From 9c5df7960abf895efe5978b6d9185cc50596c22b Mon Sep 17 00:00:00 2001 From: pvtroshin Date: Mon, 13 Jun 2011 15:50:35 +0000 Subject: [PATCH] Adding IUPred executables for the new web service git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4262 e3abac25-378b-4346-85de-24260fe3988d --- binaries/src/iupred/LICENSE | 76 +++ binaries/src/iupred/Makefile | 25 + binaries/src/iupred/README | 86 ++++ binaries/src/iupred/histo | 1074 ++++++++++++++++++++++++++++++++++++++++ binaries/src/iupred/histo_casp | 1071 +++++++++++++++++++++++++++++++++++++++ binaries/src/iupred/histo_sum | 1074 ++++++++++++++++++++++++++++++++++++++++ binaries/src/iupred/iupred | Bin 0 -> 17738 bytes binaries/src/iupred/iupred.c | 639 ++++++++++++++++++++++++ binaries/src/iupred/ss | 400 +++++++++++++++ binaries/src/iupred/ss_casp | 400 +++++++++++++++ 10 files changed, 4845 insertions(+) create mode 100644 binaries/src/iupred/LICENSE create mode 100644 binaries/src/iupred/Makefile create mode 100644 binaries/src/iupred/README create mode 100644 binaries/src/iupred/histo create mode 100644 binaries/src/iupred/histo_casp create mode 100644 binaries/src/iupred/histo_sum create mode 100644 binaries/src/iupred/iupred create mode 100644 binaries/src/iupred/iupred.c create mode 100644 binaries/src/iupred/ss create mode 100644 binaries/src/iupred/ss_casp diff --git a/binaries/src/iupred/LICENSE b/binaries/src/iupred/LICENSE new file mode 100644 index 0000000..9fcbdd1 --- /dev/null +++ b/binaries/src/iupred/LICENSE @@ -0,0 +1,76 @@ + ACADEMIC LICENSE AGREEMENT + for the program + IUPred + +A nonexclusive, nontransferable right to use the IUPred executable, source +code and related documentation ("Licensed Material") is granted +by Zsuzsanna Dosztanyi ("Author") to + + + .................................... + +in exchange of the following commitments: + +I hereby certify and accept that + + 1. I am an academic user at an academic research institution. In using the + Licensed Material, I will respect the interests of the Author and the + Institute of Enzymology. + + 2. All rights, title, and interest in and to the Licensed Material shall at + all times remain with the Author. + + 3. I may, for internal use only, execute, enhance, modify, or expand the + Licensed Material, may merge it into other material, and may use the + Licensed Material as modified. All such modifications shall include the + Author copyright notice. + + 4. There is no warranty or other guarantee of fitness of the Licensed + Material. It is provided solely "as is". The Author disclaims all res- + ponsibility and liability with respect to this software's usage or its + effect upon hardware or computer systems. The Author has no obligation + to provide support or maintenance services for the Licensed Material. + + 5. I will not use the software in commercial activities. Incorporation of + the Software into a commercial Web site or other fee paying service is + not allowed. + + 6. The program shall not be made available to users outside the recipient's + laboratory. I will suggest to other interested research groups to + contact the authors directly. + + 7. I will not alter or suppress the run-time copyright message. + + 8. I will acknowledge the program authors on any publication of scientific + results based in part on use of the program and cite the article in + which the program was described: + +The Pairwise Energy Content Estimated from Amino Acid Composition Discriminates +between Folded and Intrinsically Unstructured Proteins +Zsuzsanna Dosztanyi, Veronika Csizmok, Peter Tompa and Istvan Simon +J. Mol. Biol. (2005) 347, 827-839. + + 9. I will report evidence of program bugs to the Author. + +Purpose of research: + + +Full name and institutional address: + + + +Internet email address: + +Date: Signature: + + + + +Mail of fax the signed form to: + +Dr Zsuzsanna Dosztanyi +Institute of Enzymology +Biological Research Center +Hungarian Academy of Sciences +H-1518 Budapest PO Box 7 +Fax: +36-1 466-5465 diff --git a/binaries/src/iupred/Makefile b/binaries/src/iupred/Makefile new file mode 100644 index 0000000..aef5c84 --- /dev/null +++ b/binaries/src/iupred/Makefile @@ -0,0 +1,25 @@ +CFLAGS = -O3 -funroll-loops -Winline +LDLIBS = -lm + +OBJ = .o +EXE = + +RM = rm -f +CP = cp + +GPP = cc +LD = $(GPP) $(CFLAGS) +CPP = $(GPP) -c $(CFLAGS) + + +all: iupred + +CPPSRC = $(sort $(wildcard *.c)) +CPPOBJ = $(subst .c,.o,$(CPPSRC)) + +$(CPPOBJ): %.o: %.c + $(CPP) $< -o $@ + +iupred: $(CPPOBJ) + $(LD) -o iupred $(CPPOBJ) $(LDLIBS) + strip iupred diff --git a/binaries/src/iupred/README b/binaries/src/iupred/README new file mode 100644 index 0000000..3489e52 --- /dev/null +++ b/binaries/src/iupred/README @@ -0,0 +1,86 @@ + IUPred RELEASE NOTES + ==================== + +IUPred Version 1.0 + +by Zsuzsanna Dosztanyi + + +IUPred is supplied in source code form along with the required data files. The +program is written in ANSI C and the code should compile on any ANSI C compiler +e.g. the GNU C compiler. To be able to run outside the source directory, the +IUPred_PATH environment variable has to be set to the location of the source +files. + +TO COMPILE: + +cc iupred.c -o iupred + +TO RUN IUPred: + +iupred seqfile type + + where seqfile is the name of the sequence file + + type is any of the option of + + long + short + glob + + for prediction of long disorder, short disorder ( e.g. missing residues in + X-ray structures) or predicting globular domains. + + +INPUT FILE: sequence_file in fasta format. One sequence per file. + +EXAMPLE RUN: + +iupred P53_HUMAN.seq long + + +INTERPRETATION OF THE OUTPUT: + +In the case of long and short types of disorder the output gives the +likelihood of disorder for each residue, i.e. it is a value between 0 and 1, +and higher values indicate higher probability of disorder. Residues with values +above 0.5 can be regarded as disordered, and at this cutoff 5% of globular +proteins is expected to be predicted to disordered (false positives). + +For the prediction type of globular domains it gives the number of globular +domains and list their start and end position in the sequence. This is followed +by the submitted sequence with residues of globular domains indicated by +uppercase letters. + + +Please see the LICENSE file for the license terms for the software. It is +basically free for academic users, but a license fee applies to commercial +users. + +THE PUBLICATION OF RESEARCH USING IUPred MUST INCLUDE AN APPROPRIATE +CITATION TO THE METHOD: + +The Pairwise Energy Content Estimated from Amino Acid Composition Discriminates +between Folded and Intrinsically Unstructured Proteins +Zsuzsanna Dosztányi, Veronika Csizmók, Péter Tompa and István Simon +J. Mol. Biol. (2005) 347, 827-839. + + +SHORT SUMMARY OF THE METHOD + +Intrinsically unstructured/disordered proteins have no single well-defined +tertiary structure in their native, functional state. Our server recognizes +such regions from the amino acid sequence based on the estimated pairwise +energy content. The underlying assumption is that globular proteins make a +large number of interresidue interactions, providing the stabilizing energy to +overcome the entropy loss during folding. In contrast, IUPs have special +sequences that do not have the capacity to form sufficient interresidue +interactions. Taking a set of globular proteins with known structure, we have +developed a simple formalism that allows the estimation of the pairwise +interaction energies of these proteins. It uses a quadratic expression in the +amino acid composition, which takes into account that the contribution of an +amino acid to order/disorder depends not only its own chemical type, but also +on its sequential environment, including its potential interaction partners. +Applying this calculation for IUP sequences, their estimated energies are +clearly shifted towards less favorable energies compared to globular proteins, +enabling the predicion of protein disorder on this ground. diff --git a/binaries/src/iupred/histo b/binaries/src/iupred/histo new file mode 100644 index 0000000..6e9782d --- /dev/null +++ b/binaries/src/iupred/histo @@ -0,0 +1,1074 @@ +# -1.1450 4.2050 1071 +# -0.0017 0.3220 +# 0.6643 0.3450 + 0 -1.1450 0.002375 0.000024 0.999976 + 1 -1.1400 0.000000 0.000024 0.999976 + 2 -1.1350 0.000000 0.000024 0.999976 + 3 -1.1300 0.002375 0.000048 0.999952 + 4 -1.1250 0.000000 0.000048 0.999952 + 5 -1.1200 0.004750 0.000095 0.999905 + 6 -1.1150 0.002375 0.000119 0.999881 + 7 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z=bgYWLx1TUivmB(LQMCwRCci)whMkbzoEd-a1gKKIEVP-5s^#_{`x5%jz}L&-|kSo zavvqw8QpgyoX&YD@UtGo{{&nmz!vCNYt@Dk`ES5swYebgEB+Zc-5+~i*r9aWCvE&R zP88nf_{IL`V;jG`->9I2)_Udr#wj*@lvzBRW5ebB#^u1Nokwi*=q?+-y!S}wmSfql zKa~C2Y~!CR>ir)!T;7M=W5ct8e?RcD&#{LWIX~>D)WbRXSte4i*~*dip0nXSqWqCq zT&;Q=6!?`kT=KhslYWlb^y4PHpp@0w=I>1$zl_nP3v2iqFMkZ9YaJBQ{E1I71fCK7 z;%BhPYZN%0mr~$orih~)=MaCCiR2C&F7Ij88OM8CThRboGj{vOtKMp<$P8;e1+^qQ@arCLEfRFp6>5mZ8a9}BTv0ZicnK)d-pE3?1aDp74Tf%AxNxa| zS!kJeLC{Z~%NORHR#ARW7;KgbOdbm$czj=9;$0l5Ww%5UA^a@K=!i_T2A75#Lv0NS zW?tm=c;v-fx^5c^@w>UDlgp6--Ln79)9@%*pmP3oyhHj6n!7rSVSZ!-VJRae9 zljHeiF0bVmne#!jcyWue#OhrUfj|i^0!CKo6z}Lp}?)^ zS0fmb@d!pkT!FUSTOQ`WfnQD@rb$USGsQ2w`4}v0SjD(ojbDZ1xsv(i>S6vHGPmxAUPmzk!{P`Rh<_V>}va#!sQG5fFS%Nc+r<9~lMR5N`~{B25fUqLISyy%4b7 z+|Dl_nc?PGK4xAP&&NU`oVW`6Fn=TGSHwFu +#include +#include +#include +#include + + + +#define AA "GAVLIFPSTCMWYNQDEKRH" +#define AAN 20 +#define MSL 40000 +#define ML 1000 + +#define DLC 1 +#define DUC 100 +#define DWS 10 +#define DMin_Ene 0.3 +#define DJOIN 45 +#define DDEL 35 + + +#define MAX(a,b) ((a)>(b)?(a):(b)) +#define MIN(a,b) ((a)<(b)?(a):(b)) + + +typedef struct +{ + char name[1000]; + int le; + char *seq; + double expscore; + double *eprof; + double *smp; + double *en; + int ngr; + int **gr; +} SEQ_STR; + + +typedef struct +{ + double **CC; + double *distro; + double min, max; + double step; + double cutoff; + int nb; +} P_STR; + + +void read_mat(char *path, char *fn, double **MAT, double *matave); +int getargs(char *line,char *args[],int max); +void read_ref(char *path, char *fn, double **REF); +void Get_Histo( P_STR *P, char *path, char *); +double **DMatrix(int n_rows, int n_cols); +void *my_malloc(size_t size); +void IUPred(SEQ_STR *SEQ, P_STR *P); +void getRegions(SEQ_STR *SEQ ); +void Get_Seq(char *fn, SEQ_STR *SEQ); + + +int LC, UC, WS; +double Min_Ene; +int JOIN, DEL; +int Flag_EP; +double EP; + + +int main(int argc, char **argv) +{ + P_STR *P; + SEQ_STR *SEQ; + int i,j; + int type; + char *path; + + + + if (argc!=3) { + printf(" Usage: %s seqfile type \n",argv[0]); + printf(" where type stands for one of the options of \n"); + printf(" \"long\", \"short\" or \"glob\"\n"); + exit(1); + } + if ((path=getenv("IUPred_PATH"))==NULL) { + fprintf(stderr,"IUPred_PATH environment variable is not set\n"); + path="./"; + } + + printf("# IUPred \n"); + printf("# Copyright (c) Zsuzsanna Dosztanyi, 2005\n"); + printf("#\n"); + printf("# Z. Dosztanyi, V. Csizmok, P. Tompa and I. Simon\n"); + printf("# J. Mol. Biol. (2005) 347, 827-839. \n"); + printf("#\n"); + printf("#\n"); + + + + + if ((strncmp(argv[2],"long",4))==0) { + type=0; + } + else if ((strncmp(argv[2],"short",5))==0) { + type=1; + } + else if ((strncmp(argv[2],"glob",4))==0) { + type=2; + } + else { + printf("Wrong argument\n");exit(1); + } + + + SEQ=malloc(sizeof(SEQ_STR)); + Get_Seq(argv[1],SEQ); + if (SEQ->le==0) {printf(" Sequence length 0\n");exit(1);} + +#ifdef DEBUG + printf("%s %d\n%s\n",SEQ->name,SEQ->le,SEQ->seq); +#endif + + + P=malloc(sizeof(P_STR)); + P->CC= DMatrix(AAN,AAN); + + if (type==0) { + + LC=1; + UC=100; + WS=10; + Flag_EP=0; + + read_ref(path,"ss",P->CC); + Get_Histo(P, path, "histo"); + + + IUPred(SEQ,P); + + printf("# Prediction output \n"); + printf("# %s\n",SEQ->name); + for (i=0;ile;i++) + printf("%5d %c %10.4f\n",i+1,SEQ->seq[i],SEQ->en[i]); + } + if (type==1) { + LC=1; + UC=25; + WS=10; + Flag_EP=1; + EP=-1.26; + + read_ref(path,"ss_casp",P->CC); + Get_Histo(P, path, "histo_casp"); + + IUPred(SEQ,P); + + printf("# Prediction output \n"); + printf("# %s\n",SEQ->name); + for (i=0;ile;i++) + printf("%5d %c %10.4f\n",i+1,SEQ->seq[i],SEQ->en[i]); + } + if (type==2) { + char *globseq; + + LC=1; + UC=100; + WS=15; + Flag_EP=0; + + + + read_ref(path,"ss",P->CC); + Get_Histo(P,path,"histo"); + + IUPred(SEQ,P); + + Min_Ene=DMin_Ene; + JOIN=DJOIN; + DEL=DDEL; + + getRegions(SEQ); + globseq=malloc((SEQ->le+1)*sizeof(char)); + for (i=0;ile;i++) globseq[i]=tolower(SEQ->seq[i]); + + printf("# Prediction output \n"); + printf("# %s\n",SEQ->name); + printf("Number of globular domains: %5d \n",SEQ->ngr); + for (i=0;ingr;i++) { + printf(" globular domain %5d. %d - %d \n", + i+1,SEQ->gr[i][0]+1,SEQ->gr[i][1]+1); + for (j=SEQ->gr[i][0];jgr[i][1]+1;j++) { + globseq[j]=toupper(globseq[j]); + } + } + printf(">%s\n",SEQ->name); + for (i=0;ile;i++) { + if ((i>0)&&(i%60==0)) printf("\n"); + else if ((i>0)&&(i%10==0)) printf(" "); + printf("%c",globseq[i]); + } + printf("\n"); + free(globseq); + + +#ifdef DEBUG + for (i=0;ile;i++) + printf("%5d %c %10.4f\n",i,SEQ->seq[i],SEQ->en[i]); +#endif + } + + free(SEQ->seq); + free(SEQ->eprof);free(SEQ->en);free(SEQ->smp); + free(SEQ); + + + return 0; +} + + +void IUPred(SEQ_STR *SEQ, P_STR *P) +{ + int i,j, a1, a2, p; + int naa; + double n2; + double min, max, step; + + naa=SEQ->le; + min=P->min; max=P->max;step=P->step; + + SEQ->eprof=malloc(naa*sizeof(double)); + for (i=0;ieprof[i]=0; + SEQ->en=malloc(naa*sizeof(double)); + for (i=0;ien[i]=0; + SEQ->smp=malloc(naa*sizeof(double)); + for (i=0;ismp[i]=0; + + + SEQ->expscore=0; + for (i=0;iseq[i]))))-AA; + if ((a1<0) || (a1>=AAN)) continue; + n2=0; + for (j=0;jLC)&&((abs(i-j))seq[j]))))-AA; + if ((a2<0) || (a2>=AAN)) continue; + SEQ->eprof[i]+=P->CC[a1][a2]; + n2++; + } + SEQ->expscore+=SEQ->eprof[i]/(naa*n2); + SEQ->eprof[i]/=n2; + + } + + if (Flag_EP==0) { + for (i=0;ismp[i]+=SEQ->eprof[j]; + n2++; + } + SEQ->smp[i]/=n2; + } + } else { + for (i=0;i=naa)) SEQ->smp[i]+=EP; + else SEQ->smp[i]+=SEQ->eprof[j]; + + n2++; + } + SEQ->smp[i]/=n2; + } + } + + for (i=0;ismp[i]<=min+2*step) SEQ->en[i]=1; + if (SEQ->smp[i]>=max-2*step) SEQ->en[i]=0; + if ((SEQ->smp[i]>min+2*step)&&(SEQ->smp[i]smp[i]-min)*(1.0/step)); + SEQ->en[i]=P->distro[p]; + } + +#ifdef DEBUG + printf("%5d %10.4f %10.4f %10.4f\n", + i,SEQ->eprof[i], SEQ->smp[i],SEQ->en[i]); + +#endif + + } + +} + + + +void getRegions(SEQ_STR *SEQ ) +{ + int naa; + int i, k,kk; + int **GR, **mGR; + int in_GR; + int nr, mnr; + int beg_GR, end_GR; + int beg,end; + + + naa=SEQ->le; + + + GR=NULL; + nr=0; + in_GR=0; + beg_GR=end_GR=0; + + + for (i=0;ismp[i]<=Min_Ene)) { + GR=realloc(GR,(nr+1)*sizeof(int *)); + GR[nr]=malloc(2*sizeof(int)); + GR[nr][0]=beg_GR; + GR[nr][1]=end_GR; + in_GR=0; + nr++; + } + else if (in_GR==1) + end_GR++; + if ((SEQ->smp[i]>Min_Ene)&&(in_GR==0)) { + beg_GR=i; + end_GR=i; + in_GR=1; + } + } + if (in_GR==1) { + GR=realloc(GR,(nr+1)*sizeof(int *)); + GR[nr]=malloc(2*sizeof(int)); + GR[nr][0]=beg_GR; + GR[nr][1]=end_GR; + in_GR=0; + nr++; + } + + + mnr=0; + k=0;mGR=NULL; + kk=k+1; + if (nr>0) { + beg=GR[0][0];end=GR[0][1]; + } + while (kngr=mnr; + SEQ->gr=mGR; + + + +} + + +void Get_Histo(P_STR *P, char *path, char *fn) +{ + FILE *f; + char ln[ML]; + int i,nb, set; + double v, min, max, cutoff, c; + char *fullfn; + int sl; + + sl=strlen(path)+strlen(fn)+2; + fullfn=malloc(sl*sizeof(char)); + sprintf(fullfn,"%s/%s",path,fn); + + if ((f=fopen(fullfn,"r"))==NULL) { + printf("Could not open %s\n",fullfn); + exit(1); + } + + + + fscanf(f,"%*s %lf %lf %d\n",&min, &max, &nb); + + P->distro=malloc(nb*sizeof(double )); + for (i=0;idistro[i]=0; + + + for (i=0,set=0;idistro[i]=v; + } + + fclose(f); + P->max=max; + P->min=min; + P->nb=nb; + P->cutoff=cutoff; + + + + P->step=(max-min)/nb; + P->cutoff-=P->step; + +} + + +void read_ref(char *path, char *fn, double **REF) +{ + + FILE *f; + int p1,p2; + double v; + char line[1000],s[20]; + int i,j; + char *fullfn; + int sl; + + sl=strlen(path)+strlen(fn)+2; + fullfn=malloc(sl*sizeof(char)); + sprintf(fullfn,"%s/%s",path,fn); + + if ((f=fopen(fullfn,"r"))==NULL) { + printf("Could not open %s\n",fullfn); + exit(1); + } + + + while (!feof(f)) { + fgets(line,1000,f); + + sscanf(line,"%d",&p1); + sscanf(&line[8],"%d",&p2); + sscanf(&line[17],"%s",s); + v=atof(s); + REF[p1][p2]=v; + + } + + + if (REF[9][9]<0) { + for (i=0;iseq=calloc(MSL,sizeof(char)); + + fgets(line,ML,f); + sscanf(&line[1],"%s",SEQ->name); + + + j=0; + while ((c!='>') && (!feof(f))) { + c=fgetc(f); + if (isalpha((int)(c))) { + SEQ->seq[j]=c; + j++; + if ((j>0)&&(j%MSL==0)) { + SEQ->seq=realloc(SEQ->seq,(j+MSL)*sizeof(char)); + } + } + } + SEQ->le=j; + +#ifdef DEBUG + printf("%s %5d\n%s\n",SEQ->name,SEQ->le,SEQ->seq); +#endif + + +} + + diff --git a/binaries/src/iupred/ss b/binaries/src/iupred/ss new file mode 100644 index 0000000..e7bfc9f --- /dev/null +++ b/binaries/src/iupred/ss @@ -0,0 +1,400 @@ + 0 G 0 G -0.19743960 + 0 G 1 A -0.40578783 + 0 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