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align3d specifications


Unique identifier OMICS_31750
Name align3d
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C, C++, MATLAB
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.1
Stability Stable
Maintained Yes




No version available


  • person_outline James Costello
  • person_outline Brian Ross

Publication for align3d

align3d citations


Structure of anthrax lethal toxin prepore complex suggests a pathway for efficient cell entry

PMCID: 5037343
PMID: 27670897
DOI: 10.1085/jgp.201611617

[…] . S2) refined with an angular sampling of 14.3° and low pass filtering at 30 Å at each iteration. Refinement was run until volumes became similar. These volumes were then aligned and merged using the align3d and avg3d commands of EMAN giving the starting model. Refinement of this initial model was conducted using XMIPPv2.3 (Fourier reconstruction method; ). Proper alignment of the gap was ensured […]


X ray computed tomography datasets for forensic analysis of vertebrate fossils

Sci Data
PMCID: 4896130
PMID: 27272251
DOI: 10.1038/sdata.2016.40

[…] Vizlab/drishti/). Volume exploration and presentation tool.SPIERS ( A useful software toolkit for tomographic visualization that generates surface models.Blob3D, Quant3D, Align3D, and MuCalc Tool ( UTCT has developed a number of specialized software packages for quantitative analysis of HRXCT datasets. Blob3D measures 3-D geom […]


Single Particle Electron Microscopy Analysis of the Bovine Anion Exchanger 1 Reveals a Flexible Linker Connecting the Cytoplasmic and Membrane Domains

PLoS One
PMCID: 3564912
PMID: 23393575
DOI: 10.1371/journal.pone.0055408

[…] s average in the −45° tilt particle set. We visually compared this projection and the class average for feature consistency and selected the best 25 OTR maps. These 25 ORT maps then aligned using the align3d program in EMAN and averaged. […]


In silico and In vitro based studies of Streptomyces peucetius CYP107N3 for oleic acid epoxidation

PMCID: 4133810
PMID: 23261061
DOI: 10.5483/BMBRep.2012.45.12.080

[…] 2ZBX, 40% identity) and CYP105P1 (PDB ID: 3E5L, 40% identity) were selected as templates to build a homology model of CYP107N3. Sequence alignment between CYP107N3 and other CYPs was performed using Align3D, followed by manual modification (A), and models were generated by MODELER . The final alignment was carefully evaluated and was found to match the conserved residues fairly well; thereafter, […]


Loss and Gain of Function in SERPINB11: An Example of a Gene under Selection on Standing Variation, with Implications for Host Pathogen Interactions

PLoS One
PMCID: 3290568
PMID: 22393410
DOI: 10.1371/journal.pone.0032518

[…] e used Each protein6 showed a sequence identity of approximately 37% with SERPINB11.Modeller 9v6 was used in all modeling tasks. Sequence and structural alignments were carried out using ALIGN2D and ALIGN3D features of Modeller and optimized through several cycles of comparative modeling. In the last cycle, 200 different models were generated and the one with the lowest value for the Modeller's o […]


Three Dimensional cryoEM Reconstruction of Native LDL Particles to 16Å Resolution at Physiological Body Temperature

PLoS One
PMCID: 3090388
PMID: 21573056
DOI: 10.1371/journal.pone.0018841

[…] of LDL at 6°C (resolution ∼16 Å) with the very recently published 3D volume (resolution 28 Å) of a complex of LDL with the LDL-receptor (LDL-LDLr) at 4°C . The result by an automatic alignment tool (Align3D in EMAN, ) is shown in . It can be seen that most of the regions of the LDL reconstruction at 6°C overlap with the corresponding regions in the LDL-LDLr complex at 4°C. The region that shows p […]


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align3d institution(s)
Computational Bioscience Program, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
align3d funding source(s)
Supported by the Boettcher Foundation, NIH grant 2T15LM009451 and a Cancer League of Colorado grant.

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