SCWRL statistics

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Citations per year

Number of citations per year for the bioinformatics software tool SCWRL
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Tool usage distribution map

This map represents all the scientific publications referring to SCWRL per scientific context
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Associated diseases

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Protocols

SCWRL specifications

Information


Unique identifier OMICS_15563
Name SCWRL
Alternative name SCWRL4
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


No version available

Maintainer


  • person_outline Roland Dunbrack Jr

Publications for SCWRL

SCWRL citations

 (231)
call_split

A1603P and K1617del, Mutations in β Cardiac Myosin Heavy Chain that Cause Laing Early Onset Distal Myopathy, Affect Secondary Structure and Filament Formation In Vitro and In Vivo

2018
J Mol Biol
PMCID: 5958240
PMID: 29660325
DOI: 10.1016/j.jmb.2018.04.006
call_split See protocol

[…] 7del model was built that used a canonical coiled-coil motif throughout this region.BEAMMOTIFCC provides a backbone structure for the coiled-coil model. Side-chain atoms were added to the model using SCWRL4 . N-termini were again capped with acetyl groups and C-termini were capped with N-methylamide. Simulations were run as for the composite model with an additional minimization and equilibration […]

library_books

Mechanistic insights into allosteric regulation of the A2A adenosine G protein coupled receptor by physiological cations

2018
Nat Commun
PMCID: 5893540
PMID: 29636462
DOI: 10.1038/s41467-018-03314-9

[…] resolved 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 recept […]

library_books

Effects of Mutations and Ligands on the Thermostability of the l Arginine/Agmatine Antiporter AdiC and Deduced Insights into Ligand Binding of Human l Type Amino Acid Transporters

2018
Int J Mol Sci
PMCID: 5877779
PMID: 29558430
DOI: 10.3390/ijms19030918

[…] ers 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. […]

library_books

A computational study for rational HIV 1 non nucleoside reverse transcriptase inhibitor selection and the discovery of novel allosteric pockets for inhibitor design

2018
Biosci Rep
PMCID: 5835713
PMID: 29437904
DOI: 10.1042/BSR20171113

[…] rug 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 with re […]

call_split

Application of Assisted Design of Antibody and Protein Therapeutics (ADAPT) improves efficacy of a Clostridium difficile toxin A single domain antibody

2018
Sci Rep
PMCID: 5797146
PMID: 29396522
DOI: 10.1038/s41598-018-20599-4
call_split See protocol

[…] maturation. 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 […]

library_books

Electrostatic Variation of Haemagglutinin as a Hallmark of the Evolution of Avian Influenza Viruses

2018
Sci Rep
PMCID: 5792503
PMID: 29386534
DOI: 10.1038/s41598-018-20225-3

[…] ructural models for the RBD regions of target HA proteins were obtained by homology modelling using SWISS-MODEL and the PDB 1JSH structure as the H9N2 HA template; such models were then refined using SCWRL, which for optimisation integrates: (i) a backbone-dependent rotamer library, (ii) a simple energy function based on rotamer frequencies and a repulsive steric energy term, as well as (iii) a gr […]


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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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