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molecular modeling software package moe  (Chemical Computing Group)

 
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    Structured Review

    Chemical Computing Group molecular modeling software package moe
    AlphaFold3 models of TNFR1-ICM11 complexes (A) Native TNFR1–TNF reference structure for epitope orientation (adapted from PDB: 1TNR ). The following contact residues defines TNF binding site: Lys18, Ser49, His52, Trp93, Glu95, Arg132, Lys143, Lys144, Glu42, Ser43, His55, Cys56, Cys59, Ser60, Lys61, Arg63, Lys64, Glu65, and Met66. (B–D) AF3 models for 1:1, 2×, and 3× TNFR1-ICM11 assemblies. The AF3 confidences are indicated in the figure: ipTM provides confidence in the interface quality, and pTM summarizes the overall complex topology. The resulting contact residues of the 1:1 complex are: Arg63, Glu65, His91, Tyr92, Trp93, Glu95, Asn96, Gln99, Phe101, Lys118, Arg132, Glu133, Glu135, Glu147, and Lys150. Shared TNFR1 hotspot residues shared by both TNF and ICM11: Arg63, Glu65, Trp93, Glu95, Arg132. Interface/contact residues were computed <t>via</t> <t>Molecular</t> Operating Environment <t>(MOE)</t> software.
    Molecular Modeling Software Package Moe, supplied by Chemical Computing Group, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/software+modeling+packages/environment+molecular+operating/pmc13053762-142-0-9
    Average 86 stars, based on 1 article reviews
    molecular modeling software package moe - by Bioz Stars, 2026-11
    86/100 stars

    Images

    1) Product Images from "Antigen-directed single domain antibody-based TNFR1 agonists elicit preferential killing of HER2-overexpressing cancer cells"

    Article Title: Antigen-directed single domain antibody-based TNFR1 agonists elicit preferential killing of HER2-overexpressing cancer cells

    Journal: iScience

    doi: 10.1016/j.isci.2026.115327

    AlphaFold3 models of TNFR1-ICM11 complexes (A) Native TNFR1–TNF reference structure for epitope orientation (adapted from PDB: 1TNR ). The following contact residues defines TNF binding site: Lys18, Ser49, His52, Trp93, Glu95, Arg132, Lys143, Lys144, Glu42, Ser43, His55, Cys56, Cys59, Ser60, Lys61, Arg63, Lys64, Glu65, and Met66. (B–D) AF3 models for 1:1, 2×, and 3× TNFR1-ICM11 assemblies. The AF3 confidences are indicated in the figure: ipTM provides confidence in the interface quality, and pTM summarizes the overall complex topology. The resulting contact residues of the 1:1 complex are: Arg63, Glu65, His91, Tyr92, Trp93, Glu95, Asn96, Gln99, Phe101, Lys118, Arg132, Glu133, Glu135, Glu147, and Lys150. Shared TNFR1 hotspot residues shared by both TNF and ICM11: Arg63, Glu65, Trp93, Glu95, Arg132. Interface/contact residues were computed via Molecular Operating Environment (MOE) software.
    Figure Legend Snippet: AlphaFold3 models of TNFR1-ICM11 complexes (A) Native TNFR1–TNF reference structure for epitope orientation (adapted from PDB: 1TNR ). The following contact residues defines TNF binding site: Lys18, Ser49, His52, Trp93, Glu95, Arg132, Lys143, Lys144, Glu42, Ser43, His55, Cys56, Cys59, Ser60, Lys61, Arg63, Lys64, Glu65, and Met66. (B–D) AF3 models for 1:1, 2×, and 3× TNFR1-ICM11 assemblies. The AF3 confidences are indicated in the figure: ipTM provides confidence in the interface quality, and pTM summarizes the overall complex topology. The resulting contact residues of the 1:1 complex are: Arg63, Glu65, His91, Tyr92, Trp93, Glu95, Asn96, Gln99, Phe101, Lys118, Arg132, Glu133, Glu135, Glu147, and Lys150. Shared TNFR1 hotspot residues shared by both TNF and ICM11: Arg63, Glu65, Trp93, Glu95, Arg132. Interface/contact residues were computed via Molecular Operating Environment (MOE) software.

    Techniques Used: Binding Assay, Software

    Related Articles

    Software:

    Article Title: The Preorganization of Atropisomers to Increase Target Selectivity
    Article Snippet: Atropisomerism is a form of chirality that arises from differential substitution around a bond that renders the rotational isomers enantiomers.. Depending on the degree of hindrance to bond rotation, atropisomers can exist as either stable isolable enantiomers or rapidly racemizing atropisomeric mixtures.. Many biologically active small molecules exist as rapidly interconverting atropisomers, however, only one of the possible atropisomers possesses the desired activity.



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    Image Search Results


    AlphaFold3 models of TNFR1-ICM11 complexes (A) Native TNFR1–TNF reference structure for epitope orientation (adapted from PDB: 1TNR ). The following contact residues defines TNF binding site: Lys18, Ser49, His52, Trp93, Glu95, Arg132, Lys143, Lys144, Glu42, Ser43, His55, Cys56, Cys59, Ser60, Lys61, Arg63, Lys64, Glu65, and Met66. (B–D) AF3 models for 1:1, 2×, and 3× TNFR1-ICM11 assemblies. The AF3 confidences are indicated in the figure: ipTM provides confidence in the interface quality, and pTM summarizes the overall complex topology. The resulting contact residues of the 1:1 complex are: Arg63, Glu65, His91, Tyr92, Trp93, Glu95, Asn96, Gln99, Phe101, Lys118, Arg132, Glu133, Glu135, Glu147, and Lys150. Shared TNFR1 hotspot residues shared by both TNF and ICM11: Arg63, Glu65, Trp93, Glu95, Arg132. Interface/contact residues were computed via Molecular Operating Environment (MOE) software.

    Journal: iScience

    Article Title: Antigen-directed single domain antibody-based TNFR1 agonists elicit preferential killing of HER2-overexpressing cancer cells

    doi: 10.1016/j.isci.2026.115327

    Figure Lengend Snippet: AlphaFold3 models of TNFR1-ICM11 complexes (A) Native TNFR1–TNF reference structure for epitope orientation (adapted from PDB: 1TNR ). The following contact residues defines TNF binding site: Lys18, Ser49, His52, Trp93, Glu95, Arg132, Lys143, Lys144, Glu42, Ser43, His55, Cys56, Cys59, Ser60, Lys61, Arg63, Lys64, Glu65, and Met66. (B–D) AF3 models for 1:1, 2×, and 3× TNFR1-ICM11 assemblies. The AF3 confidences are indicated in the figure: ipTM provides confidence in the interface quality, and pTM summarizes the overall complex topology. The resulting contact residues of the 1:1 complex are: Arg63, Glu65, His91, Tyr92, Trp93, Glu95, Asn96, Gln99, Phe101, Lys118, Arg132, Glu133, Glu135, Glu147, and Lys150. Shared TNFR1 hotspot residues shared by both TNF and ICM11: Arg63, Glu65, Trp93, Glu95, Arg132. Interface/contact residues were computed via Molecular Operating Environment (MOE) software.

    Article Snippet: molecular modeling software package MOE (Molecular Operating Environment) , Chemical Computing Group Inc. , RRID: SCR_014882.

    Techniques: Binding Assay, Software