Tools p3DAlign Structure-based alignment of protein sequences 1. Paste protein sequences in Fasta format: >ProteinX KFKVINVDDDGNELGSGIMELTDTELILYTRKRDSVKWHYLCLRRYGYDSNLFSFESGRRCQTGQGIFA >ProteinY SQFWVTSQKTEASERCGLQGSYILRVEAEKLTLLTLGAQSQILEPLLFWPYTLLRRYGRDKVMFSFEAG >ProteinZ SFFLVKEKMKGKNKLVPRLLGITKECVMRVDEKTKEVIQEWSLTNIKRWAASPKSFTLDFGDYQDGYYS 2. Paste PDB identifiers (the last letter indicates chain ID): >ProteinX _P_ 1XR0B >ProteinY _P_ 1P5TA Pairwise Sequence Alignment Methods Mlalign_id_pair Mfast_pair Mclustalw_pair Mslow_pair Pairwise Structural Alignment Methods Msap_pair Mfugue_pair Multiple Alignment Methods Mclustalw_msa Alignment Format clustalw_aln pir_aln pir_seq score_pdf gcg fasta_aln fasta_seq score_ascii msf_aln phylip score_html Case upper lower Residue Number on off Order input aligned The above macro is based on 3DCoffee algorithm.

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