- Molecular operating environment installation guide manual#
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If the sequence identity of a V L + V H result is within 10% of the target sequence then a homo template (V L and V H belong to the same structure) is used, otherwise hetero templates (V L and V H from different structures) are considered. Only the top 10 scoring framework candidates from each of respective result set are retained. Since the template search is confined to the content of the Fab Database, the time required to find suitable templates takes on average <0.5 s per query. The hypervariable loop scores are calculated as similarity of the query loop compared to the corresponding hypervariable loop sequences of the same length in the Fab Database. The scores for the FRs are calculated as the identity with prealigned framework clusters in the Fab Database, factoring gaps into the calculation. Two different scores are used for framework and hypervariable loop regions.
A sequence alignment with the BLOSUM62 substitution matrix is performed. Separate results are collected for V L, V H, and V L + V H as well as the hypervariable loop regions. Given the V L and V H amino acid sequences of the antibody to be modeled, the Fab database is searched for suitable templates. , For structural clustering, the Structural Composition of Protein database SCOP, was used as seed clusters followed augmented with single linkage clustering. If detected as a V L chain, further subclassification into either κ or λ subclasses is achieved by aligning to reference germline sequences originating from the Immunogenetics database. The cutoffs in the antibody detection as described above ensured no contamination of other immunoglobulin-like structures such as T-cell receptor sequences. Classifying an F V chain as either V L or V H requires a framework sequence identity of at least 60% with one class and <50% with the opposite class. Protein chains are classified as antibody chains if the overall sequence identity with one chain of the reference collections exceeds 40%. The sequence of each protein chain is aligned against the V L and V H reference sets and the sequence identity is calculated as a percentage of identical residues within the aligned F V domain as well as within the respective FRs FR 1, FR 2, and FR 3. The entire PDB was then screened for immunoglobulin structures.
Molecular operating environment installation guide manual#
Molecular Operating Environment Manual 2017.
Molecular operating environment installation guide crack#
Molecular operating environment installation guide software#
Molecular Operating Environment ( MOE) is a drug discovery software platform that integrates visualization, modeling and simulations, as well as methodology development, in one package. Material moe molecular operating environment manual unified operations.
MOE, the Molecular Operating Environment, is a comprehensive software system for Life. MOE is a drug discovery software platform that integrates visualization, modeling and simulations, as well as methodology development, in one package.
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