aa	amino acids
CLIP	cross-linking immunoprecipitation
CH domain	cysteine-histidine-rich domain
CHARMm	Chemistry at Harvard Macromolecular Mechanics
DECID	decay-inducing complex
EJC	exon–exon junction complex
eRF1	eukaryotic translation termination factor 1
H-bond	hydrogen bond
LINCS	linear constraint solver
mRNP	messenger ribonucleoprotein
MDS	molecular dynamics simulation
MOE	Molecular Operating Environment
NGD	no-go decay
NMD	nonsense-mediated mRNA decay
NSD	non-stop decay
ns	nanosecond
PAB1	poly(A)-binding protein cytoplasmic 1
pdb	protein data bank
PME	particle mesh Ewald
PTC	premature termination codon
ps	picosecond
RMSD	root-mean-square deviation
RMSF	root-mean-square fluctuations
SMG	suppressors with morphogenetic effect on genitalia
SPC	simple point charge
uORF	upstream open reading frames
UPF1	UP-frameshift 1
UTR	untranslated region
VMD	Visual Molecular Dynamics