shunsunsun / display-of-preset-rosetta-ncaas

What exactly are the non-canonical amino acids in the Rosetta database folder?

Display of the preset Rosetta NCAAs

What exactly are the non-canonical amino acids in the Rosetta database folder?

Names like V02 really do not help... So there is only one way to find out, manually generate a figure for each by recycling a large amount of code.

Script

The file generate.py does the work. To do this, it used both pyrosetta and RDKit. In the case of RDKit the bond order is guessed using a function for a blog post of mine.

In the case of pyrosetta, the mover pyrosetta.rosetta.protocols.simple_moves.MutateResidue is used as the argument new_res can be a custom parameterised residue. Shamefully, I do not know how one can pass the argument extra_res_fa to pyrosetta after it gets initialised as setting it as an option afterward simply failed.

A cool detail is that for once I am not using PyMOL. In fact, the line pyrosetta.rosetta.core.pose.make_pose_from_sequence(pose, 'A', 'fa_standard') generates the pose from scratch.

The fix_bond_order method has a problem with tryptophans due to a valence of 5 carbon. Makes sense though.

Gallery

3-Letter	Image of non-canonical amino acid	File	SMILES
A34		2-aminomethyl-phenylalanine.params	N[C@@H](Cc1ccccc1C[NH3+])C(=O)[O-]
A33		2-amino-heptanoic_acid.params	CCCCC[C@H](N)C(=O)[O-]
NVL		NVL.params	CCC[C@H](N)C(=O)[O-]
C94		trifluoro-leucine_ent2.params	CC(C[C@H](N)C(=O)[O-])C(F)(F)F
B27		4-methyl-phenylalanine.params	Cc1ccc(C[C@H](N)C(=O)[O-])cc1
A20		2-allyl-glycine.params	C=CC[C@H](N)C(=O)[O-]
B57		alpha-methyl-leucine.params	CC(C)CC(C)(N)C(=O)[O-]
C26		homocysteine.params	N[C@@H](CCS)C(=O)[O-]
A31		2-amino-5-phenyl-pentanoic_acid.params	N[C@@H](CCCc1ccccc1)C(=O)[O-]
B97		beta-chloro-alanine.params	N[C@@H](CCl)C(=O)[O-]
B58		alpha-methyl-phenylalanine.params	CC(N)(Cc1ccccc1)C(=O)[O-]
B19		4-fluoro-proline.params_rot	CC(F)C[C@H](N)C(=O)[O-]
C00		beta-cyclohexyl-alanine.params	N[C@@H](CC1CCCCC1)C(=O)[O-]
A80		3-hydroxy-tyrosine.params	N[C@@H](Cc1ccc(O)c(O)c1)C(=O)[O-]
NLU		NLU.params	CCCC[C@H](N)C(=O)[O-]
B96		beta.beta-diphenyl-alanine.params	N[C@H](C(=O)[O-])C(c1ccccc1)c1ccccc1
C27		homophenylalanine.params	N[C@@H](CCc1ccccc1)C(=O)[O-]
B54		alpha-methyl-3-hydroxy-tyrosine.params	CC(N)(Cc1ccc(O)c(O)c1)C(=O)[O-]
C30		homoserine.params	N[C@@H](CCO)C(=O)[O-]
B61		alpha-methyl-tyrosine.params	CC(N)(Cc1ccc(O)cc1)C(=O)[O-]
BMAA		2-amino-3-methylamino-propanoic_acid.params	C[NH2+]C[C@H](N)C(=O)[O-]
C04		beta-hydroxy-norvaline.params	CCC(O)[C@H](N)C(=O)[O-]
A30		2-amino-4-bromo-4-pentenoic_acid.params	C=C(Br)C[C@H](N)C(=O)[O-]
V04		V04.params	N[C@H](C(=O)[O-])C(O)c1ccc(O)c(Cl)c1
DAB		2.4-diaminobutyric_acid.params	N[C@@H](CC[NH3+])C(=O)[O-]
C89		4-fluoro-proline_puck.params_rot	CC(F)C[C@H](N)C(=O)[O-]
HLU		HLU.params	CC(C)CC[C@H](N)C(=O)[O-]
A32		2-amino-octanoic_acid.params	CCCCCC[C@H](N)C(=O)[O-]
B95		beta-beta-dicyclohexyl-alanine.params	N[C@H](C(=O)[O-])C(C1CCCCC1)C1CCCCC1
A43		2-hydroxy-phenylalanine.params	N[C@@H](Cc1ccccc1O)C(=O)[O-]
C93		hexafluoro-leucine.params	N[C@@H](CC(C(F)(F)F)C(F)(F)F)C(=O)[O-]
C20		ethionine.params	CCSCC[C@H](N)C(=O)[O-]
B74		beta-(2-naphthyl)-alanine.params	N[C@@H](Cc1ccc2ccccc2c1)C(=O)[O-]
C55		tert-butyl-glycine.params	CC(C)(C)[C@H](N)C(=O)[O-]
B44		9-anthryl-alanine.params	N[C@@H](Cc1c2ccccc2cc2ccccc12)C(=O)[O-]
C92		fluoro-leucine_ent2.params	CC(CF)C[C@H](N)C(=O)[O-]
B62		alpha-methyl-valine.params	CC(C)C(C)(N)C(=O)[O-]
C41		penicillamine.params	CC(C)(S)[C@H](N)C(=O)[O-]
ABA		ABA.params	CC[C@H](N)C(=O)[O-]
A98		4-amino-piperidine-4-carboxylic-acid.params	C[NH2+]CCC(C)(N)C(=O)[O-]
A83		3-methyl-histidine_prot.params	CN1CNC=C1C[C@H](N)C(=O)[O-]
B59		alpha-methyl-proline.params	CCCC(C)(N)C(=O)[O-]
B56		alpha-methyl-histidine.params	CC(N)(Cc1c[nH]cn1)C(=O)[O-]
A45		2-indanyl-glycine_puck2.params	N[C@H](C(=O)[O-])C1Cc2ccccc2C1
BB8		phenyl-serine.params	N[C@H](C(=O)[O-])C(O)c1ccccc1
C54		tert-butyl-cysteine.params	CC(C)(C)SC[C@H](N)C(=O)[O-]
MPA		MPA.params	Cc1ccc(C[C@H](N)C(=O)[O-])cc1
TES		TES.params	CC(=O)NC1C(NC(=O)C[C@H](N)C(=O)[O-])OC(CO)C(OC2OC(CO)C(OC3OC(COC4OC(COC5OC(CO)C(O)C(O)C5O)C(O)C(OC5OC(CO)C(O)C(O)C5O)C4O)C(O)C(OC4OC(CO)C(O)C(O)C4O)C3O)C(O)C2NC(C)=O)C1O
C89		4-fluoro-proline_puck.params	CC(F)C[C@H](N)C(=O)[O-]
C53		tert-butyl-alanine.params	CC(C)(C)C[C@H](N)C(=O)[O-]
A06		1-methyl-histidine.params	Cn1cnc(C[C@H](N)C(=O)[O-])c1
A69		3-amino-tyrosine.params	Nc1cc(C[C@H](N)C(=O)[O-])ccc1O
HTY		HTY.params	N[C@@H](Cc1ccc(O)cc1O)C(=O)[O-]
B02		4-amino-tetrahydropyran-4-carboxylic_acid.params	COCCC(C)(N)C(=O)[O-]
HPR		HPR.params	CC(O)C[C@H](N)C(=O)[O-]
C60		trifluoro-alanine.params	N[C@H](C(=O)[O-])C(F)(F)F
C01		beta-cyclopentyl-alanine.params	N[C@@H](CC1CCCC1)C(=O)[O-]
A12		2.4-dimethyl-phenylalanine.params	Cc1ccc(C[C@H](N)C(=O)[O-])c(C)c1
A07		1-methyl-histidine_prot.params	CN1C=C(C[C@H](N)C(=O)[O-])NC1
A68		3-aminomethyl-phenylalanine.params	N[C@@H](Cc1cccc(C[NH3+])c1)C(=O)[O-]
V01		V01.params	N[C@H](C(=O)[O-])C(O)c1ccc(O)c(Cl)c1
C12		cyclohexyl-glycine.params	N[C@H](C(=O)[O-])C1CCCCC1
A84		3-methyl-phenylalanine.params	Cc1cccc(C[C@H](N)C(=O)[O-])c1
C61		trifluoro-leucine.params	CC(C[C@H](N)C(=O)[O-])C(F)(F)F
BCS		BCS.params	N[C@@H](CSCc1ccccc1)C(=O)[O-]
A78		3-hydroxy-phenylalanine.params	N[C@@H](Cc1cccc(O)c1)C(=O)[O-]
C95		3-chloro-phenylalanine.params	N[C@@H](Cc1cccc(Cl)c1)C(=O)[O-]
A91		4.5-dehydro-leucine.params	C=C(C)C[C@H](N)C(=O)[O-]
B63		amino-ethyl-cysteine.params	N[C@@H](CSCC[NH3+])C(=O)[O-]
B19		4-fluoro-proline.params	CC(F)C[C@H](N)C(=O)[O-]
C03		beta-fluoro-alanine.params	N[C@@H](CF)C(=O)[O-]
C91		fluoro-leucine_ent1.params	CC(CF)C[C@H](N)C(=O)[O-]
A94		4-aminomethyl-phenylalanine.params	N[C@@H](Cc1ccc(C[NH3+])cc1)C(=O)[O-]
ORN		ornithine.params	N[C@@H](CCC[NH3+])C(=O)[O-]
DPP		2.3-diaminopropionic_acid.params	N[C@@H](C[NH3+])C(=O)[O-]
IGL		2-indanyl-glycine_puck1.params	N[C@H](C(=O)[O-])C1Cc2ccccc2C1
C05		beta-iodo-alanine.params	N[C@@H](CI)C(=O)[O-]
A04		1-amino-cyclopentane-carboxylic_acid.params	CCCC(C)(N)C(=O)[O-]
A92		4.5-dehydro-lysine.params	N[C@@H](CC=CC[NH3+])C(=O)[O-]
A48		2-methyl-phenylalanine.params	Cc1ccccc1C[C@H](N)C(=O)[O-]
B67		beta-(1-naphthyl)-alanine.params	N[C@@H](Cc1cccc2ccccc12)C(=O)[O-]
B31		4-tert-butyl-phenylalanine.params	CC(C)(C)c1ccc(C[C@H](N)C(=O)[O-])cc1
APA		APA.params	Nc1ccc(C[C@H](N)C(=O)[O-])cc1
C16		dipropyl-glycine.params	CC.CCCC(C)(N)C(=O)[O-]