# # EASE-MM: sequence-based prediction of mutation-induced stability changes with feature-based multiple models # # This file describes the input format for the EASE-MM web-server. # If the line starts with '#' (hash), the line is ignored. # If the line does NOT start with '#' (hash), it must start with 'SEQ:' or 'MUT:'. # There must be an equal number of 'SEQ:' and 'MUT:' lines, and a 'MUT:' line must always follow a corresponding 'SEQ:' line. # 'SEQ:' line defines the target protein sequence in a one-letter code: 'SEQ: unique_sequence_name protein_sequence'. # 'MUT:' line defines the mutations which are to be predicted for the protein sequence specified on the previous line: 'MUT: XnY ...'. # The mutation format 'XnY' stands for X: wild-type amino acid, n: 1-based sequence position, Y: mutated amino acid. # Multiple mutations per line are allowed, however, they are always predicted as single-site mutations at a time. # The whole protein sequence must be specified on a single line, i.e., line-breaks are not allowed. ############################################################################ # Please note that the input size is limited to 20 proteins per submission # ############################################################################ ############ # Examples # ############ # Example of a query with three mutations (each mutation is predicted as a single-site mutation): SEQ: my_short_seq RDSGTVWGALGHGINLNIPNFQMTDDIDEVRWERGSTLVAEFKRKMKPFLKSGAFEILANGDLKIKNLTRDDSGTYNVTVYSTNGTRILDKALDLRILE MUT: A40G L16V G4A # The use of wild-card '*' is allowed in three different ways: # 1) carry out all possible substitutions for the given position 'n' of amino acid 'X': 'Xn*' # Example: SEQ: my_short_seq RDSGTVWGALGHGINLNIPNFQMTDDIDEVRWERGSTLVAEFKRKMKPFLKSGAFEILANGDLKIKNLTRDDSGTYNVTVYSTNGTRILDKALDLRILE MUT: N60* # 2) carry out substitutions to amino acid 'Y' for all possible positions in the give protein sequence: '*Y' # Example: SEQ: my_short_seq RDSGTVWGALGHGINLNIPNFQMTDDIDEVRWERGSTLVAEFKRKMKPFLKSGAFEILANGDLKIKNLTRDDSGTYNVTVYSTNGTRILDKALDLRILE MUT: *A # 3) carry out all possible substitutions of all possible positions in the give protein sequence: '**' # Example: SEQ: my_short_seq RDSGTVWGALGHGINLNIPNFQMTDDIDEVRWERGSTLVAEFKRKMKPFLKSGAFEILANGDLKIKNLTRDDSGTYNVTVYSTNGTRILDKALDLRILE MUT: ** # The use of wild-cards can be used alongside specific mutations: SEQ: my_short_seq RDSGTVWGALGHGINLNIPNFQMTDDIDEVRWERGSTLVAEFKRKMKPFLKSGAFEILANGDLKIKNLTRDDSGTYNVTVYSTNGTRILDKALDLRILE MUT: A40G L16V G4A N60* *A ** # More examples: SEQ: my_short_seq RDSGTVWGALGHGINLNIPNFQMTDDIDEVRWERGSTLVAEFKRKMKPFLKSGAFEILANGDLKIKNLTRDDSGTYNVTVYSTNGTRILDKALDLRILE MUT: D62Y Y76A R96* SEQ: my_long_seq MPEGSLYEMAVEQFNRAASLMDLESDLAEVLRRPKRVLIVEFPVRMDDGHVEVFTGYRVQHNVARGPAKGGIRYHPDVTLDEVKALAFWMTWKTAVMNLPFGGGKGGVRVDPKKLSRNELERLSRRFFSEIQVIIGPYNDIPAPDVNTNADVIAWYMDTYSMNVGHTVLGIVTGKPVELGGSKGREEATGRGVKVCAGLAMDVLGIDPKKATVAVQGFGNVGQFAALLISQE MUT: E52A G4A L27* SEQ: seq_to_ala MSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPGATL MUT: *A