We offer a standalone version, available here, for predicting structures locally. TCR-pMHC Complex: Class I TCR-pMHC Complex: Class II Unbound TCR Enter sequence Select from gene Enter TCR α sequence Enter TCR β sequence Enter peptide sequence Species Human Mouse Choose MHC class IHLA-A*01:01HLA-A*02:01HLA-A*02:03HLA-A*02:06HLA-A*03:01HLA-A*11:01HLA-A*23:01HLA-A*24:02HLA-A*26:01HLA-A*29:02HLA-A*30:01HLA-A*30:02HLA-A*31:01HLA-A*32:01HLA-A*33:01HLA-A*68:01HLA-A*68:02HLA-B*07:02HLA-B*08:01HLA-B*14:02HLA-B*15:01HLA-B*15:02HLA-B*18:01HLA-B*27:03HLA-B*27:05HLA-B*27:06HLA-B*27:09HLA-B*35:01HLA-B*35:08HLA-B*37:01HLA-B*39:01HLA-B*40:01HLA-B*40:02HLA-B*41:03HLA-B*41:04HLA-B*42:01HLA-B*44:02HLA-B*44:03HLA-B*44:05HLA-B*46:01HLA-B*51:01HLA-B*53:01HLA-B*57:01HLA-B*58:01HLA-B*81:01HLA-C*05:01HLA-C*06:02HLA-C*07:02HLA-C*08:02HLA-C*14:02HLA-E*01:03HLA-F*01:01HLA-G*01:01 Enter MHC I sequence or select gene from above As an alternative to entering sequences, you can upload a FASTA file instead. Make sure to use the correct sequence order indicated here. FASTA input: FASTA example: FASTA input Advanced options Perform Amber energy minimization Click to view lists of class I and class II pMHC templates. pMHC PDB templates to exclude: pMHC PDB templates to include: PDB templates date cutoff: Example input: TCR / HLA-A*01 - SARS-CoV-2 ORF3 peptide complex (reference) Example output: TCR / HLA-A*01 - SARS-CoV-2 ORF3 peptide complex Select TCR α sequence from gene Species Human Mouse Choose TRAVTRAV1-1*01TRAV1-1*02TRAV1-2*01TRAV10*01TRAV12-1*01TRAV12-1*02TRAV12-2*01TRAV12-2*02TRAV12-3*01TRAV12-3*02TRAV13-1*01TRAV13-1*02TRAV13-2*01TRAV13-2*02TRAV14/DV4*01TRAV14/DV4*02TRAV14/DV4*03TRAV16*01TRAV17*01TRAV18*01TRAV19*01TRAV2*01TRAV2*02TRAV20*01TRAV21*01TRAV22*01TRAV23/DV6*01TRAV23/DV6*02TRAV23/DV6*03TRAV24*01TRAV24*02TRAV25*01TRAV26-1*01TRAV26-1*02TRAV26-2*01TRAV27*01TRAV27*02TRAV29/DV5*01TRAV29/DV5*02TRAV3*01TRAV30*01TRAV34*01TRAV35*01TRAV36/DV7*01TRAV36/DV7*02TRAV36/DV7*04TRAV38-1*01TRAV38-1*02TRAV38-1*03TRAV38-2/DV8*01TRAV39*01TRAV4*01TRAV40*01TRAV41*01TRAV5*01TRAV6*01TRAV7*01TRAV8-1*01TRAV8-2*01TRAV8-2*02TRAV8-3*01TRAV8-3*02TRAV8-4*01TRAV8-4*02TRAV8-4*04TRAV8-4*05TRAV8-6*01TRAV8-6*02TRAV8-7*01TRAV9-1*01TRAV9-2*01TRAV9-2*04 Choose TRAJTRAJ1*01TRAJ10*01TRAJ11*01TRAJ12*01TRAJ13*01TRAJ13*02TRAJ14*01TRAJ15*01TRAJ15*02TRAJ16*01TRAJ17*01TRAJ18*01TRAJ19*01TRAJ2*01TRAJ20*01TRAJ21*01TRAJ22*01TRAJ23*01TRAJ23*02TRAJ24*01TRAJ24*02TRAJ25*01TRAJ26*01TRAJ27*01TRAJ28*01TRAJ29*01TRAJ3*01TRAJ30*01TRAJ31*01TRAJ32*01TRAJ32*02TRAJ33*01TRAJ34*01TRAJ36*01TRAJ37*01TRAJ37*02TRAJ38*01TRAJ39*01TRAJ4*01TRAJ40*01TRAJ41*01TRAJ42*01TRAJ43*01TRAJ44*01TRAJ45*01TRAJ46*01TRAJ47*01TRAJ47*02TRAJ48*01TRAJ49*01TRAJ5*01TRAJ50*01TRAJ52*01TRAJ53*01TRAJ54*01TRAJ56*01TRAJ57*01TRAJ59*01TRAJ6*01TRAJ7*01TRAJ8*01TRAJ9*01 Generate sequence Select TCR β sequence from gene Species Human Mouse TRBVTRBV10-1*01TRBV10-1*02TRBV10-2*01TRBV10-3*01TRBV10-3*02TRBV10-3*03TRBV10-3*04TRBV11-1*01TRBV11-2*01TRBV11-2*03TRBV11-3*01TRBV12-3*01TRBV12-4*01TRBV12-4*02TRBV12-5*01TRBV13*01TRBV13*02TRBV14*01TRBV14*02TRBV15*01TRBV15*02TRBV15*03TRBV16*01TRBV16*03TRBV18*01TRBV19*01TRBV19*02TRBV19*03TRBV2*01TRBV2*02TRBV2*03TRBV20-1*01TRBV20-1*03TRBV20-1*04TRBV20-1*06TRBV20-1*07TRBV24-1*01TRBV25-1*01TRBV27*01TRBV28*01TRBV29-1*01TRBV29-1*02TRBV3-1*01TRBV30*01TRBV30*02TRBV30*05TRBV4-1*01TRBV4-2*01TRBV4-2*02TRBV4-3*01TRBV4-3*02TRBV4-3*03TRBV5-1*01TRBV5-1*02TRBV5-4*01TRBV5-4*02TRBV5-5*01TRBV5-5*02TRBV5-5*03TRBV5-6*01TRBV5-8*01TRBV6-1*01TRBV6-2*01TRBV6-3*01TRBV6-4*01TRBV6-4*02TRBV6-5*01TRBV6-6*01TRBV6-6*02TRBV6-6*03TRBV6-6*04TRBV6-6*05TRBV6-8*01TRBV6-9*01TRBV7-2*01TRBV7-2*02TRBV7-2*03TRBV7-2*04TRBV7-3*01TRBV7-3*04TRBV7-4*01TRBV7-6*01TRBV7-6*02TRBV7-7*01TRBV7-7*02TRBV7-8*01TRBV7-8*02TRBV7-8*03TRBV7-9*01TRBV7-9*02TRBV7-9*03TRBV7-9*04TRBV7-9*05TRBV7-9*06TRBV9*01TRBV9*02TRBV9*03 TRBJTRBJ1-1*01TRBJ1-2*01TRBJ1-3*01TRBJ1-4*01TRBJ1-5*01TRBJ1-6*01TRBJ1-6*02TRBJ2-1*01TRBJ2-2*01TRBJ2-3*01TRBJ2-4*01TRBJ2-5*01TRBJ2-6*01TRBJ2-7*01 Generate sequence Enter peptide sequence Species Human Mouse Choose MHC class IHLA-A*01:01HLA-A*02:01HLA-A*02:03HLA-A*02:06HLA-A*03:01HLA-A*11:01HLA-A*23:01HLA-A*24:02HLA-A*26:01HLA-A*29:02HLA-A*30:01HLA-A*30:02HLA-A*31:01HLA-A*32:01HLA-A*33:01HLA-A*68:01HLA-A*68:02HLA-B*07:02HLA-B*08:01HLA-B*14:02HLA-B*15:01HLA-B*15:02HLA-B*18:01HLA-B*27:03HLA-B*27:05HLA-B*27:06HLA-B*27:09HLA-B*35:01HLA-B*35:08HLA-B*37:01HLA-B*39:01HLA-B*40:01HLA-B*40:02HLA-B*41:03HLA-B*41:04HLA-B*42:01HLA-B*44:02HLA-B*44:03HLA-B*44:05HLA-B*46:01HLA-B*51:01HLA-B*53:01HLA-B*57:01HLA-B*58:01HLA-B*81:01HLA-C*05:01HLA-C*06:02HLA-C*07:02HLA-C*08:02HLA-C*14:02HLA-E*01:03HLA-F*01:01HLA-G*01:01 Enter MHC I sequence or select gene from above Advanced options Perform Amber energy minimization Click to view lists of class I and class II pMHC templates. pMHC PDB templates to exclude: pMHC PDB templates to include: PDB templates date cutoff: Example input: TCR / HLA-A*01 - SARS-CoV-2 ORF3 peptide complex (reference) Example output: TCR / HLA-A*01 - SARS-CoV-2 ORF3 peptide complex Enter sequence Select from gene Enter TCR α sequence Enter TCR β sequence Enter peptide sequence Species Human Mouse Choose MHC II αHLA-DRA*01:01HLA-DQA1*05:01HLA-DQA1*03:01HLA-DQA1*04:01HLA-DQA1*01:01HLA-DQA1*01:02HLA-DPA1*02:01HLA-DPA1*01:03HLA-DPA1*03:01 Choose MHC II βHLA-DRB1*01:01HLA-DRB1*03:01HLA-DRB1*04:01HLA-DRB1*04:05HLA-DRB1*07:01HLA-DRB1*08:02HLA-DRB1*09:01HLA-DRB1*11:01HLA-DRB1*12:01HLA-DRB1*13:01HLA-DRB1*13:02HLA-DRB1*15:01HLA-DRB3*01:01HLA-DRB3*02:02HLA-DRB4*01:01HLA-DRB5*01:01HLA-DQB1*02:01HLA-DQB1*03:01HLA-DQB1*03:02HLA-DQB1*04:02HLA-DQB1*05:01HLA-DQB1*06:02HLA-DPB1*01:01HLA-DPB1*02:01HLA-DPB1*04:01HLA-DPB1*04:02HLA-DPB1*05:01HLA-DPB1*14:01 Enter MHC II α sequence or select gene from above Enter MHC II β sequence or select gene from above As an alternative to entering sequences, you can upload a FASTA file instead. Make sure to use the correct sequence order indicated here. Upload a FASTA file: FASTA example: Example fasta input Advanced options Perform Amber energy minimization Click to view lists of class I and class II pMHC templates. pMHC PDB templates to exclude: pMHC PDB templates to include: PDB templates date cutoff: Example input: 4285 TCR - R175H neoantigen peptide complex (reference) Example output: 4285 TCR - R175H neoantigen peptide complex Select TCR α sequence from gene Species Human Mouse Choose TRAVTRAV1-1*01TRAV1-1*02TRAV1-2*01TRAV10*01TRAV12-1*01TRAV12-1*02TRAV12-2*01TRAV12-2*02TRAV12-3*01TRAV12-3*02TRAV13-1*01TRAV13-1*02TRAV13-2*01TRAV13-2*02TRAV14/DV4*01TRAV14/DV4*02TRAV14/DV4*03TRAV16*01TRAV17*01TRAV18*01TRAV19*01TRAV2*01TRAV2*02TRAV20*01TRAV21*01TRAV22*01TRAV23/DV6*01TRAV23/DV6*02TRAV23/DV6*03TRAV24*01TRAV24*02TRAV25*01TRAV26-1*01TRAV26-1*02TRAV26-2*01TRAV27*01TRAV27*02TRAV29/DV5*01TRAV29/DV5*02TRAV3*01TRAV30*01TRAV34*01TRAV35*01TRAV36/DV7*01TRAV36/DV7*02TRAV36/DV7*04TRAV38-1*01TRAV38-1*02TRAV38-1*03TRAV38-2/DV8*01TRAV39*01TRAV4*01TRAV40*01TRAV41*01TRAV5*01TRAV6*01TRAV7*01TRAV8-1*01TRAV8-2*01TRAV8-2*02TRAV8-3*01TRAV8-3*02TRAV8-4*01TRAV8-4*02TRAV8-4*04TRAV8-4*05TRAV8-6*01TRAV8-6*02TRAV8-7*01TRAV9-1*01TRAV9-2*01TRAV9-2*04 Choose TRAJTRAJ1*01TRAJ10*01TRAJ11*01TRAJ12*01TRAJ13*01TRAJ13*02TRAJ14*01TRAJ15*01TRAJ15*02TRAJ16*01TRAJ17*01TRAJ18*01TRAJ19*01TRAJ2*01TRAJ20*01TRAJ21*01TRAJ22*01TRAJ23*01TRAJ23*02TRAJ24*01TRAJ24*02TRAJ25*01TRAJ26*01TRAJ27*01TRAJ28*01TRAJ29*01TRAJ3*01TRAJ30*01TRAJ31*01TRAJ32*01TRAJ32*02TRAJ33*01TRAJ34*01TRAJ36*01TRAJ37*01TRAJ37*02TRAJ38*01TRAJ39*01TRAJ4*01TRAJ40*01TRAJ41*01TRAJ42*01TRAJ43*01TRAJ44*01TRAJ45*01TRAJ46*01TRAJ47*01TRAJ47*02TRAJ48*01TRAJ49*01TRAJ5*01TRAJ50*01TRAJ52*01TRAJ53*01TRAJ54*01TRAJ56*01TRAJ57*01TRAJ59*01TRAJ6*01TRAJ7*01TRAJ8*01TRAJ9*01 Generate sequence Select TCR β sequence from gene Species Human Mouse TRBVTRBV10-1*01TRBV10-1*02TRBV10-2*01TRBV10-3*01TRBV10-3*02TRBV10-3*03TRBV10-3*04TRBV11-1*01TRBV11-2*01TRBV11-2*03TRBV11-3*01TRBV12-3*01TRBV12-4*01TRBV12-4*02TRBV12-5*01TRBV13*01TRBV13*02TRBV14*01TRBV14*02TRBV15*01TRBV15*02TRBV15*03TRBV16*01TRBV16*03TRBV18*01TRBV19*01TRBV19*02TRBV19*03TRBV2*01TRBV2*02TRBV2*03TRBV20-1*01TRBV20-1*03TRBV20-1*04TRBV20-1*06TRBV20-1*07TRBV24-1*01TRBV25-1*01TRBV27*01TRBV28*01TRBV29-1*01TRBV29-1*02TRBV3-1*01TRBV30*01TRBV30*02TRBV30*05TRBV4-1*01TRBV4-2*01TRBV4-2*02TRBV4-3*01TRBV4-3*02TRBV4-3*03TRBV5-1*01TRBV5-1*02TRBV5-4*01TRBV5-4*02TRBV5-5*01TRBV5-5*02TRBV5-5*03TRBV5-6*01TRBV5-8*01TRBV6-1*01TRBV6-2*01TRBV6-3*01TRBV6-4*01TRBV6-4*02TRBV6-5*01TRBV6-6*01TRBV6-6*02TRBV6-6*03TRBV6-6*04TRBV6-6*05TRBV6-8*01TRBV6-9*01TRBV7-2*01TRBV7-2*02TRBV7-2*03TRBV7-2*04TRBV7-3*01TRBV7-3*04TRBV7-4*01TRBV7-6*01TRBV7-6*02TRBV7-7*01TRBV7-7*02TRBV7-8*01TRBV7-8*02TRBV7-8*03TRBV7-9*01TRBV7-9*02TRBV7-9*03TRBV7-9*04TRBV7-9*05TRBV7-9*06TRBV9*01TRBV9*02TRBV9*03 TRBJTRBJ1-1*01TRBJ1-2*01TRBJ1-3*01TRBJ1-4*01TRBJ1-5*01TRBJ1-6*01TRBJ1-6*02TRBJ2-1*01TRBJ2-2*01TRBJ2-3*01TRBJ2-4*01TRBJ2-5*01TRBJ2-6*01TRBJ2-7*01 Generate sequence Enter peptide sequence Species Human Mouse Choose MHC II αHLA-DRA*01:01HLA-DQA1*05:01HLA-DQA1*03:01HLA-DQA1*04:01HLA-DQA1*01:01HLA-DQA1*01:02HLA-DPA1*02:01HLA-DPA1*01:03HLA-DPA1*03:01 Choose MHC II βHLA-DRB1*01:01HLA-DRB1*03:01HLA-DRB1*04:01HLA-DRB1*04:05HLA-DRB1*07:01HLA-DRB1*08:02HLA-DRB1*09:01HLA-DRB1*11:01HLA-DRB1*12:01HLA-DRB1*13:01HLA-DRB1*13:02HLA-DRB1*15:01HLA-DRB3*01:01HLA-DRB3*02:02HLA-DRB4*01:01HLA-DRB5*01:01HLA-DQB1*02:01HLA-DQB1*03:01HLA-DQB1*03:02HLA-DQB1*04:02HLA-DQB1*05:01HLA-DQB1*06:02HLA-DPB1*01:01HLA-DPB1*02:01HLA-DPB1*04:01HLA-DPB1*04:02HLA-DPB1*05:01HLA-DPB1*14:01 Enter MHC II α sequence or select gene from above Enter MHC II β sequence or select gene from above Advanced options Perform Amber energy minimization Click to view lists of class I and class II pMHC templates. pMHC PDB templates to exclude: pMHC PDB templates to include: PDB templates date cutoff: Example input: 4285 TCR - R175H neoantigen peptide complex (reference) Example output: 4285 TCR - R175H neoantigen peptide complex Enter TCR sequence Select from Germline gene Enter TCR α sequence Enter TCR β sequence As an alternative to entering sequences, you can upload a FASTA file instead. Make sure to use the correct sequence order indicated here. Upload a FASTA file: FASTA example: Example fasta input Advanced options Perform Amber energy minimization PDB templates date cutoff: Example input: BV9–CDR3β TCR (reference) Example output: BV9–CDR3β TCR Select TCR α sequence from gene Species Human Mouse Choose TRAVTRAV1-1*01TRAV1-1*02TRAV1-2*01TRAV10*01TRAV12-1*01TRAV12-1*02TRAV12-2*01TRAV12-2*02TRAV12-3*01TRAV12-3*02TRAV13-1*01TRAV13-1*02TRAV13-2*01TRAV13-2*02TRAV14/DV4*01TRAV14/DV4*02TRAV14/DV4*03TRAV16*01TRAV17*01TRAV18*01TRAV19*01TRAV2*01TRAV2*02TRAV20*01TRAV21*01TRAV22*01TRAV23/DV6*01TRAV23/DV6*02TRAV23/DV6*03TRAV24*01TRAV24*02TRAV25*01TRAV26-1*01TRAV26-1*02TRAV26-2*01TRAV27*01TRAV27*02TRAV29/DV5*01TRAV29/DV5*02TRAV3*01TRAV30*01TRAV34*01TRAV35*01TRAV36/DV7*01TRAV36/DV7*02TRAV36/DV7*04TRAV38-1*01TRAV38-1*02TRAV38-1*03TRAV38-2/DV8*01TRAV39*01TRAV4*01TRAV40*01TRAV41*01TRAV5*01TRAV6*01TRAV7*01TRAV8-1*01TRAV8-2*01TRAV8-2*02TRAV8-3*01TRAV8-3*02TRAV8-4*01TRAV8-4*02TRAV8-4*04TRAV8-4*05TRAV8-6*01TRAV8-6*02TRAV8-7*01TRAV9-1*01TRAV9-2*01TRAV9-2*04 Choose TRAJTRAJ1*01TRAJ10*01TRAJ11*01TRAJ12*01TRAJ13*01TRAJ13*02TRAJ14*01TRAJ15*01TRAJ15*02TRAJ16*01TRAJ17*01TRAJ18*01TRAJ19*01TRAJ2*01TRAJ20*01TRAJ21*01TRAJ22*01TRAJ23*01TRAJ23*02TRAJ24*01TRAJ24*02TRAJ25*01TRAJ26*01TRAJ27*01TRAJ28*01TRAJ29*01TRAJ3*01TRAJ30*01TRAJ31*01TRAJ32*01TRAJ32*02TRAJ33*01TRAJ34*01TRAJ36*01TRAJ37*01TRAJ37*02TRAJ38*01TRAJ39*01TRAJ4*01TRAJ40*01TRAJ41*01TRAJ42*01TRAJ43*01TRAJ44*01TRAJ45*01TRAJ46*01TRAJ47*01TRAJ47*02TRAJ48*01TRAJ49*01TRAJ5*01TRAJ50*01TRAJ52*01TRAJ53*01TRAJ54*01TRAJ56*01TRAJ57*01TRAJ59*01TRAJ6*01TRAJ7*01TRAJ8*01TRAJ9*01 Generate sequence Select TCR β sequence from gene Species Human Mouse TRBVTRBV10-1*01TRBV10-1*02TRBV10-2*01TRBV10-3*01TRBV10-3*02TRBV10-3*03TRBV10-3*04TRBV11-1*01TRBV11-2*01TRBV11-2*03TRBV11-3*01TRBV12-3*01TRBV12-4*01TRBV12-4*02TRBV12-5*01TRBV13*01TRBV13*02TRBV14*01TRBV14*02TRBV15*01TRBV15*02TRBV15*03TRBV16*01TRBV16*03TRBV18*01TRBV19*01TRBV19*02TRBV19*03TRBV2*01TRBV2*02TRBV2*03TRBV20-1*01TRBV20-1*03TRBV20-1*04TRBV20-1*06TRBV20-1*07TRBV24-1*01TRBV25-1*01TRBV27*01TRBV28*01TRBV29-1*01TRBV29-1*02TRBV3-1*01TRBV30*01TRBV30*02TRBV30*05TRBV4-1*01TRBV4-2*01TRBV4-2*02TRBV4-3*01TRBV4-3*02TRBV4-3*03TRBV5-1*01TRBV5-1*02TRBV5-4*01TRBV5-4*02TRBV5-5*01TRBV5-5*02TRBV5-5*03TRBV5-6*01TRBV5-8*01TRBV6-1*01TRBV6-2*01TRBV6-3*01TRBV6-4*01TRBV6-4*02TRBV6-5*01TRBV6-6*01TRBV6-6*02TRBV6-6*03TRBV6-6*04TRBV6-6*05TRBV6-8*01TRBV6-9*01TRBV7-2*01TRBV7-2*02TRBV7-2*03TRBV7-2*04TRBV7-3*01TRBV7-3*04TRBV7-4*01TRBV7-6*01TRBV7-6*02TRBV7-7*01TRBV7-7*02TRBV7-8*01TRBV7-8*02TRBV7-8*03TRBV7-9*01TRBV7-9*02TRBV7-9*03TRBV7-9*04TRBV7-9*05TRBV7-9*06TRBV9*01TRBV9*02TRBV9*03 TRBJTRBJ1-1*01TRBJ1-2*01TRBJ1-3*01TRBJ1-4*01TRBJ1-5*01TRBJ1-6*01TRBJ1-6*02TRBJ2-1*01TRBJ2-2*01TRBJ2-3*01TRBJ2-4*01TRBJ2-5*01TRBJ2-6*01TRBJ2-7*01 Generate sequence Advanced options Perform Amber energy minimization PDB templates date cutoff: Example input: BV9–CDR3β TCR (reference) Example output: BV9–CDR3β TCR