Tag: Atom

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.

ATOM – Association Test via Optimally-weighted Markers

ATOM

:: DESCRIPTION

ATOM is a software of powerful gene-based Association Test by combining Optimally Weighted Markers within a genomic region. Due to variation in linkage disequilibrium, different markers often associate with the trait of interest at different levels.

::DEVELOPER

Chun Li, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 ATOM

:: MORE INFORMATION

Citation

Li M, Wang K, Grant SF, Hakonarson H, Li C (2009)
ATOM: A powerful gene-based association test by combining optimally weighted markers.
Bioinformatics 25:497-503 (PMID: 19074959)

 

DEPTH 2.8.7 – Measure Extent of Atom/Residue Burial within Protein

DEPTH 2.8.7

:: DESCRIPTION

Depth measures the extent of atom/residue burial within a protein. It correlates with properties such as protein stability, hydrogen exchange rate, protein–protein interaction hot spots, post-translational modification sites and sequence variability.

::DEVELOPER

Bioinformatics Institute of Singapore.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 DEPTH

:: MORE INFORMATION

Citation:

Kuan Pern Tan; Raghavan Varadarajan; M. S. Madhusudhan
DEPTH: a web server to compute depth and predict small-molecule binding cavities in proteins
Nucleic Acids Research 2011; doi: 10.1093/nar/gkr356

SOESA 0.21b – Structure Optimization and Evaluation using Separations of Atoms

SOESA 0.21b

:: DESCRIPTION

Soesa is a program for use in evaluating and refining atomic models of protein structures. The program calculates an estimated prior probability of the interatomic distances in the structure by reference to an interatomic distance probability density function (PDF) database compiled from known structures. It also calculates derivatives with respect to atomic position vectors for use in molecular dynamics simulations and structure refinement.

::DEVELOPER

Michael Wall

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SOESA

:: MORE INFORMATION

Citation

Michael E. Wall, Shankar Subramaniam, and George N. Phillips, Jr.
Protein structure determination using a database of interatomic distance probabilities. 1999.
Protein Science 12:2720-27.

MapVol 1.1 – Awk Script to Assign Volume by Atom

MapVol 1.1

:: DESCRIPTION

Mapvol is an awk script which reads a PDB file and tries to assign a volume to each atom based on residue and atom names. The output is a table, listing the volume and the atomic coordinates, which can be contoured with Kin3Dcont to show the distribution of atomic volume in a protein.

::DEVELOPER

Richardson Lab

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

:: DOWNLOAD

MapVol

:: MORE INFORMATION

MapVol is free software available under the terms of its own BSD-style license.

AtVol 1.2 – Atomic Volume Calculation

AtVol 1.2

:: DESCRIPTION

AtVol performs atomic volume calculations by separating each atom from neighboring atoms where their van der Waals spheres join and performing Monte Carlo integration to estimate the volume.

::DEVELOPER

Richardson Lab

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Linux/ MacOsX/SGI-irix/Sun-SPARC

:: DOWNLOAD

AtVol

:: MORE INFORMATION

AtVol is free software available under the terms of its own BSD-style license.