concepts

This Vocabulary describes concepts used in Rosetta like Pose, AtomTree and ScoreFunction.
Click one of the letters above to advance the page to terms beginning with that letter.

A

abinitio stage
AtomTree

The AtomTree reflects the chemical and kinematic structure of the Pose and stores internal degrees of freedom on its edges.

autoNOE

An iterative protocol building on RASREC that uses the low-energy pool of structures to improve NOE peak assignments

B

broken chain sampling
bulge

C

centroid
chainbreak

A chainbreak is between consecutive residues (in the protein sequence) that are not connected in the AtomTree/FoldTree.

chainbreak energy

Penalty energy term computed for non-physical chainbreaks.

chemical shifts
constraint

D

de-novo structure predicition

F

fasta file
folding
FoldTree

A low-resolution abstraction of the AtomTree with peptide- and jump-edges.

fragment

is a particular conformation of short pieces of protein, RNA or DNA backbone

fragment library

A file that contains many possible conformations (fragments) for a given set of degrees of freedom.

fragments
fullatom

G

gradient based minimization

I

ideal
installation

J

job-distributor
jumping

sampling with non-trivial FoldTree

L

loop modelling

M

method

A choice of a structure calculation protocol (abrelax, rasrec, autoNOE) in the automated setup tools.

molecular fragment replacement
Mover

N

nmr

Nuclear Magnetic Resonance

P

packing
pose

The Pose is the container of the molecular system including its chemical-, kinematic- and conformational structure.

protocol

A recipe for structure calculation.

R

rasrec

An iterative protocol that recombines structural features found in the (genetic) pool of low-energy structures

re-reference
register
resampling stage
residue type patch
residue type variant
residue-type
residue-type-patch
residue-type-set
residue-type-variant
restraint

A bias energy contribution usually based on experimental data

restraint guided structure calculation
rosetta database

place for storage of common ROSETTA data files

rotamers
run (automated setup)

S

score

An energy computed for a given Pose using the ScoreFunction.

score patch

A patch file to change individual weights of the ScoreFunction.

score0

Weight-set for centroid scoring used during stage I of abrelax protocol.
score0 uses only vdw forces: ( env 0.0, pair 0.0, cbeta 0.0, cenpack 0.0, vdw 0.1, rg 0.0, hs_pair 0.0, ss_pair 0.0, rsigma 0.0, sheet 0.0 )

score1

used during abrelax protocol.
( env 1.0, pair 1.0, cbeta 0.0, vdw 1.0, rg 0.0, cenpack 0.0, hs_pair 1.0, ss_pair 0.3, rsigma 0.0, sheet 1.0 )
STRAND_STRAND_WEIGHTS 1 11

score12

The weight-set used for full-atom scoring in Rosetta

score13_env_hb

A deprecated weight-set for full-atom scoring. Although using different weights its performance in discrimination of structures is not significant altered vs. score12.

score2

Weight-set for centroid scoring used during stage III of abrelax protocol.

( env 1.0, pair 1.0, cbeta 0.25, cenpack 0.5, vdw 1.0, rg 0.0, hs_pair 1.0, ss_pair 1.0, rsigma 0.0, sheet 1.0 )
STRAND_STRAND_WEIGHTS 1 6

score3

Weight-set for centroid scoring used during stage IV of abrelax protocol.

( env 1.0, pair 1.0, cbeta 1.0, cenpack 1.0, vdw 1.0, rg 3.0, hs_pair 1.0, ss_pair 1.0, rsigma 1.0, sheet 1.0 )
STRAND_STRAND_WEIGHTS 0 6

score5

Weight-set for centroid scoring used during stage III of abrelax protocol.

( env 1.0, pair 1.0, cbeta 0.25, cenpack 0.5, vdw 1.0, rg 0.0, hs_pair 1.0, ss_pair 1.0, rsigma 0.0, sheet 1.0 )
STRAND_STRAND_WEIGHTS 1 11

scoring

Scoring is an application of a ScoreFunction to a pose.

setup
silent file

Rosetta specific trajectory format.

silent io

Structure IO using a ROSETTA specific trajectory format

silent-files
strand-strand contact

a beta-sheet forming contact between two residues in extended conformation.

T

target

V

vall