – Protein Docking using a density-based descriptor for Atoms Charge and Dynamics

JabberDock

:: DESCRIPTION

JabberDock tackles the problem of protein-protein docking while accommodating for rearrangements upon binding including side chain reorientations and backbone flexibility.

::DEVELOPER

Degiacomi Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Python

:: DOWNLOAD

JabberDock

:: 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.

Biobox – Toolbox for Biomolecular Modelling

Biobox

:: DESCRIPTION

Biobox is a Python-based toolbox facilitating the implementation of biomolecular modelling methods.

::DEVELOPER

Degiacomi Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Python

:: DOWNLOAD

Biobox

:: 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.

CNSsolve 1.3 – X-ray Crystallography Suite

CNSsolve 1.3

:: DESCRIPTION

CNSsolve (Crystallography & NMR System or CNS) is an X-ray crystallography suite used for refinement, phasing, and molecular replacement

::DEVELOPER

CNSsolve Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 CNSsolve

:: MORE INFORMATION

Citation:

A.T. Brunger,
Version 1.2 of the Crystallography and NMR System,
Nature Protocols 2, 2728-2733 (2007).

WHAT IF 8.3 – Protein Structure Analysis program

WHAT IF 8.3

:: DESCRIPTION

WHAT IF is a versatile protein structure analysis program that can be used for mutant prediction, structure verification, molecular graphics, etc.

::DEVELOPER

Gert Vriend

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 WHAT IF

:: MORE INFORMATION

Citation

G.Vriend,
WHAT IF: A molecular modeling and drug design program.
J Mol Graph. 1990 Mar;8(1):52-6, 29.

ModeRNA 1.7.1 – Comparative RNA 3D Modeling

ModeRNA 1.7.1

:: 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

Bujnicki Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

ModeRNA

:: 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

FiltRest3D – Filtering Protein Models by Fuzzy Restraints

FiltRest3D

:: 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.)

FiltRest3D Web Server

::DEVELOPER

Bujnicki Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

FiltRest3D

:: 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

Raster3D 3.0-7 – Generate High Quality Raster Images of Proteins or other Molecules

Raster3D 3.0-7

:: 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

Raster3D Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsx/Linux/Windows

:: DOWNLOAD

  Raster3D

:: MORE INFORMATION

Citation

Merritt, Ethan A. and Bacon, David J. (1997).
Raster3D: Photorealistic Molecular Graphics
Methods in Enzymology 277, 505-524.

LIGPLOT 4.5.3 / LIGPLOT+ 2.2 – Plot Schematic Diagrams of Protein-ligand Interactions

LIGPLOT 4.5.3 / LIGPLOT+ 2.2

:: 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

Roman Laskowski

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 LIGPLOT  / LIGPLOT+

:: 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.