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MolIDE specifications


Unique identifier OMICS_06952
Name MolIDE
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Medium
Stability No
Maintained No


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Publication for MolIDE

MolIDE citations


Rapid optimization and prototyping for therapeutic antibody like molecules

PMCID: 3893234
PMID: 23392215
DOI: 10.4161/mabs.23363

[…] consensus sequences or canonical structures were considered candidates for mutations and were further analyzed in the context of structural models. The initial homology models of scFvs were built by MolIDE using independent zero-gap templates for VH and VL domains and energy-refined using SCWRL- or using Chiron. The potential impact of the candidate mutations to most frequent, canonical or consen […]


Design, Synthesis and Characterization of a Highly Effective Inhibitor for Analog Sensitive (as) Kinases

PLoS One
PMCID: 3117834
PMID: 21698101
DOI: 10.1371/journal.pone.0020789

[…] e created based on four structure templates (pdb codes 1cm8, 1m7q, 1p38 and 3erk) to provide a better understanding of the orthogonal ligands' affinities. Template selection was carried out using the MolIDE program , which is an interface to programs that performs psi-blast searches against the nr database and stores the generated alignment profiles, searches the pdb sequences using the profiles, […]


Modeling Single Nucleotide Polymorphisms in the Human AKR1C1 and AKR1C2 Genes: Implications for Functional and Genotyping Analyses

PLoS One
PMCID: 3013106
PMID: 21217827
DOI: 10.1371/journal.pone.0015604

[…] a. shows the AKR1C2 SNPs and SNDs modeled, the corresponding amino acid change, and a summary of our findings along with those of Takahashi et al.Each variant of the AKR1C2 protein was modeled using MolIDE and the following procedure. The FASTA format sequence of AKR1C2 was taken from UniProt (accession number: P52895) and edited to reflect the amino acid change in the variant. The edited sequenc […]


Numb Independently Antagonizes Sanpodo Membrane Targeting and Notch Signaling in Drosophila Sensory Organ Precursor Cells

Mol Biol Cell
PMCID: 2828966
PMID: 20053677
DOI: 10.1091/mbc.E09-09-0831

[…] oduced using a multiple alignment editor Jalview (). Multiple sequence alignments of Sanpodo were performed with ClustalW (). The sequence of Numb was aligned to potential templates using the program MolIDE (), and side chain conformations of the protein and peptide were predicted with the program SCWRL (; ), allowing all side chains to move. Structure figures were produced with the program Chimer […]


In Vitro and in Vivo Characterization of Molecular Interactions between Calmodulin, Ezrin/Radixin/Moesin, and L selectin*S⃞

PMCID: 2659241
PMID: 19129194
DOI: 10.1074/jbc.M806983200

[…] roteins remain unchanged, and none of the proteins were “ejected.” A low energy of the total complex was obtained from the dynamics simulation (∼-28,858 kcal/mol). All modeling was performed using MolIDE () and Accelrys Discovery Studio and Yasra (). A detailed breakdown of the hydrogen bonds can be found in supplemental Fig. S2.FIGURE 1.FIGURE 2.Cell Culture, Transfection, Immunoblotting, a […]


MultiSeq: unifying sequence and structure data for evolutionary analysis

BMC Bioinformatics
PMCID: 1586216
PMID: 16914055
DOI: 10.1186/1471-2105-7-382

[…] , including RASMOL [], STAMP [], STRIDE [], and 3DNA [].There are also a few programs that combine sequence and structure data either for specific purposes, such as Swiss-PdbViewer/SWISS-MODEL [] and MolIDE/SCWRL3 [,] for homology modeling, or as part of a pre-computed database of attributes, of which STING [] is the primary example. Modeller [] allows structural features to be built using sequenc […]


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MolIDE institution(s)
Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA, USA

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