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{"sheet":"Intro","index":0,"n_rows":17,"n_cols":1,"rows_kept":17,"cut":false,"hidden":false,"merged":[]}
["Peptide Companion - Excel Version"]
[]
["There is a program called Peptide Companion (written by Michal Lebl, Viktor Krchnak, and Jiri Lebl in 1992) installed on many peptide chemist's computers across laboratories everywhere. However, upgrades to new versions of Windows have made it unusable. Therefore we are including this macro based peptide chemist friendly tool which you can use if you have Excel installed on your computer.  "]
[]
["This spreadsheet version is intended to become a community project. If you feel that something should be added to this spreadsheet, just ask and we will try to implement it. Or even better, if you already have written something which may be beneficial to other peptide enthusiasts, let us know, send it to us and we will incorporate it to the spreadsheet collection. The newest version of the project will be always available on our website. You will always be credited for your work."]
[]
["This spreadsheet will be always free. It can be downloaded from: http://www.spyderinstitute.com/software.html"]
[]
["For any questions feel free to contact us at michallebl@gmail.com"]
[]
["At this moment our spreadsheet can:"]
[]
["Calculate molecular weights of peptides"]
[]
["Predict difficult couplings of peptides to be synthesized"]
[]
["Predict peptide HPLC retention times "]

{"sheet":"HPLC Prediction","index":1,"n_rows":24,"n_cols":23,"rows_kept":24,"cut":false,"hidden":false,"merged":[]}
["Sequence",null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,"Sequence"]
["AAA",3.57,1,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,0,0]
["AAAAA",5.14,0.7,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,{"$f":"V4-0.2","v":3.3699999999999997},0]
["DSAF",11.63,1,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,"AAA",3.57,1]
["AQWSAQWSA",17.16,0.7,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,{"$f":"V4+0.2","v":3.77},0]
["YGGFL",18.39,1,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,{"$f":"V7-0.2","v":4.9399999999999995},0]
["ASDERTFGYIPLKMN",24.77,0.7,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,"AAAAA",5.14,0.7]
["FFFF",30,1,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,{"$f":"V7+0.2","v":5.34},0]
[null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,{"$f":"V10-0.2","v":11.430000000000001},0]
[null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,"DSAF",11.63,1]
[null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,{"$f":"V10+0.2","v":11.83},0]
[null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,{"$f":"V13-0.2","v":16.96},0]
[null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,"AQWSAQWSA",17.16,0.7]
[null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,{"$f":"V13+0.2","v":17.36},0]
[null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,{"$f":"V16-0.2","v":18.190000000000001},0]
[null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,"YGGFL",18.39,1]
[null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,{"$f":"V16+0.2","v":18.59},0]
[null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,{"$f":"V19-0.2","v":24.57},0]
[null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,"ASDERTFGYIPLKMN",24.77,0.7]
[null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,{"$f":"V19+0.2","v":24.97},0]
[null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,{"$f":"V22-0.2","v":29.8},0]
[null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,"FFFF",30,1]
[null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,{"$f":"V22+0.2","v":30.2},0]
[null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,{"$f":"V23+1","v":31.2},0]

{"sheet":"Molecular Weights","index":2,"n_rows":22,"n_cols":14,"rows_kept":22,"cut":false,"hidden":false,"merged":[]}
["Sequence",null,null,null,null,null,null,null,null,"AA-3-Letter","AA-1-Letter","Fmoc-AA","MW Fmoc","MW AA"]
["AAAASSDS",678.67,null,null,null,null,null,null,null,"Ala","A","Fmoc-Ala",311.3,71.08]
["Ala-Gly-Pro-Tyr-His-Arg",699.78,null,null,null,null,null,null,null,"Cys","C","Fmoc-Cys(Trt)",585.70000000000005,103.15]
["ASDF",438.44,null,null,null,null,null,null,null,"Asp","D","Fmoc-Asp(OBut)",411.4,115.09]
[null,null,null,null,null,null,null,null,null,"Glu","E","Fmoc-Glu(OBut)",425.5,129.12]
[null,null,null,null,null,null,null,null,null,"Phe","F","Fmoc-Phe",387.4,147.18]
[null,null,null,null,null,null,null,null,null,"Gly","G","Fmoc-Gly",297.3,57.05]
[null,null,null,null,null,null,null,null,null,"His","H","Fmoc-His(Trt)",619.70000000000005,137.13999999999999]
[null,null,null,null,null,null,null,null,null,"Ile","I","Fmoc-Ile",353.4,113.16]
[null,null,null,null,null,null,null,null,null,"Lys","K","Fmoc-Lys(Boc)",468.5,128.18]
[null,null,null,null,null,null,null,null,null,"Leu","L","Fmoc-Leu",353.4,113.16]
[null,null,null,null,null,null,null,null,null,"Met","M","Fmoc-Met",371.4,131.19999999999999]
[null,null,null,null,null,null,null,null,null,"Asn","N","Fmoc-Asn(Trt)",596.70000000000005,114.11]
[null,null,null,null,null,null,null,null,null,"Pro","P","Fmoc-Pro",337.4,97.12]
[null,null,null,null,null,null,null,null,null,"Gln","Q","Fmoc-Gln(Trt)",610.70000000000005,128.13]
[null,null,null,null,null,null,null,null,null,"Arg","R","Fmoc-Arg(Pbf)",648.70000000000005,156.19]
[null,null,null,null,null,null,null,null,null,"Ser","S","Fmoc-Ser(But)",383.4,87.08]
[null,null,null,null,null,null,null,null,null,"Thr","T","Fmoc-Thr(But)",397.5,101.11]
[null,null,null,null,null,null,null,null,null,"Val","V","Fmoc-Val",339.4,99.13]
[null,null,null,null,null,null,null,null,null,"Trp","W","Fmoc-Trp(Boc)",526.6,186.22]
[null,null,null,null,null,null,null,null,null,"Tyr","Y","Fmoc-Tyr(But)",459.5,163.18]
[null,null,null,null,null,null,null,null,null,"Nle",1,"Fmoc-Nle",353.4,113.16]

{"sheet":"Difficulty (Sheet)","index":3,"n_rows":5,"n_cols":15,"rows_kept":5,"cut":false,"hidden":false,"merged":[]}
["Sequence"]
["CASDERTFAAADSA","C 0.97","A 0.84","S 0.81","D 0.88","E 1.02","R 1.07","T 1.25","F 1.14","A 1.07","A 1.07","A 0.88","D 0.88","S 0.88","A 0.88"]
["LKVHGFDSA","L 1.15","K 1.12","V 0.98","H 0.77","G 0.91","F 0.88","D 0.88","S 0.88","A 0.88"]
["VQAAIDYING","V 1.36","Q 1.14","A 1.20","A 1.25","I 1.18","D 1.02","Y 0.88","I 0.88","N 0.88","G 0.88"]
["ASDFGHKL","A 0.91","S 0.77","D 0.89","F 1.01","G 0.88","H 0.88","K 0.88","L 0.88"]

{"sheet":"Difficulty (Detail)","index":4,"n_rows":11,"n_cols":3,"rows_kept":11,"cut":false,"hidden":false,"merged":[]}
["VQAAIDYING"]
[null,"V",1.36]
[null,"Q",1.1399999999999999]
[null,"A",1.2]
[null,"A",1.25]
[null,"I",1.18]
[null,"D",1.02]
[null,"Y",0.88]
[null,"I",0.88]
[null,"N",0.88]
[null,"G",0.88]

{"sheet":"HPLC Instructions","index":5,"n_rows":13,"n_cols":1,"rows_kept":13,"cut":false,"hidden":false,"merged":[]}
["HPLC retention times predictor"]
["Macro written by M. Lebl based on Tripet B. et al. J. Chromatography A, 1141, 212 (2007)."]
[]
["Your Excel must have macro capability enabled. See e.g. http://www.ehow.com/how_8160192_enable-excel-macros.html"]
[]
["There is no algorithm which would precisely predict HPLC trace of your peptide on your column. However, this algorithm will show you very reliably the relative retention of the \"new\" peptide in comparison to your \"standart\" peptide, which you have analyzed on the same column using the same gradient earlier."]
["Predicts HPLC of up to 100 peptides in one sheet. Just paste your list in the first column of the \"HPLC Prediction\" sheet and click the button in the sheet. List of retention times will be created, sorted and theoretical HPLC trace will be generated."]
[]
["The algorithm will generate the \"ideal\" chromatogram using \"ideal\" gradient of 0.2% TFA in acetonitrile. It cannot know what column and gradient will be used by you and therefore the retention times will be only relative to your situation. It does not make sense to predict HPLC of just one peptide, it will show it eluted at 30 minutes.  If you analyze peptide with no retention, it will be eluted at the dead volume of the fictional column, which is 1 minute. "]
[]
["Make sure that the carboxy terminus is defined by selecting (or unselecting) \"C-Terminal Amide\" checkbox. If you are comparing acetylated peptides, check the checkbox \"N-Terminus Acetylated\"."]
[]
["Sequences should be written in one-letter code. You can use lower case or upper case letters, the algorithm does not know the difference between D and L amino acids. Diastereomeric peptides are eluted very close to each other, but there is no guarantee that you can say which one is which (If they separate at all)."]

{"sheet":"Difficult Coupling Instructions","index":6,"n_rows":14,"n_cols":1,"rows_kept":14,"cut":false,"hidden":false,"merged":[]}
["Difficult couplings predictor"]
["Macro written by M. Lebl based on Krchnak, V., Flegelova, Z., Vagner, J., Int. J.Peptide Protein Res. 42, 450, 1993."]
[]
["Your Excel must have macro capability enabled. See e.g. http://www.ehow.com/how_8160192_enable-excel-macros.html"]
[]
["Predicts up to 100,000 peptides in one sheet. Just paste your list in the \"Sheet Calculation\" sheet (or any other new sheet) and click \"ctrl + s\" (or click the button in the sheet). List of difficulty coefficients will be created and original sequence will be labeled with red and green for difficult and easy couplings. "]
[]
["If you are interested only in one peptide, or want to see graphical representation of the profile, paste its sequence in the \"Individual Peptides\" sheet (or any other new sheet) and press \"ctrl + i\" (or click the button in the sheet). To compare more peptides, use always new sheet."]
[]
["If your prediction shows potential problem, try inserting pseudoproline (Ser - based, or Thr - based) in the place of Ser or Thr in the sequence. Exchange Ser for \"X\" and Thr for \"Z\" and run the calculation again to see the improvement. Another option is the use of N-substituted amino acids (e.g. ). In this case insert \"J\" in the sequence."]
[]
["Sequences should be written in one-letter code."]
[]
["The following rules are used in the prediction of difficult sequences: (i) Coupling difficulties begin at residue number five from the carboxy terminus. A pendent peptide chain starts to be prone to aggregation after acquiring its fifth residue and its susceptibility to aggregation declines with the increasing peptide length. (ii) The carboxyterminal six to nine residues dominantly influence the character of the whole sequence.  (iii) Sequence starts being potentially difficult after two or three consecutive potentials have exceeded the value 1.1 and ends with the same number of consecutive potentials being below 0.9. With the higher aggregation potential comes the higher proportion of pendent peptide chains tending to aggregate.  The result is the slower aminoacylation. (iv) In most cases aggregation profiles with seven or more consecutive average potentials greater than 1.1 will cause difficult couplings for the entire sequence (even if the potential drops below 0.9 for the rest of the sequence). (v) Residues more than ten amino acids distant from the carboxy terminus can be coupled without significant problems even if the aggregation profiles show four consecutive values over 1.1 (but do not show strong aggregation in the carboxyterminal decapeptide). (vi) The type of the coupled amino acid contributes significantly to the overall aminoacylation rate. Since prediction of difficult sequences by using the aggregation profile eliminates the effect of random coupling problems, the relative reactivity of a coupled amino acid has to be considered.  This effect is particularly pronounced when slow reacting amino acids are coupled to a difficult sequence. Evaluating \"Individual Sequences\" will show graphical representation of aggregation potential for amino acids starting from the fifth position in the peptide chain. If it is difficult to associate the point on the graph with the amino acid residue on x axis, point the particular position with the mouse pointer, and the amino acid label will be displayed.  Only sequences containing natural unprotected amino acids can be evaluated correctly since the aggregation parameters are not defined for unnatural building blocks. (Program will use the value of 0.9.) If you want to use this program to evaluate unnatural sequences, replace unnatural building blocks with natural amino acids having similar coupling properties (make a qualified guess)."]

{"sheet":"Parameters","index":7,"n_rows":27,"n_cols":11,"rows_kept":27,"cut":false,"hidden":false,"merged":[]}
[null,null,"X-OH","X-NH2","Ac-X","NH2-X","X",null,null,"Meek 7.4","Meek 2.1"]
["A","Ala",5,3,3.4,1.5,2.8,null,"A",0.5,-0.1]
["C","Cys",10.8,8.6,8.1,4.3,6,null,"C",-6.8,-2.2000000000000002]
["D","Asp",1.4,1.9,1.7,1.4,1.5,null,"D",-8.1999999999999993,-2.8]
["E","Glu",2.1,3.8,3.1,1.4,2.2999999999999998,null,"E",-16.899999999999999,-7.5]
["F","Phe",37,32.9,29.6,22.3,20.6,null,"F",13.2,13.9]
["G","Gly",0,0,0,0,0,null,"G",0,-0.5]
["H","His",0,1.2,0,1.4,"−2.4",null,"H",-3.5,0.8]
["I","Ile",30.5,25.2,21.8,14.2,15.3,null,"I",13.9,11.8]
["K","Lys","−1.0",0,"−0.3",1.3,"−2.3",null,"K",0.1,-3.2]
["L","Leu",32.200000000000003,26,23.7,15.8,16.8,null,"L",8.8000000000000007,10]
["M","Met",21.2,18,16.5,11.8,11.2,null,"M",4.8,7.1]
["N","Asn","−2.3",0,"−0.5",0,"−0.5",null,"N",0.8,-1.6]
["P","Pro",12.2,7.5,10.199999999999999,4.5,3.6,null,"P",6.1,8]
["Q","Gln",0,1.6,0.7,1.4,0.8,null,"Q",-4.8,-2.5]
["R","Arg",2.5,3.7,2.4,3,"−1.1",null,"R",0.8,-4.5]
["S","Ser","−0.8",0,0,0,0.6,null,"S",1.2,-3.7]
["T","Thr",3.6,3.3,2.8,1.9,1.5,null,"T",2.7,1.5]
["V","Val",20,15.4,13.8,8.1,8.6,null,"V",2.7,3.3]
["W","Trp",40,36.5,33.200000000000003,27.9,22.9,null,"W",14.9,18.100000000000001]
["Y","Tyr",18.899999999999999,16.399999999999999,15.6,12.8,8.1999999999999993,null,"Y",6.1,8.1999999999999993]
["Parameters are hidden and cannot be changed",null,null,null,null,null,null,null,"amino",2.4,-0.4]
[null,null,null,null,null,null,null,null,"cooh",-3,6.9]
[null,null,null,null,null,null,null,null,"conh2",7.8,5]
[null,null,null,null,null,null,null,null,"Ac",5.6,3.9]
[null,null,null,null,null,null,null,null,"tyrso3",10.9,6.5]
[null,null,null,null,null,null,null,null,"pyGlu",-1.1000000000000001,-2.8]