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C-alpha Building

Building a Peptide (by Homology)

Moloc offers the possibility to build peptides on a residue level without having to bother about single atoms. The resulting C-alpha structures can then be transferred directly to all atom models. Let us build a model for Oxytocin (sequence CYIQNCPLG) which is cyclized by a disulfide bond. Now the topology of your peptide is specified. Depending on your choice of secondary structure for elongating the sequence the conformation may need more or less adjustment to conform with the cyclic condition. The peptide force field offers the possibility to obtain a reasonable first order proposal for the conformation:

Using Non-Natural Amino Acids

Moloc allows to build peptides containing non-natural amino acid residues. These must be provided in file(s) witn neutral amino- and acid groups. The names of these structures must start with a letter and have at least three characters (preferably all letters).

Homology Building

From a known protein structure a structural model for a homologous protein can be built, provided a sequence alignment is given. The alignment must be given in a file in which each line is interpreted as single letter code sequence of the original protein or of the homologous one, provided the line starts with either #1 or #2 respectively. All other lines are interpreted as comments. In case of deletions or insertions, missing residues must be indicated by a dot. For deletions the program simply connects the two ends of the last and first residues present. Insertions are positioned near a circle of appropriate size. It is understood that these regions are subjected to subsequent energy minimization within the Calf force field to generate acceptable geometries. The program automatically generates a user set which contains the residues in the homologous structure, which may be kept fixed under a subsequent minimization. This set must be activated (definition of fixed residues) prior to minimization. Loop Search