MD	molecular dynamics
GPU	graphics processing unit
PCA	principal component analysis
RIP-MD	residue interaction network in protein molecular dynamics
VMD	visual molecular dynamics
JED	Java-based Essential Dynamics
scFv	single-chain variable-fragment
PDB	protein data bank
RMSD	root-mean-square deviation
SPM	shortest path map
CAMERRA	computation of allosteric mechanism by evaluating residue–residue associations
DAAO	D-amino acid oxidase
MC	Monte Carlo
FixBB	fixed backbone
D&R	Design-and-relax
PCC	Pearson correlation coefficient
ΔΔG	change in binding free energy
RMSE	root-mean-square error
SSD	single-state design
MSD	multistate design
NMR	nuclear magnetic resonance
NSR	native sequence recovery
NSSR	native sequence similarity recovery
FlexiBaL-GP	flexible backbone learning by Gaussian processes
SHADES	structural homology algorithm for protein design
ITEM	In-contact amino acid residue tertiary motif
DEE	dead-end elimination
DEEPer	dead-end elimination with perturbations
CATS	coordinates of atoms by Taylor series
NMA	normal mode analysis