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ir classes ~. - - - ~ - - -of ~ oroteins if one wished to obtain more refined probabilities for structure prediction within a class.Simply addine more nroteins to tbis same table did little to improve p&dic;ive ac'curacy (8). Using both Chou and (1) and Kvte and Doolittle (2) methods together one can attempt t o make some intelligent guesses about regions with ambieuous scores. For instance. alternating hvdrophilic and hydrophobic residues will give 'an intermdiite hidropathy value hut may well be strongly predicted as a-helical. This might represent a helix lying along the surface of a protein with one side buried and the other exposed. The program Protein Structure prediction is available from Project SERAPHIM a t $5 for a 5'14-in. disk plus $2 domestic-or $10 foreign postage. Make checks payable to Project SERAPHIM. T o order or to get a Project SERAPHIM Catalogue write to Project SERAPHIM, Department of Chemistry, Eastern Michigan University, Ypsilanti, MI 48197. ~~
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asm man
Flgure I Strucl.re predlct ons tor DOvlne rhwopsln comparea ~s ng the Chod method T k unaer ned and Fasman ( 11 memod ano ins W e and Dooim e (4 regoons are tnose prwleted oy hargrave el ai (6)to oe memaane-spannmg helices. In the tap line upper case italic is the helix, lower case italic is undetermined, and upper case bold is &sheet. For the lower line the upper case italic is most hydraphilic, lower case italic is moderately hydrophilic. lower case bold is maderately hydrophobic, and upper case bald is sUongly hydrophobic.
Acknowledgment
dents and faculty can gain a feeling for their reliability and sensitivity. Data entry and editing are sufficiently easy that it is possible for a student to enter quickly, for instance, four variants of a particular sequence, and to see how the amino acid substitutions alter the predicted conformation of a pnlgpeptide. \Vt. haw found thisof use in designing synthetic oeptides instudies of bovine rhodopsin ( 3 )and in romparin; &leotide binding domains in nitrogenase (4). The use of color in presenting a structure prediction of a sequence has a decided advantage over other methods because the human eye is able to take in and process more information with a ranee of colors than with simple blacka n d - w h i t r - p r e s e n t a h .I h i i allows more compact presentation tlf results. Karlier oresentations 01 Chou and Fasman predictions (5)typically showed the protein sequence on one line and on a separate line some series of symbols indicating probable conformation. Using color, it is possible to contain the same information on a single line, facilitating comparisons of different sequences one above the other. The eye then detects regularities in the color distribution of the four sequences as agestalt, rather than character by character. Earlier presentations of the Kyte and Doolittle (2) prediction typically showed a graph of hydropathy vs. sequence position number. With color, the pattern of alternating domains becomes readily apparent while still showing the amino acid sequence. The nature of the moving average means that there are no rapid fluctuations, so blocking out the scores arbitrarily as we have done produces no significant loss of information. The cutoff values that we have assigned for purple (hydrophobic) and red (hydrophilic) correspond very closely to known crystallographic domains, either buried or exposed, as discussed by Kyte and Doolittle (2) and give very few false positive predictions. Within the transitional score regions (green and blue) there is much less certainty, and no reliable prediction can be made without further information. When comparing predicted helical regions and hydrophobic regions for a protein such as bovine rhodopsin, it i s apparent that the Chou and Fasman method fails to predict the membrane-spanning helices of this molecule (6), presumably because the method was based on crystal structure of mostly globular protein (7). Argos et al. (7) showed, using hacterio rhodopsin, that the membrane-spanning helices had an amino acid distribution that correlated only weakly with either predicted a or j3 regions using the Chou and Fasman criteria. They developed an empirical set of predictors, similar to that used by Kyte and Doolittle but slightly different in rank order. In a similar way i t would be simple to rrplilre the prohahility table oiChou and Fasman with another tahlr 11usedon more recent cystral structuresofspecif~~~~
584
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This work was supported in part by NIH Grant GM 23039 and by the Kansas Agricultural Experiment Station. This is contribution 86-117j from the Kansas Agricultural Experiment Station.
Computer Programming in General Chemistry G. L. Breneman and 0. J. Parker Eastern Washington University Cheney, WA 99004
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Journal of Chemical Education
Computer availability has increased to the point where most general chemistry students have easy access to them. Many of these students also know something about programming. It may be time to take advantage of this and have students start . oroerammine comouters to solve problems as an integral part of their general chemistry course. The possibilitv of students doing their own programming and how to introduce this into the-curriculum-are discuss& in tbis paper.
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Are Pocket Computers tor Real?
Most people scoff at the mention of pocket computers; they envision the old programmable calculator. But there have been great advances recently in producing a true computer the size of a calculator. These have an alphanumeric keyboard, an excellent version of BASIC in ROM (more sophisticated than Applesoft), and enough memory in RAM to handle all the nroerammine we have in our . .. .. assignments .. I'hysizal Chemistry I.ab rourin easily. The Share K.:1.-5500ll u,ith a 10K ROM and 4.2K RAM is typical. It ailows several programs to be stored in memory at the same time and has a separate calculator mode with keys for all of the usual scientific functions including standard deviation and linear least squares. It has been selling for $70, and a combination small printer and cassette recorder interface is available for $55. The inexpensive pocket computer will lead to everybody having his or her own computer just as everybody had to have a calculator during the last decade. lmplementatlon
In a typical school a mixture of terminals, microcomputers, and pocket computers furnished. by the school andlor the students will be available. However, this could involve as many as 10 different types of computers and student programming ability from none to expert. An approach that gives everybody access to the programming projects must be carefully designed.
BASIC is the only computer language generally available on a wide range of computers. Fortunately i t is also one of the easiest t o learn and allows programs of modest length to be quite significant. These factors cannot be underestimated when we are dealing with nonprogrammers. We need to convince them that some programming is worth their time and that means they must see significant results with reasonable effort on their part. A chemistry classroom is not a computer science classroom. Thus most of the exercises should not involve the student writing all of the programs needed to do the work. Initiallv the student is furnished with programs that he enters,-debugs, and runs. Subsequent p r ~ b l i m swould require small changes in the program to handle some of the exercises and finally, depending on the group of students, there could b e a few situations where the students write their own programs. As the ability of incoming students increases, assignments can shift toward more actual program writing. Our Approach We have a number of terminals on a VAX minicomputer available in our department and in several other campus locations. This is the main resource we provide to the students. Some of our students have their own microcomputers and increasingly their own pocket computers. During a classroom demonstration showing how to use the chemistry department's program library, we show students how to access BASIC and then enter, debug, and edit a simole oroeram for calculatine density. Students follow this demon&aiion step by step o n a TV monitor and on a printed handout that they keep for future reference. Each programming exercise shows the program listing followed by a sample run with typical data. This sample run is used b; the student to determine whether his program is running correctly after he has entered i t into a computer. We assume there is no way to save the programs after they are used. Our class is not provided this option on our VAX, and manv students' own comouters mav not have a disk or tape storage. This, along with some students' inexperience, make short oroerams and modest-length assianments desirable. If storage isavailable, students could b&d up a substantial library of chemistry programs. We have started out with three extra-credit assignments oer quarter, often . giving.students a choice between two so they can choose a topic of more interdifferent est to them. As computer access becomes even more available, we expect to make these assignments a regular part of the course work.
Table 5. 10 20 30 40 50 55 60 65 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220 230 240 250
Listing ot Weak Acid Titration Curve Program
PRINT "WEAK ACID TITRATION" INPUT "KA=";KA INPUT "CONC=":CA INPUT "VOL=";VA KW=IE-14 KB=KWIKA CB=.l NA=CASVA PRINT" 0 2 4 6 8 10 12 14 PH" PRINT" FOR VB=O TO 65 STEP 5 IF VB=O THEN H=SQR(KA'CA)\GOTO 150 NB=CB'VB IF NB.Biochem.1982,128,565. 8. Arga,P.:Hsnei,M.;Garevito, R. M F E B S L a l f . 1978.3(1), 19.
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Electronic Journal To Be Produced The Journal of Chemical Education and Project SERAPHIM will be jointly producing an electronicjournalunder the sponsorship of the Dreyfuss Foundation. Details are given in a note on page 644 of this issue.
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Journal of Chemical Education
