SCWRL protocols

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SCWRL specifications

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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

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Maintainer


  • person_outline Roland Dunbrack Jr <>

Publications for SCWRL

SCWRL in pipelines

 (15)
2018
PMCID: 5893540
PMID: 29636462
DOI: 10.1038/s41467-018-03314-9

[…] in crystal structures were removed. missing backbone atoms were modeled with the program loopy,. missing side chain atoms and side chain reversions to wild-type were modeled with the program scwrl4. disulfide bonds (c71-c159, c74-c146, c77-c166, and c259-c262) and all hydrogen atoms were placed with the gromacs tool pdb2gmx, and the receptor was then energy minimized. the simulated […]

2017
PMCID: 5404884
PMID: 28406899
DOI: 10.1371/journal.pntd.0005539

[…] twenty virtual structural models with modeller 9v10 [], from which we selected the one with the lowest normalized dope-score (zdope, z-score of discrete optimized protein energy). the software scwrl4.0 [] was applied to the selected virtual model to improve protein side-chain conformations and kobamim [] was used to refine the structure. finally the virtual model of smezh2 set domain […]

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

[…] by thermosetting the system using a stochastic velocity rescaling (). the starting conformations were taken from the available nmr structures (pdb code 1kbh and 2c52) and mutated accordingly using scwrl4 (). 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 for each structure […]

2017
PMCID: 5531539
PMID: 28750054
DOI: 10.1371/journal.pone.0181490

[…] infinite cutoff for non-bonded interactions. non-hydrogen atoms were restrained at their crystallographic positions with a harmonic force constant of 5 kcal/(mol.a2)., we used three protocols (sie-scwrl, foldx and rosetta) for modeling mutants and scoring their binding affinities. for each of these protocols, additional refinement of the amber-refined parent structure was carried […]

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

[…] with a database approach and are then adapted to the environment using ccd and a final candidate gets selected using statistical potentials of mean force. the sidechain modelling is inspired by scwrl4. a final energy minimization is performed using the openmm molecular mechanics library. each model is annotated with the qs-score to the native structure and the set of features described […]


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SCWRL in publications

 (120)
PMCID: 5893540
PMID: 29636462
DOI: 10.1038/s41467-018-03314-9

[…] in crystal structures were removed. missing backbone atoms were modeled with the program loopy,. missing side chain atoms and side chain reversions to wild-type were modeled with the program scwrl4. disulfide bonds (c71-c159, c74-c146, c77-c166, and c259-c262) and all hydrogen atoms were placed with the gromacs tool pdb2gmx, and the receptor was then energy minimized. the simulated […]

PMCID: 5877779
PMID: 29558430
DOI: 10.3390/ijms19030918

[…] and the adic structure using promals3d [] (default settings), which was subsequently refined based on structural considerations. initial lat1 models were built using modeller [] and refined using scwrl4 []. the final model was selected based on its ability to distinguish between known ligands and decoy compounds, capturing its relevance for describing protein-ligand interactions., […]

PMCID: 5869410
PMID: 29533999
DOI: 10.3390/toxins10030122

[…] structural models were generated and the best dope score was selected and analyzed using classical approaches [,]., the different mutations were performed with pymol 1.7.1 software [] using the scwrl 4.0 tool [] for (i) simple mutant s720n, (ii) double mutants s720n and s723e, and (iii) double mutants k726s and s727i. amino acid accessibilities were computed using the dssp 2.2.1 tool [] […]

PMCID: 5835713
PMID: 29437904
DOI: 10.1042/BSR20171113

[…] m05. after missing residues were added using modeller [], computational mutagenesis was performed on these rt-nnrti complexes with the 2017 clinically reported nnrti resistance mutations [] using scwrl4 [], which successfully reproduced the side chain of the control rt structure (with rmsd ~0 å)., a total of 14 mutant complexes (shown in supplementary table s1) and 4 wild-type (complexed […]

PMCID: 5797146
PMID: 29396522
DOI: 10.1038/s41598-018-20599-4

[…] in the first round of affinity optimization, single-point scanning mutagenesis simulations were carried out at several positions within the cdrs of vhh a26.8. we used three protocols, sie-scwrl–, foldx,, and rosetta,, for building the structures and evaluating the energies of single-point mutations to 17 other possible natural amino acids (cys and pro were excluded) at these positions […]


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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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