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Protocols

ACCpro specifications

Information


Unique identifier OMICS_04653
Name ACCpro
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Pierre Baldi

Information


Unique identifier OMICS_04653
Name ACCpro
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Pierre Baldi

Publications for ACCpro

ACCpro citations

 (28)
library_books

A sparse autoencoder based deep neural network for protein solvent accessibility and contact number prediction

2017
BMC Bioinformatics
PMCID: 5751690
PMID: 29297299
DOI: 10.1186/s12859-017-1971-7

[…] ded weighting scheme (SPINE-X) [], a nearest neighbor method by using sequence profiles (SANN) [], an ensemble of Bidirectional Recursive Neural Networks using both sequence and structure similarity (ACCpro5) [], and a conditional neural fields model (AcconPred) []. For contact number prediction, we compare our method with Kinjo’s method which applied linear regression scheme based on multiple seq […]

library_books

Hydrogen Bond Variations of Influenza A Viruses During Adaptation in Human

2017
Sci Rep
PMCID: 5662722
PMID: 29085020
DOI: 10.1038/s41598-017-14533-3

[…] Relative solvent accessibility (RSA) of a residue was calculated using the program NAccess (unpublished, S. Hubbard and J. Thornton 1992–6, http://www.wolf.bms.umist.ac.uk/naccess/) and ACCpro. A site was regarded as exposed if its RSA was above 25%. […]

library_books

Accurate prediction of functional effects for variants by combining gradient tree boosting with optimal neighborhood properties

2017
PLoS One
PMCID: 5470696
PMID: 28614374
DOI: 10.1371/journal.pone.0179314

[…] n probabilities; 9) solvent accessible surface area, secondary structure and local backbone angles generated by SPIDER2 []; 10) predicted the relative solvent accessibility of protein residues by the ACCpro and ACCpro20 from the SCRATCH package []; 11)evolutionary conservation scores calculated based on PSSM [] and Jensen-Shannon divergence [, ]. […]

library_books

Sorting protein decoys by machine learning to rank

2016
Sci Rep
PMCID: 4987638
PMID: 27530967
DOI: 10.1038/srep31571

[…] MQA-SS-total score is also used as a feature. For solvent accessibility features, the absolute solvent accessibility of the model is computed by DSSP and relative solvent accessibility is computed by ACCpro5. These two vectors are compared and transformed into a Pearson Correlation Coefficient and a cosine value as two features.The SIFT is a program that uses averaged (i.e. amino acid independent) […]

library_books

Cell Wall Anchoring of the Campylobacter Antigens to Lactococcus lactis

2016
Front Microbiol
PMCID: 4757695
PMID: 26925040
DOI: 10.3389/fmicb.2016.00165

[…] ndary structure prediction and tertiary fold-recognition (FR) were carried out via the GeneSilico metaserver gateway (). Solvent accessibility for the individual residues was predicted with SABLE (), ACCPRO2 (), and JNET (). Disordered residues were predicted from consensus of results generated with disprot (), DISpro (), DisEMBL (), RONN (), and disopred () methods. Secondary structure was predic […]

library_books

ProQ2: estimation of model accuracy implemented in Rosetta

2016
Bioinformatics
PMCID: 4848402
PMID: 26733453
DOI: 10.1093/bioinformatics/btv767

[…] here is also a similar feature for predicted surface accessibility. To calculate all the features needed for a prediction ProQ2, used many different external programs such as PSI-BLAST (), PSIPRED () ACCpro (), Naccess (), ProQres (), Stride () and SVM-light (). These dependencies made it difficult to distribute the program, to run large batches and to incorporate in novel modeling protocols.Here, […]


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ACCpro institution(s)
Department of Computer Science and Institute for Genomics and Bioinformatics, University of California, Irvine, CA, USA

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