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Protocols

Naccess specifications

Information


Unique identifier OMICS_18981
Name Naccess
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use Academic or non-commercial use
Output data An atomic accessibility file, a residue accessibility file and a log file.
Output format ASA, RSA, LOG
Operating system Unix/Linux
Programming languages Fortran
Computer skills Advanced
Version 2.1.1
Stability Stable
Source code URL http://www.bioinf.manchester.ac.uk/naccess/download/naccess.rar.gz
Maintained Yes

Download


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Versioning


No version available

Maintainers


  • person_outline Simon Hubbard
  • person_outline Marina Santilli

Additional information


http://www.bioinf.manchester.ac.uk/naccess/nac_intro.html http://www.bioinf.manchester.ac.uk/naccess/nac_readme.html

Naccess citations

 (342)
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

[…] in seven (i) residues and their (i + 7) residue partners in the sequence. The inter-heptad angles were measured between Cα atoms in residues at sequence positions (i – 7), i, and (i + 7). The program Naccess was used to show which residues make up the hydrophobic core of the protein ( and Hubbard, S. J.; Thornton, J. M. Naccess; Department of Biochemistry and Molecular Biology, University College […]

library_books

Computational Protein Design with Deep Learning Neural Networks

2018
Sci Rep
PMCID: 5910428
PMID: 29679026
DOI: 10.1038/s41598-018-24760-x

[…] ect to the central residue. cos and sin values of the dihedrals were used because the dihedrals that range from −180 to 180 are not continuous at −180 and 180. The SASA value was calculated using the Naccess program on the whole protein structure (not on a structural cluster) with the sidechain atom removed, because during protein design, the identity of a residue and thus its sidechain atoms are […]

library_books

Exploration of the effect of sequence variations located inside the binding pocket of HIV 1 and HIV 2 proteases

2018
Sci Rep
PMCID: 5893546
PMID: 29636521
DOI: 10.1038/s41598-018-24124-5

[…] quantified the global pocket hydrophobicity based on residue properties, and hydrophobicity_pocket_pocket quantified the global pocket hydrophobicity based on the solvent accessibility computed using NACCESS. The three descriptors provided complementary information. For example, a pocket can have a high hydrophobic_kyte value but a small p_hydrophobic_residues value, indicating that this pocket is […]

library_books

Mutations Conferring Increased Sensitivity to Tripartite Motif 22 Restriction Accumulated Progressively in the Nucleoprotein of Seasonal Influenza A (H1N1) Viruses between 1918 and 2009

2018
PMCID: 5885024
PMID: 29624498
DOI: 10.1128/mSphere.00110-18

[…] quare deviation (RMSD) tolerance on heavy atom of 0.3 Å was performed. To evaluate the accessibilities of the four lysines (K98, K293, K422, and K446), we calculated the solvent-accessible area using Naccess V2.1.1 (). […]

library_books

Building protein protein interaction networks for Leishmania species through protein structural information

2018
BMC Bioinformatics
PMCID: 5840830
PMID: 29510668
DOI: 10.1186/s12859-018-2105-6

[…] egadock [] tool version 4.0.2.The Prism Protocol requires as input atomic coordinates of two proteins, and a template set formed by pairs of proteins that are known to interact. This tool applies the Naccess [] and Multiprot [] softwares to compare the residues responsible for the interaction in the template set with the surface residues of a pair of target proteins, and then Prism Protocol uses t […]

call_split

Cytochrome c speeds up caspase cascade activation by blocking 14 3 3ε dependent Apaf 1 inhibition

2018
PMCID: 5840378
PMID: 29511177
DOI: 10.1038/s41419-018-0408-1
call_split See protocol

[…] g standard criteria. Random exclusion of AIRs was not employed. Cc residues labeled as active were those showing 1H ΔΔν1/2Binding ≥ 59.2 Hz and a solvent accessibility larger than 50% calculated with NACCESS. These active residues were Gln16, Gln42, Ser47, Ala50, Gly77, Lys79, Ile81, and Val83. Cc residues located at <4 Å from the active ones and showing high-solvent accessible surface (>50%) were […]

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