MotiveValidator 1.1.15.8.8e – Validate Ligand and Residue Structure in Biomolecular Complexes

MotiveValidator 1.1.15.8.8e

:: DESCRIPTION

MotiveValidator is a platform for a set of applications designed to help you determine whether a residue or a ligand in a biomolecule or biomolecular complex is structurally complete and correctly annotated according to its models stored in the wwPDB Chemical Component Dictionary (wwPDB CCD).

::DEVELOPER

MotiveValidator team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

MotiveValidator

:: MORE INFORMATION

Citation

MotiveValidator: interactive web-based validation of ligand and residue structure in biomolecular complexes.
Vařeková RS, Jaiswal D, Sehnal D, Ionescu CM, Geidl S, Pravda L, Horský V, Wimmerová M, Koča J.
Nucleic Acids Res. 2014 Jul;42(Web Server issue):W227-33. doi: 10.1093/nar/gku426.

POPSCOMP v.3.2 – Automated Interaction analysis of Biomolecular Complexes

POPSCOMP v.3.2

:: DESCRIPTION

POPSCOMP is a method to analyse interactions between individual complex components of proteins and/or nucleic acids by calculating the solvent accessible surface area (SASA) buried upon complex formation. It is based on POPS, which calculates SASAs of individual proteins and nucleic acid molecules at atomic (default) and residue (coarse-grained) level.

::DEVELOPER

Fraternali lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/ Linux /MacOsX
R

:: DOWNLOAD

POPSCOMP

:: MORE INFORMATION

Citation

Kleinjung, J, Fraternali, F.
POPSCOMP: An automated interaction analysis of biomolecular complexes.
Nuc. Acids Res. 33:W342-W346, 2005 PMID: 15980485

HADDOCK 2.2 – Docking approach for the Modeling of Biomolecular Complexes

HADDOCK 2.2

:: DESCRIPTION

HADDOCK (High Ambiguity Driven protein-protein DOCKing) is an information-driven flexible docking approach for the modeling of biomolecular complexes. HADDOCK distinguishes itself from ab-initio docking methods in the fact that it encodes information from identified or predicted protein interfaces in ambiguous interaction restraints (AIRs) to drive the docking process. HADDOCK can deal with a large class of modeling problems including protein-protein, protein-nucleic acids and protein-ligand complexes.

Haddock Server

::DEVELOPER

BONVIN LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ MacOsX
Python

:: DOWNLOAD

HADDOCK

:: MORE INFORMATION

Citation

The HADDOCK2.2 web server: User-friendly integrative modeling of biomolecular complexes.
van Zundert GC, Rodrigues JP, Trellet M, Schmitz C, Kastritis PL, Karaca E, Melquiond AS, van Dijk M, de Vries SJ, Bonvin AM.
J Mol Biol. 2015 Sep 24. pii: S0022-2836(15)00537-9. doi: 10.1016/j.jmb.2015.09.014

Cyril Dominguez, Rolf Boelens and Alexandre M.J.J. Bonvin (2003).
HADDOCK: a protein-protein docking approach based on biochemical and/or biophysical information.
J. Am. Chem. Soc. 125, 1731-1737

S.J. de Vries, A.D.J. van Dijk, M. Krzeminski, M. van Dijk, A. Thureau, V. Hsu, T. Wassenaar and A.M.J.J. Bonvin
“HADDOCK versus HADDOCK: New features and performance of HADDOCK2.0 on the CAPRI targets.”
Proteins: Struc. Funct. & Bioinformatic 69, 726-733 (2007).

Dynamical Network Analysis – Characterizing Allosteric Signalling through Biomolecular Complexes

Dynamical Network Analysis

:: DESCRIPTION

Dynamical Network Analysis is a method of characterizing allosteric signalling through biomolecular complexes.

::DEVELOPER

The Luthey-Schulten Group – University of Illinois at Urbana-Champaign

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/Linux/MacOsX

:: DOWNLOAD

Dynamical Network Analysis

:: MORE INFORMATION

Citation

Dynamical networks in tRNA:protein complexes.
Sethi A, Eargle J, Black AA, Luthey-Schulten Z.
Proc Natl Acad Sci U S A. 2009 Apr 21;106(16):6620-5