Prime Glossary

alignment—The optimal matching of residue positions between sequences, typically a query sequence and one or more template sequences.

all-atom structure—A structure in which all atoms, including hydrogen atoms, are explicitly represented. This means that the structure must have coordinates for all atoms. PDB files often do not have coordinates for hydrogen atoms, and some force fields can merge the hydrogens into the heavy atoms in a “united atom” model.

anchor—A constraint on alignment set at a given residue position. Alignment changes must preserve the query-template pairing at that residue until the anchor is removed.

ASL—Atom Specification Language.

cofactor—The complement of an enzyme reaction, usually a metal ion or metal complex.

Comparative Modeling—Protein structure modeling based on a query-template match with a substantial percentage of identical residues (usually 50% or greater sequence identity).

constraints—Tools to keep regions of a sequence (alignment constraints) or structure (during minimization) in a particular configuration.

deletions—The residues missing from a query sequence that are present in a template sequence.

gaps—The spaces in an alignment resulting from insertions and deletions.

HETATOMs—The atoms of residues, including amino acids, that are not one of the standard 20 amino acids. In PDB files, HETATM.

homolog—A sequence/structure related to the query sequence; i.e., a sequence with many of the same residues in the same patterns as the query sequence. Usually these sequences are derived from the same family and may have similar function.

insertions—The extra residues found in a query sequence that are not found in a template sequence.

ligand—A small molecule that binds to a protein; e.g., an antigen, hormone, neurotransmitter, substrate, inhibitor, and so on.

loop—A region of undefined secondary structure.

project—A collection of related data, such as structures with their associated properties. In Prime a project comprises one or more runs (executions of the Prime workflow). The project may include data that does not appear in the project table.

Project Table—The Maestro panel associated with a project, featuring a table with rows of entries and columns of properties. In Prime, project table entries are usually model structures.

query sequence—A sequence of unknown structure or fold.

refinement—An improvement of a model structure through energy-based optimization of selected regions.

run—A single execution of the Prime workflow using a particular set of choices (of templates, of paths, and of settings). Each run belongs to a project. Runs cannot be saved without saving the project to which they belong.

SSA—Secondary structure assignment.

SSP—Secondary structure prediction.

template sequence—A sequence of known structure and fold used as a basis for building a model of the query.

Workspace—The open area in the center of the Maestro window in which structures are displayed.

Z-Score—Measures the compatibility of the query sequence with the model structure, relative to the compatibility of randomly shuffled sequences of the same composition.