SwissSidechain包含了230种非标准氨基酸的gromacs和CHARMM的拓扑文件。在引入非标准氨基酸突变及分子动力学模拟中有极大的应用。为了方便查阅SwissSidechain的残基缩写所指代的真正内容，故整理下表：
| 缩写 | 指代内容 |
| ASPP | protonated ASP |
| CYS2 | disulfide cystine |
| CYS3 | cystein bound to CYT (Cys-mesitylene) |
| CYT | Cys-mesitylene |
| CYT3 | Cys-mesitylene bound to two CYS (CYS3) |
| GLUP | protonated GLU |
| LSN | neutral lysine residue |
| ALAD | Alanine dipeptide |
| O2 | O2 ligand for HEME |
| CO | CO ligand for HEME |
| 004 | Phenylglycine |
| 0A1 | 4-methoxy-beta-Phe |
| 0AF | 7-hydroxy-l-tryptophan |
| 0BN | 4-carbamimidoyl-l-phenylalanine |
| 200 | 4-chloro-Phenylalanine |
| 26P | 2-amino-6-oxopimelic acid |
| 2AG | 2-Allyl-glycine |
| 2AS | 3-methyl-aspartic acid |
| 2FM | s-(difluoromethyl)homocysteine |
| 2HF | 2-fluoro-l-histidine (NE2-ND1) |
| 2HF1 | 2-fluoro-l-histidine (ND1) |
| 2HF2 | 2-fluoro-l-histidine (NE2) |
| 2NP | l-2-amino-6-methylene-pimelic acid |
| 32T | (s)-2-amino-3-(4h-thieno[3,2-b]-pyrrol-6-yl)-propionic acid |
| 3CF | 3-cyano-phenylalanine |
| 3FG | (2s)-amino(3,5-dihydroxyphenyl)ethanoic acid |
| 3GL | 4-hydroxy-glutamic-acid |
| 3MY | 3-Chloro-tyrosine |
| 4BF | 4-Bromo-phenylalanine |
| 4CF | 4-cyano-phenylalanine |
| 4CY | nitrilo-l-methionine |
| 4FW | 4-fluorotryptophane |
| 4HMP | 4-(Hydroxymethyl)-phenylalanine |
| 4HT | 4-hydroxytryptophan |
| 4IN | 4-amino-l-tryptophan |
| 4PH | 4-Methyl-phenylalanine |
| 6CL | 6-carboxylysine |
| 6CW | 6-chloro-l-tryptophan |
| AA4 | 2-amino-5-hydroxypentanoic acid |
| ABA | 2-Aminobutyric acid |
| ACZ | cis-amiclenomycin |
| ADAM | Adamanthane |
| AGM | 5-methyl-arginine |
| AHB | beta-hydroxyasparagine |
| AHP | 2-Aminoheptanoic acid |
| ALC | 3-cyclohexyl-alanine |
| ALN | 1-Naphtalene |
| ALO | Allo-threonine |
| ANTH | 3-(9-anthryl)-alanine |
| APD | 3-Methyl-phenylalanine |
| APM | m-amidinophenyl-3-alanine |
| ARO | c-gamma-hydroxy arginine |
| AS2 | (2r)-2-amino-4-oxobutanoic acid |
| AZDA | azido-alanine |
| BB8 | Phenylserine |
| BCS | benzylcysteine |
| BHD | beta-hydroxyaspartic acid |
| BIF | biphenylalanine |
| BIU | 5-bromo-l-isoleucine |
| BTH3 | 3-(3-benzothienyl)-alanine |
| BTR | 6-bromo-tryptophan |
| BUG | Tertleucine |
| C2N | 3-chloro-d-alanine |
| CAN | canaline |
| CCS | carboxymethylated cysteine |
| CHG | Cyclohexylglycine |
| CHP | 3-chloro-4-hydroxyphenylglycine |
| CIR | Citrulline |
| CNP2 | 2-cyano-phenylalanine |
| CP24 | 2,4-chloro-phenylalanine |
| CP34 | 3,4-chloro-phenylalanine |
| CPA3 | 3-Cyclopentyl-alanine |
| CPG2 | 2-Chlorophenylglycine |
| CPG3 | 3-Chlorophenylglycine |
| CPG4 | 4-Chlorophenylglycine |
| CPH2 | 2-chloro-Phenylalanine |
| CSA | s-acetonylcysteine |
| CTE | 7-chlorotryptophan |
| CTH | 4-chlorothreonine |
| D4P | 4-Hydroxy-phenylglycine |
| DAB | Diaminobutyric acid |
| DAH | 3,4-Dihydroxy-phenylalanine |
| DBY | 3,5 dibromotyrosine |
| DDZ | 3,3-dihydroxy l-alanine |
| DILE | Diethylalanine |
| DIPH | di-phenylalanine |
| DMK | 3,3-dimethyl aspartic acid |
| DMP3 | Dimethyl-phenylalanine |
| DPP | 2,3-Diaminopropanoic acid |
| ESC | 2-amino-4-ethyl sulfanyl butyric acid |
| F2F | 3,4-Difluoro-phenylalanine |
| FCL | 3-chloro-Phenylalanine |
| FGA4 | 4-Fluoro-glutamic acid |
| FGL | 2-aminopropanedioic acid |
| FLA | Trifluoro-alanine |
| FPG2 | 2-Fluoro-phenylglycine |
| FPG3 | 3-Fluoro-phenylglycine |
| FPG4 | 4-Fluoro-phenylglycine |
| FPH2 | 2-Fluoro-Phenylalanine |
| FPH3 | 3-Fluoro-Phenylalanine |
| FT6 | 6-fluoro-l-tryptophan |
| FTR | 5-Fluoro-tryptophan |
| FUA2 | (2-furyl)-alanine |
| FVAL | 3-Fluoro-valine |
| GBUT | Guanidinobutryric |
| GDPR | 2-Amino-3-guanidinopropionic acid |
| GGB | Canavanine |
| GHG | (2s,4s)-2,5-diamino-4-hydroxy-5-oxopentanoic acid |
| GME | 5-o-methyl-glutamic acid |
| HCS | homocysteine |
| HGA | glutamine hydroxamate |
| HHK | (2s)-2,8-diaminooctanoic acid |
| HIL4 | 4-Hydroxy-L-isoleucine |
| HL2 | (2s,3r)-2-amino-3-hydroxy-4-methylpentanoic acid |
| HLEU | Homoleucine |
| HLU | 2s,3s)-2-amino-3-hydroxy-4-methylpentanoic acid |
| HOX | 4-amino-L-phenylalanine |
| HPE | Homophenylalanine |
| HQA | 3-(8-hydroxyquinolin-3-yl)-l-alanine |
| HRG | homoarginine |
| HRP | 5-Hydroxy-tryptophan |
| HSER | homoserine |
| HTR | beta-hydroxytryptophane |
| HVA | 3-hydroxy-l-valine |
| I2M | 3-methyl-l-alloisoleucine |
| IGL | 3-methyl-l-alloisoleucine |
| IIL | Allo-Isoleucine |
| ILX | 4,5-dihydroxyisoleucine |
| IYR | 3-iodo-tyrosine |
| KYN | kynurenine |
| LDO | 6-hydroxy-l-norleucine |
| LE1 | Penicillamine |
| LED | (4r)-5-oxo-l-leucine |
| LEF | (4s)-5-fluoro-l-leucine |
| LME | (3r)-3-methyl-l-glutamic acid |
| LMQ | 3-methyl-l-glutamine |
| LVG | vinylglycine |
| LVN | 4-oxo-l-valine |
| M2S | 3-{[(r)-methylsulfinyl]methyl}-l-valine |
| ME0 | hydroxy-l-methionine |
| MEG | (3s)-3-methyl-l-glutamic acid |
| MEN | n-methyl asparagine |
| MEQ | n5-methylglutamine |
| MHO | s-oxymethionine |
| MOT5 | 5-Methoxy-tryptophan |
| MP34 | 3,4-Dimethyl-phenylalanine |
| MPH2 | 2-Methyl-phenylalanine |
| MTR5 | 5-Methyl-tryptophan |
| MTR6 | 6-Methyl-tryptophan |
| MTY | m-Tyrosine |
| NAL | 2-Naphtalene |
| NIY | meta-nitro-tyrosine |
| NLE | Nor-leucine |
| NVA | Norvaline |
| OAS | o-acetylserine |
| OBF | (2s)-2-amino-4,4-difluorobutanoic acid |
| OCY | s-(2-hydroxyethyl)-l-cysteine |
| OLT | o-methyl-l-threonine |
| OMT | Methionine sulfone |
| OMX | (betar)-beta-hydroxy-l-tyrosine |
| OMY | (betar)-3-chloro-beta-hydroxy-l-tyrosine |
| ONL | 5-oxo-l-norleucine |
| ORN | Ornithine |
| OTYR | o-Tyrosine |
| PBF | 4-benzoyl-Phe |
| PF5 | pentafluoro-phenylalanine |
| PFF | 4-Fluoro-Phenylalanine |
| PHI | 4-Iodo-Phe |
| PPN | 4-Nitrophenylalanine |
| PTR | phosphonotyrosine (charge: -1) |
| PTR2 | phosphonotyrosine (charge: -2) |
| PYR2 | 3-(2-Pyridyl)-alanine |
| PYR3 | 3-(3-Pyridyl)-alanine |
| PYR4 | 3-(4-Pyridyl)-alanine |
| PYZ1 | 3-(1-Pyrazolyl)-alanine |
| QU32 | 3-(2-Quinolyl)-alanine |
| QU33 | 3-(3-quinolyl)-alanine |
| QU34 | 3-(4-quinolyl)-alanine |
| QU35 | 3-(5-Quinolyl)-alanine |
| QU36 | 3-(6-Quinolyl)-alanine |
| QX32 | 3-(2-quinoxalyl)-alanine |
| SEP | phosphoserine (charge: -1) |
| SEP2 | phosphoserine (charge: -2) |
| SLZ | thialysine |
| SME | Methionine sulfoxide |
| STYA | styryl-alanine |
| SYM | 2s,4r-4-methylglutamate |
| TBP4 | 4-tert-butyl-phenylalanine |
| TEZA | 3-(2-Tetrazolyl)-alanine |
| TFG2 | 2-(Trifluoromethyl)-phenylglycine |
| TFG3 | 3-(Trifluoromethyl)-phenylglycine |
| TFG4 | 4-(Trifluoromethyl)-phenylglycine |
| TFLE | 5,5,5-Trifluoro-DL-leucine |
| TFP2 | 2-(Trifluoromethyl)-phenylalanine |
| TFP3 | 3-(Trifluoromethyl)-phenylalanine |
| TFP4 | 4-(Trifluoromethyl)-phenylalanine |
| TH6 | 4-hydroxy-l-threonine |
| THA3 | 3-(3-thienyl)-alanine |
| THG2 | 2-thienylglycine |
| THG3 | 3-thienylglycine |
| THIC | Thio-citrulline |
| TIH | 3-(2-thienyl)-alanine |
| TPO | phosphothreonine (charge: -1) |
| TPO2 | phosphothreonine (charge: -1) |
| TRO | 2-hydroxy-tryptophan |
| TRX | 6-hydroxytryptophan |
| TRZ4 | 3-(1,2,4-Triazol-1-yl)-alanine |
| TTQ | 6-amino-7-hydroxy-l-tryptophan |
| TY2 | 3-Amino-L-tyrosine |
| TYI | 3,5-diiodotyrosine |
| TYQ | 3-amino-6-hydroxy-tyrosine |
| TZA4 | (4-thiazolyl)-alanine |
| UN1 | 2-Aminoadipic acid |
| VAH | Hydroxynorvaline |
| WFP | 3,5-Difluoro-phenylalanine |
| YCM | cysteine-s-acetamide |
| YOF | 3-fluorotyrosine |
Souce: 纽普生物 2020-03-18