Deep Mutational Landscape data from 28 standardised deep mutational scans

A dataset containing combined results from 28 deep mutational scanning studies. The fitness scores are transformed into the same format and normalised.

deep_landscape

Format

A data frame with 6357 rows

cluster

Amino acid subtype

study

Source study

gene

Gene tested

position

Position in gene

wt

Wild type amino acid

A

Normalised fitness score when mutating to alanine

C

Normalised fitness score when mutating to cysteine

D

Normalised fitness score when mutating to aspartate

E

Normalised fitness score when mutating to glutamate

F

Normalised fitness score when mutating to phenylalanine

G

Normalised fitness score when mutating to glycine

H

Normalised fitness score when mutating to histidine

I

Normalised fitness score when mutating to isoleucine

K

Normalised fitness score when mutating to lysine

L

Normalised fitness score when mutating to leucine

M

Normalised fitness score when mutating to methionine

N

Normalised fitness score when mutating to asparagine

P

Normalised fitness score when mutating to proline

Q

Normalised fitness score when mutating to glutamine

R

Normalised fitness score when mutating to arginine

S

Normalised fitness score when mutating to serine

T

Normalised fitness score when mutating to threonine

V

Normalised fitness score when mutating to valine

W

Normalised fitness score when mutating to tryptophan

Y

Normalised fitness score when mutating to tyrosine

mean_score

Mean normalised fitness score

mean_sift

Mean SIFT4G score for the position

total_energy

Mean FoldX total ddG for mutations to this position

backbone_hbond

Mean FoldX backbone_hbond term

sidechain_hbond

Mean FoldX sidechain_hbond term

van_der_waals

Mean FoldX van_der_waals term

electrostatics

Mean FoldX electrostatics term

solvation_polar

Mean FoldX solvation_polar term

solvation_hydrophobic

Mean FoldX solvation_hydrophobic term

van_der_waals_clashes

Mean FoldX van_der_waals_clashes term

entropy_sidechain

Mean FoldX entropy_sidechain term

entropy_mainchain

Mean FoldX entropy_mainchain term

cis_bond

Mean FoldX cis_bond term

torsional_clash

Mean FoldX torsional_clash term

backbone_clash

Mean FoldX backbone_clash term

helix_dipole

Mean FoldX helix_dipole term

disulfide

Mean FoldX disulfide term

electrostatic_kon

Mean FoldX electrostatic_kon term

partial_covalent_bonds

Mean FoldX partial_covalent_bonds term

energy_ionisation

Mean FoldX energy_ionisation term

phi

Phi backbone angle

psi

Psi backbone angle

all_atom_rel

Relative surface accessibility

hydrophobicity

Residue hydrophobicity

PC1

PC1 of the principal component analysis of A-Y

PC2

PC2 of the principal component analysis of A-Y

PC3

PC3 of the principal component analysis of A-Y

PC4

PC4 of the principal component analysis of A-Y

PC5

PC5 of the principal component analysis of A-Y

PC6

PC6 of the principal component analysis of A-Y

PC7

PC7 of the principal component analysis of A-Y

PC8

PC8 of the principal component analysis of A-Y

PC9

PC9 of the principal component analysis of A-Y

PC10

PC10 of the principal component analysis of A-Y

PC11

PC11 of the principal component analysis of A-Y

PC12

PC12 of the principal component analysis of A-Y

PC13

PC13 of the principal component analysis of A-Y

PC14

PC14 of the principal component analysis of A-Y

PC15

PC15 of the principal component analysis of A-Y

PC16

PC16 of the principal component analysis of A-Y

PC17

PC17 of the principal component analysis of A-Y

PC18

PC18 of the principal component analysis of A-Y

PC19

PC19 of the principal component analysis of A-Y

PC20

PC20 of the principal component analysis of A-Y

tSNE1

First tSNE dimension of dimensionality reduction of A-Y

tSNE2

Second tSNE dimension of dimensionality reduction of A-Y

umap1

First UMAP dimension of dimensionality reduction of A-Y

umap2

Second UMAP dimension of dimensionality reduction of A-Y

Source

Dunham and Beltrao (2020)