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ANOLEA specifications

Information


Unique identifier OMICS_34400
Name ANOLEA
Alternative name Atomic Non-Local Environment Assessment
Interface Web user interface
Restrictions to use None
Input data A file containing one or more protein chains.
Input format PDB
Output data An energy profile, which gives an energy value for each amino acid of the protein.
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Francisco Melo

Publication for Atomic Non-Local Environment Assessment

ANOLEA citations

 (37)
library_books

Accurate prediction of functional, structural, and stability changes in PITX2 mutations using in silico bioinformatics algorithms

2018
PLoS One
PMCID: 5903617
PMID: 29664915
DOI: 10.1371/journal.pone.0195971

[…] v/; provided in the public domain by the Swiss Institute of Bioinformatics, Geneva, Switzerland). Model structures of wild-type and mutants were created in Swiss-Pdb Viewer and investigated using the ANOLEA server (http://melolab.org/anolea). For structure predictions of PITX2, sequence in FASTA format was obtained from NCBI database (NP_001191327.1). […]

library_books

Comparative Analysis of CDPK Family in Maize, Arabidopsis, Rice, and Sorghum Revealed Potential Targets for Drought Tolerance Improvement

2017
PMCID: 5742180
PMID: 29312925
DOI: 10.3389/fchem.2017.00115

[…] d on distant homology recognition techniques with secondary structure prediction and domain analysis of each CDPK protein model (Kelley and Sternberg, ). The predicted structures were evaluated using Atomic Non-Local Environment assessment (ANOLEA; Melo and Feytmans, ), Verify-3D (Eisenberg et al., ) and Protein structure analysis (ProSA) program (Wiederstein and Sippl, ) and validated using Ramac […]

library_books

Alternative oxidase (AOX) constitutes a small family of proteins in Citrus clementina and Citrus sinensis L. Osb

2017
PLoS One
PMCID: 5411082
PMID: 28459876
DOI: 10.1371/journal.pone.0176878

[…] []. The α-carbon chain RMSD between targets and their respective templates was calculated using PyMOL V3.0 []. The stereochemical quality of both AOX models was calculated by Procheck 3.4 [] and the Atomic Non-Local Environment Assessment (ANOLEA) program []. The validation of the secondary structure was performed using the Protein Structure Prediction Server-PSIPRED program []. […]

library_books

Insight into SNPs and epitopes of E protein of newly emerged genotype I isolates of JEV from Midnapur, West Bengal, India

2017
BMC Immunol
PMCID: 5339996
PMID: 28264652
DOI: 10.1186/s12865-017-0197-9

[…] n the Right panel of the Fig. . Energetic profile of the model (green trace) and the template (red trace) are seen to be almost identical when plotted as a function of residue position as obtained by ANOLEA [] (Fig. : D1) and VERIFY3D analysis [] (Fig. : D2). Ramachandran plot for main chain dihedral angles and PROCHECK analysis [] (Fig. : D3 and D4 respectively) show amino acid residues, occupyin […]

library_books

Pharmacoinformatics, Adaptive Evolution, and Elucidation of Six Novel Compounds for Schizophrenia Treatment by Targeting DAOA (G72) Isoforms

2017
Biomed Res Int
PMCID: 5288522
PMID: 28197415
DOI: 10.1155/2017/5925714

[…] ms were minimized by AMBER [] software. The structures were evaluated by MolProbity []. The poor ramachandran outliers and rotamers were removed by utilizing WinCoot [] tool. Rampage [], ProCheck [], Anolea [], and ERRAT [] were used for the overall assessment of protein structure verifications and model quality. The generated ramachandran plots for evaluation of predicted models showed residues d […]

library_books

Flurbiprofen–antioxidant mutual prodrugs as safer nonsteroidal anti inflammatory drugs: synthesis, pharmacological investigation, and computational molecular modeling

2016
Drug Des Devel Ther
PMCID: 4968865
PMID: 27555750
DOI: 10.2147/DDDT.S109318

[…] e reliable 3D crystal structures of both COX-1 and COX-2 were modeled using Modeller 9v8. Furthermore, the validity of predicted structures was confirmed using various evaluation tools such as ERRAT, Anolea, ProCheck, and Rampage.– The energy minimization of these structures was performed using Vega-ZZ. UCSF Chimera 1.6 was used to visualize these predicted structures. The overall stereochemical p […]

Citations

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ANOLEA institution(s)
Facultés Universitaires Notre Dame de la Paix, Department of Biology, Laboratoire de Biologie Moléculaire Structurale, Namur, Belgium; Universidad Católica de Chile, Laboratorio de Bioinformática Molecular, Santiago, Chile

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