SCWRL pipeline

SCWRL specifications

Information


Unique identifier OMICS_15563
Name SCWRL
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input data A protein backbone, with or without sidechains, cofactors, or solvent.
Input format PDB
Output data Backbone with predicted coordinates for the sidechains.
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Version 4.0
Stability Stable
Maintained Yes

Versioning


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Maintainer


  • person_outline Roland Dunbrack Jr <>

Publications for SCWRL

SCWRL IN pipelines

 (6)
2017
PMCID: 5419745
PMID: 28398197
DOI: 10.7554/eLife.16059.028

[…] the system using a stochastic velocity rescaling (bussi et al., 2007). the starting conformations were taken from the available nmr structures (pdb code 1kbh and 2c52) and mutated accordingly using scwrl4 (krivov et al., 2009). the structures were solvated with 5000 water molecules and ions were added to neutralize the total charge. two preliminary 100 ns long simulations were run […]

2017
PMCID: 5585393
PMID: 28874689
DOI: 10.1038/s41598-017-09654-8

[…] with a database approach and are then adapted to the environment using ccd76 and a final candidate gets selected using statistical potentials of mean force. the sidechain modelling is inspired by scwrl477. a final energy minimization is performed using the openmm molecular mechanics library78. each model is annotated with the qs-score to the native structure and the set of features described […]

2015
PMCID: 4519324
PMID: 26222439
DOI: 10.1371/journal.pone.0134506

[…] mean values., the structural model of apo-akr1b15 was obtained from the akr1b10 ternary complex crystallographic structure (pdb id: 1zua), used as a template for homology modeling, by running the scwrl program [28]. because of the high sequence identity (92%) between the two proteins, the approach that keeps invariant the conformation of the conserved residues was adopted. the flexibility […]

2015
PMCID: 4519324
PMID: 26222439
DOI: 10.1371/journal.pone.0134506

[…] with the aim to compare the substrate-binding site of akr1b15 with that of akr1b10, and upon unsuccessful attempts of protein crystallization, a 3d homology model of akr1b15 was built (fig 4a). the scwrl server was chosen, as it is designed specifically for predicting side-chain conformations, provided a fixed backbone usually obtained from an experimental structure. in practical terms, […]

2013
PMCID: 3705615
PMID: 23847399
DOI: 10.6026/97320630009456

[…] [15] that generate a 3-d model by satisfaction of spatial restraints. the models were further refined by loop modelling, side chain modelling and energy minimization with the aid of modeler9v8, scwrl-4.0 [16] and swiss- pdbviewer4.0 gromacs96 program [17], respectively for getting more optimized and energetically favoured structures. structure analysis and verification server (saves) […]

SCWRL institution(s)
Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA, USA; Moscow Engineering Physics Institute (MEPHI), Moscow, Russia
SCWRL funding source(s)
This work was funded by NIH grants R01 HG02302, R01 GM84453, and P20 GM76222.

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