LovoAlign statistics

Tool stats & trends

Looking to identify usage trends or leading experts?

Protocols

LovoAlign specifications

Information


Unique identifier OMICS_03658
Name LovoAlign
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 Leandro Martínez

Information


Unique identifier OMICS_03658
Name LovoAlign
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Leandro Martínez

Publication for LovoAlign

LovoAlign citations

 (6)
library_books

An effective sequence alignment free superpositioning of pairwise or multiple structures with missing data

2016
PMCID: 4915111
PMID: 27330544
DOI: 10.1186/s13015-016-0079-3

[…] gnment can help characterize the role of many proteins.There are two ways for protein structure alignments, sequence-based alignments and non-sequence-based alignments (i.e. Structal [], TM-align [], LovoAlign []). For closely related proteins, sequence-based alignments give consistent answers, reflecting evolutionary divergence. For distantly related proteins, however, sequence-based alignments l […]

library_books

Molecular characterization of a family 5 glycoside hydrolase suggests an induced fit enzymatic mechanism

2016
Sci Rep
PMCID: 4817029
PMID: 27032335
DOI: 10.1038/srep23473

[…] lCel5B structure complexed with cellotetraose as the starting configuration for the MD simulations. The missing residues were taken from the apo BlCel5B structure after structural alignment using the LovoAlign server. Hydrogen atoms were then added according to the protonation states determined at the optimum pH of 4.0 using the H + + server. The following residues were considered protonated: H55, […]

library_books

Allosteric Pathways in the PPARγ RXRα nuclear receptor complex

2016
Sci Rep
PMCID: 4731802
PMID: 26823026
DOI: 10.1038/srep19940

[…] The Ω-loops (residues 242 to 265 in PPARγ and 260 to 275 in RXRα) – which were missing in the full-length structure – were taken from 1FM6 after an alignment of the structures had been performed with LovoAlign. Hydrogen atoms were added and protonation states of ionizable groups were estimated using the server H++ at pH 7.Complete simulation boxes were built with VMD. Structures were solvated with […]

call_split

Vestigialization of an Allosteric Switch: Genetic and Structural Mechanisms for the Evolution of Constitutive Activity in a Steroid Hormone Receptor

2014
PLoS Genet
PMCID: 3886901
PMID: 24415950
DOI: 10.1371/journal.pgen.1004058
call_split See protocol

[…] ules rotated to different orientations prior to the VOIDOO cavity calculation. Values are shown as mean ± standard deviation. Pymol (Schrödinger, LLC) was used to construct all structure figures, and LOVOalign was used to calculate the RMSD between human ERα (1GWR) and the CgER LBD (4N1Y) . MODELLER , was used to make a homology model of the mutated CgER LBD. The mutated CgER LBD was modelled ont […]

call_split

Medium Chain Fatty Acids Are Selective Peroxisome Proliferator Activated Receptor (PPAR) γ Activators and Pan PPAR Partial Agonists

2012
PLoS One
PMCID: 3359336
PMID: 22649490
DOI: 10.1371/journal.pone.0036297
call_split See protocol

[…] PPARγ chain A X-ray structural model. The missing loop (262–273) was modeled from residues 257–277 of a previous structure (PPARγ 1PRG model ), which fit well into the structure after alignment with LovoAlign . A solvation shell of at least 15 Å was created using VMD and Sodium and Chloride ions added in a concentration close to 0.15 mol L−1 to render the system electrically neutral. The final s […]

library_books

GQ 16, a Novel Peroxisome Proliferator activated Receptor γ (PPARγ) Ligand, Promotes Insulin Sensitization without Weight Gain

2012
PMCID: 3431672
PMID: 22584573
DOI: 10.1074/jbc.M111.332106

[…] complex) from the PDB. Missing residues in the GQ-16 complex structure (206–209 and 258–276) were taken from the structure of the rosiglitazone complex, which fit well after structural alignment with LovoAlign (). Hydrogen atoms were added, and the protonation states of the histidine residues were estimated with H++ () at pH 7. For all of the neutral histidines, the position of the hydrogen atoms […]

Citations

Looking to check out a full list of citations?

LovoAlign institution(s)
Institute of Chemistry, State University of Campinas, Campinas, SP, Brazil

LovoAlign reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review LovoAlign