************************************************************************* * This program is to identify the best alignment of two protein * structures to give the best TM-score. By default, TM-score is * normalized by the second protein. The program can be freely * copied or modified or redistributed. * (For comments, please email to: yzhang@ku.edu) * * Reference: * Yang Zhang, Jeffrey Skolnick, Nucl. Acid Res. 2005 33: 2303-9 * ************************ updating history ******************************* * 2005/06/01: A small bug of two-point superposition was fixed. * 2005/10/19: the program was reformed so that the alignment * results are not dependent on the specific compilers. * 2006/06/20: select 'A' if there is altLoc when reading PDB file. * 2007/02/27: rotation matrix from Chain-1 to Chain-2 is added. * 2007/04/18: add options with TM-score normalized by average * length, shorter length, or longer length of two * structures. * 2007/05/23: add additional output file 'TM.sup_all' for showing * all atoms while 'TM.sup' is only for aligned atoms * 2007/09/19: add a new feature alignment to deal with the problem * of aligning fractional structures (e.g. protein * interfaces). ************************************************************************* program compares PARAMETER(nmax=5000) PARAMETER(nmax2=10000) COMMON/BACKBONE/XA(3,nmax,0:1) common/dpc/score(nmax,nmax),gap_open,invmap(nmax) common/alignrst/invmap0(nmax) common/length/nseq1,nseq2 common/d0/d0,anseq common/d0min/d0_min common/d00/d00,d002 character*100 fnam,pdb(100),outname character*3 aa(-1:20),aanam,ss1(nmax),ss2(nmax) character*100 s,du character*200 outnameall_tmp,outnameall character seq1(0:nmax),seq2(0:nmax) character aseq1(nmax2),aseq2(nmax2),aseq3(nmax2) dimension xx(nmax),yy(nmax),zz(nmax) dimension m1(nmax),m2(nmax) dimension xtm1(nmax),ytm1(nmax),ztm1(nmax) dimension xtm2(nmax),ytm2(nmax),ztm2(nmax) common/init/invmap_i(nmax) common/TM/TM,TMmax common/n1n2/n1(nmax),n2(nmax) common/d8/d8 common/initial4/mm1(nmax),mm2(nmax) ccc RMSD: double precision r_1(3,nmax),r_2(3,nmax),r_3(3,nmax),w(nmax) double precision u(3,3),t(3),rms,drms !armsd is real data w /nmax*1.0/ ccc data aa/ 'BCK','GLY','ALA','SER','CYS','VAL','THR','ILE', & 'PRO','MET','ASP','ASN','LEU', & 'LYS','GLU','GLN','ARG', & 'HIS','PHE','TYR','TRP','CYX'/ character*1 slc(-1:20) data slc/'X','G','A','S','C','V','T','I', & 'P','M','D','N','L','K','E','Q','R', & 'H','F','Y','W','C'/ call getarg(1,fnam) if(fnam.eq.' '.or.fnam.eq.'?'.or.fnam.eq.'-h')then write(*,*) write(*,*)'Brief instruction for running TM-align program:' write(*,*)'(For detail: Zhang & Skolnick, Nucl. Acid Res.', & '2005 33, 2303)' write(*,*) write(*,*)'1. Align ''structure.pdb'' to ''target.pdb''' write(*,*)' (By default, TM-score is normalized by the ', & 'length of ''target.pdb'')' write(*,*)' >TMalign structure.pdb target.pdb' write(*,*) write(*,*)'2. Run TM-align and output the superposition ', & 'to ''TM.sup'' and ''TM.sup_all'':' write(*,*)' >TMalign structure.pdb target.pdb -o TM.sup' write(*,*)' To view the superimposed structures of the', & ' aligned regions by rasmol:' write(*,*)' >rasmol -script TM.sup)' write(*,*)' To view the superimposed structures of all', & ' regions by rasmol:' write(*,*)' >rasmol -script TM.sup_all)' write(*,*) write(*,*)'3. If you want TM-score normalized by ', & 'an assigned length, e.g. 100 aa:' write(*,*)' >TMalign structure.pdb target.pdb -L 100' write(*,*)' If you want TM-score normalized by the ', & 'average length of two structures:' write(*,*)' >TMalign structure.pdb target.pdb -a' write(*,*)' If you want TM-score normalized by the ', & 'shorter length of two structures:' write(*,*)' >TMalign structure.pdb target.pdb -b' write(*,*)' If you want TM-score normalized by the ', & 'longer length of two structures:' write(*,*)' >TMalign structure.pdb target.pdb -c' write(*,*) c write(*,*)'5. If you want to set a minimum cutoff for d0, ', c & 'e.g. d0>3.0' c write(*,*)' (By default d0>0.5, this option need ', c & 'be considered only when L<35 aa)' c write(*,*)' >TMalign structure.pdb target.pdb -dmin 3.0' c write(*,*) write(*,*)'(All above options does not change the ', & 'final structure alignment result)' write(*,*) goto 9999 endif ******* options -----------> m_out=-1 !decided output m_fix=-1 !fixed length-scale only for output m_ave=-1 !using average length m_d0_min=-1 !diminum d0 for search m_d0=-1 !given d0 for both search and output narg=iargc() i=0 j=0 115 continue i=i+1 call getarg(i,fnam) if(fnam.eq.'-o')then m_out=1 i=i+1 call getarg(i,outname) elseif(fnam.eq.'-L')then !change both L_all and d0 m_fix=1 i=i+1 call getarg(i,fnam) read(fnam,*)L_fix elseif(fnam.eq.'-dmin')then m_d0_min=1 i=i+1 call getarg(i,fnam) read(fnam,*)d0_min_input elseif(fnam.eq.'-d0')then m_d0=1 i=i+1 call getarg(i,fnam) read(fnam,*)d0_fix elseif(fnam.eq.'-a')then ! this will change the superposed output but not the alignment m_ave=1 i=i+1 elseif(fnam.eq.'-b')then m_ave=2 i=i+1 elseif(fnam.eq.'-c')then m_ave=3 i=i+1 else j=j+1 pdb(j)=fnam endif if(i.lt.narg)goto 115 ccccccccc read data from first CA file: open(unit=10,file=pdb(1),status='old') i=0 do while (.true.) read(10,9001,end=1010) s if(i.gt.0.and.s(1:3).eq.'TER')goto 1010 if(s(1:3).eq.'ATO')then if(s(13:16).eq.'CA '.or.s(13:16).eq.' CA '.or & .s(13:16).eq.' CA')then if(s(17:17).eq.' '.or.s(17:17).eq.'A')then i=i+1 read(s,9000)du,aanam,du,mm1(i),du, $ xa(1,i,0),xa(2,i,0),xa(3,i,0) do j=-1,20 if(aanam.eq.aa(j))seq1(i)=slc(j) enddo ss1(i)=aanam if(i.ge.nmax)goto 1010 endif endif endif enddo 1010 continue 9000 format(A17,A3,A2,i4,A4,3F8.3) 9001 format(A100) close(10) nseq1=i c^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ccccccccc read data from the second CA file: open(unit=10,file=pdb(2),status='old') i=0 do while (.true.) read(10,9001,end=1011) s if(i.gt.0.and.s(1:3).eq.'TER')goto 1011 if(s(1:3).eq.'ATO')then if(s(13:16).eq.'CA '.or.s(13:16).eq.' CA '.or. & s(13:16).eq.' CA')then if(s(17:17).eq.' '.or.s(17:17).eq.'A')then i=i+1 read(s,9000)du,aanam,du,mm2(i),du, $ xa(1,i,1),xa(2,i,1),xa(3,i,1) do j=-1,20 if(aanam.eq.aa(j))seq2(i)=slc(j) enddo ss2(i)=aanam if(i.ge.nmax)goto 1011 endif endif endif enddo 1011 continue close(10) nseq2=i c^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ *!!! Scale of TM-score in search is based on the smaller protein ---------> d0_min=0.5 if(m_d0_min.eq.1)then d0_min=d0_min_input !for search endif anseq_min=min(nseq1,nseq2) anseq=anseq_min !length for defining TMscore in search d8=1.5*anseq_min**0.3+3.5 !remove pairs with dis>d8 during search & final if(anseq.gt.15)then d0=1.24*(anseq-15)**(1.0/3.0)-1.8 !scale for defining TM-score else d0=d0_min endif if(d0.lt.d0_min)d0=d0_min if(m_d0.eq.1)d0=d0_fix d00=d0 !for quickly calculate TM-score in searching if(d00.gt.8)d00=8 if(d00.lt.4.5)d00=4.5 d002=d00**2 nseq=max(nseq1,nseq2) do i=1,nseq n1(i)=i n2(i)=i enddo ***** do alignment ************************** CALL super_align !to find invmap(j) ************************************************************ *** resuperpose to find residues of dis n_al=0 do j=1,nseq2 if(invmap0(j).gt.0)then i=invmap0(j) n_al=n_al+1 xtm1(n_al)=xa(1,i,0) ytm1(n_al)=xa(2,i,0) ztm1(n_al)=xa(3,i,0) xtm2(n_al)=xa(1,j,1) ytm2(n_al)=xa(2,j,1) ztm2(n_al)=xa(3,j,1) m1(n_al)=i !for recording residue order m2(n_al)=j endif enddo d0_input=d0 call TMscore8(d0_input,n_al,xtm1,ytm1,ztm1,n1,n_al, & xtm2,ytm2,ztm2,n2,TM,Rcomm,Lcomm) !TM-score with dis d0_min=0.5 !for output anseq=nseq2 !length for defining final TMscore if(m_ave.eq.1)anseq=(nseq1+nseq2)/2.0 ! if(m_ave.eq.2)anseq=min(nseq1,nseq2) if(m_ave.eq.3)anseq=max(nseq1,nseq2) if(anseq.lt.anseq_min)anseq=anseq_min if(m_fix.eq.1)anseq=L_fix !input length if(anseq.gt.15)then d0=1.24*(anseq-15)**(1.0/3.0)-1.8 !scale for defining TM-score else d0=d0_min endif if(d0.lt.d0_min)d0=d0_min if(m_d0.eq.1)d0=d0_fix *** remove dis>d8 in normal TM-score calculation for final report-----> j=0 n_eq=0 do i=1,n_al dis2=sqrt((xtm1(i)-xtm2(i))**2+(ytm1(i)-ytm2(i))**2+ & (ztm1(i)-ztm2(i))**2) if(dis2.le.d8)then j=j+1 xtm1(j)=xtm1(i) ytm1(j)=ytm1(i) ztm1(j)=ztm1(i) xtm2(j)=xtm2(i) ytm2(j)=ytm2(i) ztm2(j)=ztm2(i) m1(j)=m1(i) m2(j)=m2(i) if(ss1(m1(i)).eq.ss2(m2(i)))then n_eq=n_eq+1 endif endif enddo seq_id=float(n_eq)/(n_al+0.00000001) n8_al=j d0_input=d0 call TMscore(d0_input,n8_al,xtm1,ytm1,ztm1,n1,n8_al, & xtm2,ytm2,ztm2,n2,TM8,Rcomm,Lcomm) !normal TMscore rmsd8_al=Rcomm TM8=TM8*n8_al/anseq !TM-score after cutoff ********* for output summary ****************************** write(*,*) write(*,*)'*****************************************************', & '*********************' write(*,*)'* TM-align ', & ' *' write(*,*)'* A protein structural alignment algorithm based on T', & 'M-score *' write(*,*)'* Reference: Y. Zhang and J. Skolnick, Nucl. Acids Re', & 's. 2005 33, 2302-9 *' write(*,*)'* Comments on the program, please email to: yzhang@ku', & '.edu *' write(*,*)'*****************************************************', & '*********************' write(*,*) write(*,101)pdb(1),nseq1 101 format('Chain 1:',A10,' Size=',I4) write(*,102)pdb(2),nseq2,int(anseq) 102 format('Chain 2:',A10,' Size=',I4, & ' (TM-score is normalized by ',I4,')') write(*,*) write(*,103)n8_al,rmsd8_al,TM8,seq_id 103 format('Aligned length=',I4,', RMSD=',f6.2, & ', TM-score=',f7.5,', ID=',f5.3) write(*,*) ********* extract rotation matrix ------------> L=0 do i=1,n8_al k=m1(i) L=L+1 r_1(1,L)=xa(1,k,0) r_1(2,L)=xa(2,k,0) r_1(3,L)=xa(3,k,0) r_2(1,L)=xtm1(i) r_2(2,L)=ytm1(i) r_2(3,L)=ztm1(i) enddo if(L.gt.3)then call u3b(w,r_1,r_2,L,1,rms,u,t,ier) !u rotate r_1 to r_2 armsd=dsqrt(rms/L) write(*,*)'-------- rotation matrix to rotate Chain-1 to ', & 'Chain-2 ------' write(*,*)'i t(i) u(i,1) u(i,2) ', & ' u(i,3)' do i=1,3 write(*,204)i,t(i),u(i,1),u(i,2),u(i,3) enddo c do i=1,nseq1 c ax=t(1)+u(1,1)*xa(1,i,0)+u(1,2)*xa(2,i,0)+u(1,3)*xa(3,i,0) c ay=t(2)+u(2,1)*xa(1,i,0)+u(2,2)*xa(2,i,0)+u(2,3)*xa(3,i,0) c az=t(3)+u(3,1)*xa(1,i,0)+u(3,2)*xa(2,i,0)+u(3,3)*xa(3,i,0) c enddo write(*,*) endif 204 format(I2,f18.10,f15.10,f15.10,f15.10) ********* for output superposition ****************************** if(m_out.eq.1)then 1237 format('ATOM ',i5,' CA ',A3,I6,4X,3F8.3) 1238 format('TER') 1239 format('CONECT',I5,I5) 900 format(A) 901 format('select atomno=',I4) 104 format('REMARK Chain 1:',A10,' Size=',I4) 105 format('REMARK Chain 2:',A10,' Size=',I4, & ' (TM-score is normalized by ',I4,')') 106 format('REMARK Aligned length=',I4,', RMSD=',f6.2, & ', TM-score=',f7.5,', ID=',f5.3) OPEN(unit=7,file=outname,status='unknown') !pdb1.aln + pdb2.aln *** script: write(7,900)'load inline' write(7,900)'select atomno<2000' write(7,900)'wireframe .45' write(7,900)'select none' write(7,900)'select atomno>2000' write(7,900)'wireframe .20' write(7,900)'color white' do i=1,n8_al dis2=sqrt((xtm1(i)-xtm2(i))**2+ & (ytm1(i)-ytm2(i))**2+(ztm1(i)-ztm2(i))**2) if(dis2.le.5)then write(7,901)m1(i) write(7,900)'color red' write(7,901)2000+m2(i) write(7,900)'color red' endif enddo write(7,900)'select all' write(7,900)'exit' write(7,104)pdb(1),nseq1 write(7,105)pdb(2),nseq2,int(anseq) write(7,106)n8_al,rmsd8_al,TM8,seq_id *** chain1: do i=1,n8_al write(7,1237)m1(i),ss1(m1(i)),mm1(m1(i)), & xtm1(i),ytm1(i),ztm1(i) enddo write(7,1238) !TER do i=2,n8_al write(7,1239)m1(i-1),m1(i) !connect atoms enddo *** chain2: do i=1,n8_al write(7,1237)2000+m2(i),ss2(m2(i)),mm2(m2(i)), $ xtm2(i),ytm2(i),ztm2(i) enddo write(7,1238) do i=2,n8_al write(7,1239)2000+m2(i-1),2000+m2(i) enddo close(7) ccc k=0 outnameall_tmp=outname//'_all' outnameall='' do i=1,200 if(outnameall_tmp(i:i).ne.' ')then k=k+1 outnameall(k:k)=outnameall_tmp(i:i) endif enddo OPEN(unit=8,file=outnameall,status='unknown') !pdb1.aln + pdb2.aln *** script: write(8,900)'load inline' write(8,900)'select atomno<2000' write(8,900)'wireframe .45' write(8,900)'select none' write(8,900)'select atomno>2000' write(8,900)'wireframe .20' write(8,900)'color white' do i=1,n8_al dis2=sqrt((xtm1(i)-xtm2(i))**2+ & (ytm1(i)-ytm2(i))**2+(ztm1(i)-ztm2(i))**2) if(dis2.le.5)then write(8,901)m1(i) write(8,900)'color red' write(8,901)2000+m2(i) write(8,900)'color red' endif enddo write(8,900)'select all' write(8,900)'exit' write(8,104)pdb(1),nseq1 write(8,105)pdb(2),nseq2,int(anseq) write(8,106)n8_al,rmsd8_al,TM8,seq_id *** chain1: do i=1,nseq1 ax=t(1)+u(1,1)*xa(1,i,0)+u(1,2)*xa(2,i,0)+u(1,3)*xa(3,i,0) ay=t(2)+u(2,1)*xa(1,i,0)+u(2,2)*xa(2,i,0)+u(2,3)*xa(3,i,0) az=t(3)+u(3,1)*xa(1,i,0)+u(3,2)*xa(2,i,0)+u(3,3)*xa(3,i,0) write(8,1237)i,ss1(i),mm1(i),ax,ay,az enddo write(8,1238) !TER do i=2,nseq1 write(8,1239)i-1,i enddo *** chain2: do i=1,nseq2 write(8,1237)2000+i,ss2(i),mm2(i), $ xa(1,i,1),xa(2,i,1),xa(3,i,1) enddo write(8,1238) do i=2,nseq2 write(8,1239)2000+i-1,2000+i enddo close(8) endif *^^^^^^^^^^^^^^^^^^ output finished ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ************ output aligned sequences ************************** ii=0 i1_old=1 i2_old=1 do i=1,n8_al do j=i1_old,m1(i)-1 ii=ii+1 aseq1(ii)=seq1(j) aseq2(ii)='-' aseq3(ii)=' ' enddo do j=i2_old,m2(i)-1 ii=ii+1 aseq1(ii)='-' aseq2(ii)=seq2(j) aseq3(ii)=' ' enddo ii=ii+1 aseq1(ii)=seq1(m1(i)) aseq2(ii)=seq2(m2(i)) dis2=sqrt((xtm1(i)-xtm2(i))**2+ & (ytm1(i)-ytm2(i))**2+(ztm1(i)-ztm2(i))**2) if(dis2.le.5)then aseq3(ii)=':' else aseq3(ii)='.' endif i1_old=m1(i)+1 i2_old=m2(i)+1 enddo do i=i1_old,nseq1 ii=ii+1 aseq1(ii)=seq1(i) aseq2(ii)='-' aseq3(ii)=' ' enddo do i=i2_old,nseq2 ii=ii+1 aseq1(ii)='-' aseq2(ii)=seq2(i) aseq3(ii)=' ' enddo write(*,50) 50 format('(":" denotes the residue pairs of distance < 5.0 ', & 'Angstrom)') write(*,10)(aseq1(i),i=1,ii) write(*,10)(aseq3(i),i=1,ii) write(*,10)(aseq2(i),i=1,ii) 10 format(10000A1) write(*,*) c^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 9999 END *********************************************************************** *********************************************************************** * Structure superposition *********************************************************************** *********************************************************************** *********************************************************************** SUBROUTINE super_align PARAMETER(nmax=5000) COMMON/BACKBONE/XA(3,nmax,0:1) common/length/nseq1,nseq2 common/dpc/score(nmax,nmax),gap_open,invmap(nmax) common/alignrst/invmap0(nmax) common/zscore/zrms,n_al,rmsd_al common/TM/TM,TMmax common/init/invmap_i(nmax) dimension gapp(100) TMmax=0 n_gapp=2 gapp(1)=-0.6 gapp(2)=0 c n_gapp=11 c do i=1,n_gapp c gapp(i)=-(n_gapp-i) c enddo *11111111111111111111111111111111111111111111111111111111 * get initial alignment from gapless threading ********************************************************** call get_initial !gapless threading do i=1,nseq2 invmap(i)=invmap_i(i) !with highest zcore enddo call get_score !TM, matrix score(i,j) if(TM.gt.TMmax)then TMmax=TM do j=1,nseq2 invmap0(j)=invmap(j) enddo endif ***************************************************************** * initerative alignment, for different gap_open: ***************************************************************** DO 111 i_gapp=1,n_gapp !different gap panalties GAP_OPEN=gapp(i_gapp) !gap panalty do 222 id=1,30 !maximum interation is 200 call DP(NSEQ1,NSEQ2) !produce alignment invmap(j) * Input: score(i,j), and gap_open * Output: invmap(j) call get_score !calculate TM-score, score(i,j) c record the best alignment in whole search ----------> if(TM.gt.TMmax)then TMmax=TM do j=1,nseq2 invmap0(j)=invmap(j) enddo endif if(id.gt.1)then diff=abs(TM-TM_old) if(diff.lt.0.000001)goto 33 endif TM_old=TM 222 continue 33 continue 111 continue *222222222222222222222222222222222222222222222222222222222 * get initial alignment from secondary structure alignment ********************************************************** call get_initial2 !DP for secondary structure do i=1,nseq2 invmap(i)=invmap_i(i) !with highest zcore enddo call get_score !TM, score(i,j) if(TM.gt.TMmax)then TMmax=TM do j=1,nseq2 invmap0(j)=invmap(j) enddo endif ***************************************************************** * initerative alignment, for different gap_open: ***************************************************************** DO 1111 i_gapp=1,n_gapp !different gap panalties GAP_OPEN=gapp(i_gapp) !gap panalty do 2222 id=1,30 !maximum interation is 200 call DP(NSEQ1,NSEQ2) !produce alignment invmap(j) * Input: score(i,j), and gap_open * Output: invmap(j) call get_score !calculate TM-score, score(i,j) c write(*,21)gap_open,rmsd_al,n_al,TM c record the best alignment in whole search ----------> if(TM.gt.TMmax)then TMmax=TM do j=1,nseq2 invmap0(j)=invmap(j) enddo endif if(id.gt.1)then diff=abs(TM-TM_old) if(diff.lt.0.000001)goto 333 endif TM_old=TM 2222 continue 333 continue 1111 continue *333333333333333333333333333333333333333333333333333333333333 * get initial alignment from invmap0+SS ************************************************************* call get_initial3 !invmap0+SS do i=1,nseq2 invmap(i)=invmap_i(i) !with highest zcore enddo call get_score !TM, score(i,j) if(TM.gt.TMmax)then TMmax=TM do j=1,nseq2 invmap0(j)=invmap(j) enddo endif ***************************************************************** * initerative alignment, for different gap_open: ***************************************************************** DO 1110 i_gapp=1,n_gapp !different gap panalties GAP_OPEN=gapp(i_gapp) !gap panalty do 2220 id=1,30 !maximum interation is 200 call DP(NSEQ1,NSEQ2) !produce alignment invmap(j) * Input: score(i,j), and gap_open * Output: invmap(j) call get_score !calculate TM-score, score(i,j) c write(*,21)gap_open,rmsd_al,n_al,TM c record the best alignment in whole search ----------> if(TM.gt.TMmax)then TMmax=TM do j=1,nseq2 invmap0(j)=invmap(j) enddo endif if(id.gt.1)then diff=abs(TM-TM_old) if(diff.lt.0.000001)goto 330 endif TM_old=TM 2220 continue 330 continue 1110 continue *444444444444444444444444444444444444444444444444444444444 * get initial alignment of pieces from gapless threading ********************************************************** call get_initial4 !gapless threading do i=1,nseq2 invmap(i)=invmap_i(i) !with highest zcore enddo call get_score !TM, matrix score(i,j) if(TM.gt.TMmax)then TMmax=TM do j=1,nseq2 invmap0(j)=invmap(j) enddo endif ***************************************************************** * initerative alignment, for different gap_open: ***************************************************************** DO 44 i_gapp=2,n_gapp !different gap panalties GAP_OPEN=gapp(i_gapp) !gap panalty do 444 id=1,2 !maximum interation is 200 call DP(NSEQ1,NSEQ2) !produce alignment invmap(j) * Input: score(i,j), and gap_open * Output: invmap(j) call get_score !calculate TM-score, score(i,j) c record the best alignment in whole search ----------> if(TM.gt.TMmax)then TMmax=TM do j=1,nseq2 invmap0(j)=invmap(j) enddo endif 444 continue 44 continue c^^^^^^^^^^^^^^^ best alignment invmap0(j) found ^^^^^^^^^^^^^^^^^^ RETURN END ************************************************************** * get initial alignment invmap0(i) from gapless threading ************************************************************** subroutine get_initial PARAMETER(nmax=5000) COMMON/BACKBONE/XA(3,nmax,0:1) common/length/nseq1,nseq2 common/dpc/score(nmax,nmax),gap_open,invmap(nmax) common/alignrst/invmap0(nmax) common/zscore/zrms,n_al,rmsd_al common/TM/TM,TMmax common/init/invmap_i(nmax) aL=min(nseq1,nseq2) idel=aL/2.5 !minimum size of considered fragment if(idel.le.5)idel=5 n1=-nseq2+idel n2=nseq1-idel GL_max=0 do ishift=n1,n2 L=0 do j=1,nseq2 i=j+ishift if(i.ge.1.and.i.le.nseq1)then L=L+1 invmap(j)=i else invmap(j)=-1 endif enddo if(L.ge.idel)then call get_GL(GL) if(GL.gt.GL_max)then GL_max=GL do i=1,nseq2 invmap_i(i)=invmap(i) enddo endif endif enddo return end ************************************************************** * get initial alignment invmap0(i) from secondary structure ************************************************************** subroutine get_initial2 PARAMETER(nmax=5000) COMMON/BACKBONE/XA(3,nmax,0:1) common/length/nseq1,nseq2 common/dpc/score(nmax,nmax),gap_open,invmap(nmax) common/alignrst/invmap0(nmax) common/zscore/zrms,n_al,rmsd_al common/TM/TM,TMmax common/sec/isec(nmax),jsec(nmax) common/init/invmap_i(nmax) ********** assign secondary structures *************** c 1->coil, 2->helix, 3->turn, 4->strand do i=1,nseq1 isec(i)=1 j1=i-2 j2=i-1 j3=i j4=i+1 j5=i+2 if(j1.ge.1.and.j5.le.nseq1)then dis13=diszy(0,j1,j3) dis14=diszy(0,j1,j4) dis15=diszy(0,j1,j5) dis24=diszy(0,j2,j4) dis25=diszy(0,j2,j5) dis35=diszy(0,j3,j5) isec(i)=make_sec(dis13,dis14,dis15,dis24,dis25,dis35) endif enddo do i=1,nseq2 jsec(i)=1 j1=i-2 j2=i-1 j3=i j4=i+1 j5=i+2 if(j1.ge.1.and.j5.le.nseq2)then dis13=diszy(1,j1,j3) dis14=diszy(1,j1,j4) dis15=diszy(1,j1,j5) dis24=diszy(1,j2,j4) dis25=diszy(1,j2,j5) dis35=diszy(1,j3,j5) jsec(i)=make_sec(dis13,dis14,dis15,dis24,dis25,dis35) endif enddo call smooth !smooth the assignment ********** score matrix ************************** do i=1,nseq1 do j=1,nseq2 if(isec(i).eq.jsec(j))then score(i,j)=1 else score(i,j)=0 endif enddo enddo ********** find initial alignment: invmap(j) ************ gap_open=-1.0 !should be -1 call DP(NSEQ1,NSEQ2) !produce alignment invmap(j) do i=1,nseq2 invmap_i(i)=invmap(i) enddo *^^^^^^^^^^^^ initial alignment done ^^^^^^^^^^^^^^^^^^^^^^ return end ************************************************************** * get initial alignment invmap0(i) from secondary structure * and previous alignments ************************************************************** subroutine get_initial3 PARAMETER(nmax=5000) COMMON/BACKBONE/XA(3,nmax,0:1) common/length/nseq1,nseq2 common/dpc/score(nmax,nmax),gap_open,invmap(nmax) common/alignrst/invmap0(nmax) common/zscore/zrms,n_al,rmsd_al common/TM/TM,TMmax common/sec/isec(nmax),jsec(nmax) common/init/invmap_i(nmax) ********** score matrix ************************** do i=1,nseq2 invmap(i)=invmap0(i) enddo call get_score1 !get score(i,j) using RMSD martix do i=1,nseq1 do j=1,nseq2 if(isec(i).eq.jsec(j))then score(i,j)=0.5+score(i,j) else score(i,j)=score(i,j) endif enddo enddo ********** find initial alignment: invmap(j) ************ gap_open=-1.0 !should be -1 call DP(NSEQ1,NSEQ2) !produce alignment invmap(j) do i=1,nseq2 invmap_i(i)=invmap(i) enddo *^^^^^^^^^^^^ initial alignment done ^^^^^^^^^^^^^^^^^^^^^^ return end ************************************************************** * get initial alignment invmap0(i) from fragment gapless threading ************************************************************** subroutine get_initial4 PARAMETER(nmax=5000) COMMON/BACKBONE/XA(3,nmax,0:1) common/length/nseq1,nseq2 common/dpc/score(nmax,nmax),gap_open,invmap(nmax) common/alignrst/invmap0(nmax) common/zscore/zrms,n_al,rmsd_al common/TM/TM,TMmax common/init/invmap_i(nmax) common/initial4/mm1(nmax),mm2(nmax) logical contin dimension ifr2(2,nmax,nmax),Lfr2(2,nmax),Lfr_max2(2),i_fr2(2) dimension ifr(nmax) dimension mm(2,nmax) fra_min=4 !>=4,minimum fragment for search fra_min1=fra_min-1 !cutoff for shift, save time dcu0=3.85 dcu_min=3.65 ccc Find the smallest continuous fragments --------> do i=1,nseq1 mm(1,i)=mm1(i) enddo do i=1,nseq2 mm(2,i)=mm2(i) enddo do k=1,2 dcu=dcu0 if(k.eq.1)then nseq0=nseq1 r_min=nseq1/3.0 !minimum fragment, in case too small protein else nseq0=nseq2 r_min=nseq2/3.0 !minimum fragment, in case too small protein endif if(r_min.gt.fra_min)r_min=fra_min 20 nfr=1 !number of fragments j=1 !number of residue at nf-fragment ifr2(k,nfr,j)=1 !what residue Lfr2(k,nfr)=j !length of the fragment do i=2,nseq0 dis=diszy(k-1,i-1,i) contin=.false. if(dcu.gt.dcu0)then if(dis.lt.dcu)then if(dis.gt.dcu_min)then contin=.true. endif endif elseif(mm(k,i).eq.(mm(k,i-1)+1))then if(dis.lt.dcu)then if(dis.gt.dcu_min)then contin=.true. endif endif endif if(contin)then j=j+1 ifr2(k,nfr,j)=i Lfr2(k,nfr)=j else nfr=nfr+1 j=1 ifr2(k,nfr,j)=i Lfr2(k,nfr)=j endif enddo Lfr_max=0 i_fr2(k)=1 !ID of the maximum piece do i=1,nfr if(Lfr_max.lt.Lfr2(k,i))then Lfr_max=Lfr2(k,i) i_fr2(k)=i endif enddo if(Lfr_max.lt.r_min)then dcu=1.1*dcu goto 20 endif enddo c^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ccc select what piece will be used (this may araise ansysmetry, but ccc only when L1=L2 and Lfr1=Lfr2 and L1 ne Lfr1 ccc if L1=Lfr1 and L2=Lfr2 (normal proteins), it will be the same as initial1 mark=1 if(Lfr2(1,i_fr2(1)).lt.Lfr2(2,i_fr2(2)))then mark=1 elseif(Lfr2(1,i_fr2(1)).gt.Lfr2(2,i_fr2(2)))then mark=2 else !Lfr1=Lfr2 if(nseq1.le.nseq2)then mark=1 else mark=2 endif endif ccc L_fr=Lfr2(mark,i_fr2(mark)) do i=1,L_fr ifr(i)=ifr2(mark,i_fr2(mark),i) enddo ccc if(mark.eq.1)then !non-redundant to get_initial1 nseq0=nseq1 else nseq0=nseq2 endif if(L_fr.eq.nseq0)then n1=int(nseq0*0.1) !0 n2=int(nseq0*0.89) !2 j=0 do i=n1,n2 j=j+1 ifr(j)=ifr(n1+j) enddo L_fr=j endif ccc get initial -------------> if(mark.eq.1)then !nseq1 as the smallest one nseq1_=L_fr aL=min(nseq1_,nseq2) idel=aL/2.5 !minimum size of considered fragment if(idel.le.fra_min1)idel=fra_min1 n1=-nseq2+idel !shift1 n2=nseq1_-idel !shift2 GL_max=0 do ishift=n1,n2 L=0 do j=1,nseq2 i=j+ishift if(i.ge.1.and.i.le.nseq1_)then L=L+1 invmap(j)=ifr(i) else invmap(j)=-1 endif enddo if(L.ge.idel)then call get_GL(GL) if(GL.gt.GL_max)then GL_max=GL do i=1,nseq2 invmap_i(i)=invmap(i) enddo endif endif enddo else !@@@@@@@@@@@@@@@@@@@@ nseq2_=L_fr aL=min(nseq1,nseq2_) idel=aL/2.5 !minimum size of considered fragment if(idel.le.fra_min1)idel=fra_min1 n1=-nseq2_+idel n2=nseq1-idel GL_max=0 do ishift=n1,n2 L=0 do j=1,nseq2 invmap(j)=-1 enddo do j=1,nseq2_ i=j+ishift if(i.ge.1.and.i.le.nseq1)then L=L+1 invmap(ifr(j))=i endif enddo if(L.ge.idel)then call get_GL(GL) if(GL.gt.GL_max)then GL_max=GL do i=1,nseq2 invmap_i(i)=invmap(i) enddo endif endif enddo endif return end ************************************************************** * smooth the secondary structure assignment ************************************************************** subroutine smooth PARAMETER(nmax=5000) common/sec/isec(nmax),jsec(nmax) common/length/nseq1,nseq2 *** smooth single --------------> *** --x-- => ----- do i=1,nseq1 if(isec(i).eq.2.or.isec(i).eq.4)then j=isec(i) if(isec(i-2).ne.j)then if(isec(i-1).ne.j)then if(isec(i+1).ne.j)then if(isec(i+1).ne.j)then isec(i)=1 endif endif endif endif endif enddo do i=1,nseq2 if(jsec(i).eq.2.or.jsec(i).eq.4)then j=jsec(i) if(jsec(i-2).ne.j)then if(jsec(i-1).ne.j)then if(jsec(i+1).ne.j)then if(jsec(i+1).ne.j)then jsec(i)=1 endif endif endif endif endif enddo *** smooth double --------------> *** --xx-- => ------ do i=1,nseq1 if(isec(i).ne.2)then if(isec(i+1).ne.2)then if(isec(i+2).eq.2)then if(isec(i+3).eq.2)then if(isec(i+4).ne.2)then if(isec(i+5).ne.2)then isec(i+2)=1 isec(i+3)=1 endif endif endif endif endif endif if(isec(i).ne.4)then if(isec(i+1).ne.4)then if(isec(i+2).eq.4)then if(isec(i+3).eq.4)then if(isec(i+4).ne.4)then if(isec(i+5).ne.4)then isec(i+2)=1 isec(i+3)=1 endif endif endif endif endif endif enddo do i=1,nseq2 if(jsec(i).ne.2)then if(jsec(i+1).ne.2)then if(jsec(i+2).eq.2)then if(jsec(i+3).eq.2)then if(jsec(i+4).ne.2)then if(jsec(i+5).ne.2)then jsec(i+2)=1 jsec(i+3)=1 endif endif endif endif endif endif if(jsec(i).ne.4)then if(jsec(i+1).ne.4)then if(jsec(i+2).eq.4)then if(jsec(i+3).eq.4)then if(jsec(i+4).ne.4)then if(jsec(i+5).ne.4)then jsec(i+2)=1 jsec(i+3)=1 endif endif endif endif endif endif enddo *** connect --------------> *** x-x => xxx do i=1,nseq1 if(isec(i).eq.2)then if(isec(i+1).ne.2)then if(isec(i+2).eq.2)then isec(i+1)=2 endif endif endif if(isec(i).eq.4)then if(isec(i+1).ne.4)then if(isec(i+2).eq.4)then isec(i+1)=4 endif endif endif enddo do i=1,nseq2 if(jsec(i).eq.2)then if(jsec(i+1).ne.2)then if(jsec(i+2).eq.2)then jsec(i+1)=2 endif endif endif if(jsec(i).eq.4)then if(jsec(i+1).ne.4)then if(jsec(i+2).eq.4)then jsec(i+1)=4 endif endif endif enddo return end ************************************************************* * assign secondary structure: ************************************************************* function diszy(i,i1,i2) PARAMETER(nmax=5000) COMMON/BACKBONE/XA(3,nmax,0:1) diszy=sqrt((xa(1,i1,i)-xa(1,i2,i))**2 & +(xa(2,i1,i)-xa(2,i2,i))**2 & +(xa(3,i1,i)-xa(3,i2,i))**2) return end ************************************************************* * assign secondary structure: ************************************************************* function make_sec(dis13,dis14,dis15,dis24,dis25,dis35) make_sec=1 delta=2.1 if(abs(dis15-6.37).lt.delta)then if(abs(dis14-5.18).lt.delta)then if(abs(dis25-5.18).lt.delta)then if(abs(dis13-5.45).lt.delta)then if(abs(dis24-5.45).lt.delta)then if(abs(dis35-5.45).lt.delta)then make_sec=2 !helix return endif endif endif endif endif endif delta=1.42 if(abs(dis15-13).lt.delta)then if(abs(dis14-10.4).lt.delta)then if(abs(dis25-10.4).lt.delta)then if(abs(dis13-6.1).lt.delta)then if(abs(dis24-6.1).lt.delta)then if(abs(dis35-6.1).lt.delta)then make_sec=4 !strand return endif endif endif endif endif endif if(dis15.lt.8)then make_sec=3 endif return end **************************************************************** * quickly calculate TM-score with given invmap(i) in 3 iterations **************************************************************** subroutine get_GL(GL) PARAMETER(nmax=5000) common/length/nseq1,nseq2 COMMON/BACKBONE/XA(3,nmax,0:1) common/dpc/score(nmax,nmax),gap_open,invmap(nmax) common/zscore/zrms,n_al,rmsd_al common/d0/d0,anseq dimension xtm1(nmax),ytm1(nmax),ztm1(nmax) dimension xtm2(nmax),ytm2(nmax),ztm2(nmax) common/TM/TM,TMmax common/n1n2/n1(nmax),n2(nmax) common/d00/d00,d002 dimension xo1(nmax),yo1(nmax),zo1(nmax) dimension xo2(nmax),yo2(nmax),zo2(nmax) dimension dis2(nmax) ccc RMSD: double precision r_1(3,nmax),r_2(3,nmax),r_3(3,nmax),w(nmax) double precision u(3,3),t(3),rms,drms !armsd is real data w /nmax*1.0/ ccc c calculate RMSD between aligned structures and rotate the structures --> n_al=0 do j=1,NSEQ2 i=invmap(j) !j aligned to i if(i.gt.0)then n_al=n_al+1 r_1(1,n_al)=xa(1,i,0) r_1(2,n_al)=xa(2,i,0) r_1(3,n_al)=xa(3,i,0) r_2(1,n_al)=xa(1,j,1) r_2(2,n_al)=xa(2,j,1) r_2(3,n_al)=xa(3,j,1) xo1(n_al)=xa(1,i,0) yo1(n_al)=xa(2,i,0) zo1(n_al)=xa(3,i,0) xo2(n_al)=xa(1,j,1) yo2(n_al)=xa(2,j,1) zo2(n_al)=xa(3,j,1) endif enddo call u3b(w,r_1,r_2,n_al,1,rms,u,t,ier) !u rotate r_1 to r_2 GL=0 do i=1,n_al xx=t(1)+u(1,1)*xo1(i)+u(1,2)*yo1(i)+u(1,3)*zo1(i) yy=t(2)+u(2,1)*xo1(i)+u(2,2)*yo1(i)+u(2,3)*zo1(i) zz=t(3)+u(3,1)*xo1(i)+u(3,2)*yo1(i)+u(3,3)*zo1(i) dis2(i)=(xx-xo2(i))**2+(yy-yo2(i))**2+(zz-zo2(i))**2 GL=GL+1/(1+dis2(i)/(d0**2)) enddo ccc for next iteration-------------> d002t=d002 21 j=0 do i=1,n_al if(dis2(i).le.d002t)then j=j+1 r_1(1,j)=xo1(i) r_1(2,j)=yo1(i) r_1(3,j)=zo1(i) r_2(1,j)=xo2(i) r_2(2,j)=yo2(i) r_2(3,j)=zo2(i) endif enddo if(j.lt.3.and.n_al.gt.3)then d002t=d002t+.5 goto 21 endif L=j call u3b(w,r_1,r_2,L,1,rms,u,t,ier) !u rotate r_1 to r_2 G2=0 do i=1,n_al xx=t(1)+u(1,1)*xo1(i)+u(1,2)*yo1(i)+u(1,3)*zo1(i) yy=t(2)+u(2,1)*xo1(i)+u(2,2)*yo1(i)+u(2,3)*zo1(i) zz=t(3)+u(3,1)*xo1(i)+u(3,2)*yo1(i)+u(3,3)*zo1(i) dis2(i)=(xx-xo2(i))**2+(yy-yo2(i))**2+(zz-zo2(i))**2 G2=G2+1/(1+dis2(i)/(d0**2)) enddo ccc for next iteration-------------> d002t=d002+1 22 j=0 do i=1,n_al if(dis2(i).le.d002t)then j=j+1 r_1(1,j)=xo1(i) r_1(2,j)=yo1(i) r_1(3,j)=zo1(i) r_2(1,j)=xo2(i) r_2(2,j)=yo2(i) r_2(3,j)=zo2(i) endif enddo if(j.lt.3.and.n_al.gt.3)then d002t=d002t+.5 goto 22 endif L=j call u3b(w,r_1,r_2,L,1,rms,u,t,ier) !u rotate r_1 to r_2 G3=0 do i=1,n_al xx=t(1)+u(1,1)*xo1(i)+u(1,2)*yo1(i)+u(1,3)*zo1(i) yy=t(2)+u(2,1)*xo1(i)+u(2,2)*yo1(i)+u(2,3)*zo1(i) zz=t(3)+u(3,1)*xo1(i)+u(3,2)*yo1(i)+u(3,3)*zo1(i) dis2(i)=(xx-xo2(i))**2+(yy-yo2(i))**2+(zz-zo2(i))**2 G3=G3+1/(1+dis2(i)/(d0**2)) enddo if(G2.gt.GL)GL=G2 if(G3.gt.GL)GL=G3 c^^^^^^^^^^^^^^^^ GL done ^^^^^^^^^^^^^^^^^^^^^^^^^^^ return end **************************************************************** * with invmap(i) calculate TM-score and martix score(i,j) for rotation **************************************************************** subroutine get_score PARAMETER(nmax=5000) common/length/nseq1,nseq2 COMMON/BACKBONE/XA(3,nmax,0:1) common/dpc/score(nmax,nmax),gap_open,invmap(nmax) common/zscore/zrms,n_al,rmsd_al common/d0/d0,anseq dimension xtm1(nmax),ytm1(nmax),ztm1(nmax) dimension xtm2(nmax),ytm2(nmax),ztm2(nmax) common/TM/TM,TMmax common/n1n2/n1(nmax),n2(nmax) ccc RMSD: double precision r_1(3,nmax),r_2(3,nmax),r_3(3,nmax),w(nmax) double precision u(3,3),t(3),rms,drms !armsd is real data w /nmax*1.0/ ccc c calculate RMSD between aligned structures and rotate the structures --> n_al=0 do j=1,NSEQ2 i=invmap(j) !j aligned to i if(i.gt.0)then n_al=n_al+1 ccc for TM-score: xtm1(n_al)=xa(1,i,0) !for TM-score ytm1(n_al)=xa(2,i,0) ztm1(n_al)=xa(3,i,0) xtm2(n_al)=xa(1,j,1) ytm2(n_al)=xa(2,j,1) ztm2(n_al)=xa(3,j,1) ccc for rotation matrix: r_1(1,n_al)=xa(1,i,0) r_1(2,n_al)=xa(2,i,0) r_1(3,n_al)=xa(3,i,0) endif enddo *** calculate TM-score for the given alignment-----------> d0_input=d0 call TMscore8_search(d0_input,n_al,xtm1,ytm1,ztm1,n1, & n_al,xtm2,ytm2,ztm2,n2,TM,Rcomm,Lcomm) !simplified search engine TM=TM*n_al/anseq !TM-score *** calculate score matrix score(i,j)------------------> do i=1,n_al r_2(1,i)=xtm1(i) r_2(2,i)=ytm1(i) r_2(3,i)=ztm1(i) enddo call u3b(w,r_1,r_2,n_al,1,rms,u,t,ier) !u rotate r_1 to r_2 do i=1,nseq1 xx=t(1)+u(1,1)*xa(1,i,0)+u(1,2)*xa(2,i,0)+u(1,3)*xa(3,i,0) yy=t(2)+u(2,1)*xa(1,i,0)+u(2,2)*xa(2,i,0)+u(2,3)*xa(3,i,0) zz=t(3)+u(3,1)*xa(1,i,0)+u(3,2)*xa(2,i,0)+u(3,3)*xa(3,i,0) do j=1,nseq2 dd=(xx-xa(1,j,1))**2+(yy-xa(2,j,1))**2+(zz-xa(3,j,1))**2 score(i,j)=1/(1+dd/d0**2) enddo enddo c^^^^^^^^^^^^^^^^ score(i,j) done ^^^^^^^^^^^^^^^^^^^^^^^^^^^ return end **************************************************************** * with invmap(i) calculate score(i,j) using RMSD rotation **************************************************************** subroutine get_score1 PARAMETER(nmax=5000) common/length/nseq1,nseq2 COMMON/BACKBONE/XA(3,nmax,0:1) common/dpc/score(nmax,nmax),gap_open,invmap(nmax) common/zscore/zrms,n_al,rmsd_al common/d0/d0,anseq common/d0min/d0_min dimension xtm1(nmax),ytm1(nmax),ztm1(nmax) dimension xtm2(nmax),ytm2(nmax),ztm2(nmax) common/TM/TM,TMmax common/n1n2/n1(nmax),n2(nmax) ccc RMSD: double precision r_1(3,nmax),r_2(3,nmax),r_3(3,nmax),w(nmax) double precision u(3,3),t(3),rms,drms !armsd is real data w /nmax*1.0/ ccc c calculate RMSD between aligned structures and rotate the structures --> n_al=0 do j=1,NSEQ2 i=invmap(j) !j aligned to i if(i.gt.0)then n_al=n_al+1 ccc for rotation matrix: r_1(1,n_al)=xa(1,i,0) r_1(2,n_al)=xa(2,i,0) r_1(3,n_al)=xa(3,i,0) r_2(1,n_al)=xa(1,j,1) r_2(2,n_al)=xa(2,j,1) r_2(3,n_al)=xa(3,j,1) endif enddo *** calculate score matrix score(i,j)------------------> call u3b(w,r_1,r_2,n_al,1,rms,u,t,ier) !u rotate r_1 to r_2 d01=d0+1.5 if(d01.lt.d0_min)d01=d0_min d02=d01*d01 do i=1,nseq1 xx=t(1)+u(1,1)*xa(1,i,0)+u(1,2)*xa(2,i,0)+u(1,3)*xa(3,i,0) yy=t(2)+u(2,1)*xa(1,i,0)+u(2,2)*xa(2,i,0)+u(2,3)*xa(3,i,0) zz=t(3)+u(3,1)*xa(1,i,0)+u(3,2)*xa(2,i,0)+u(3,3)*xa(3,i,0) do j=1,nseq2 dd=(xx-xa(1,j,1))**2+(yy-xa(2,j,1))**2+(zz-xa(3,j,1))**2 score(i,j)=1/(1+dd/d02) enddo enddo c^^^^^^^^^^^^^^^^ score(i,j) done ^^^^^^^^^^^^^^^^^^^^^^^^^^^ return end ************************************************************************* ************************************************************************* * This is a subroutine to compare two structures and find the * superposition that has the maximum TM-score. * * L1--Length of the first structure * (x1(i),y1(i),z1(i))--coordinates of i'th residue at the first structure * n1(i)--Residue sequence number of i'th residue at the first structure * L2--Length of the second structure * (x2(i),y2(i),z2(i))--coordinates of i'th residue at the second structure * n2(i)--Residue sequence number of i'th residue at the second structure * TM--TM-score of the comparison * Rcomm--RMSD of two structures in the common aligned residues * Lcomm--Length of the common aligned regions * * Note: * 1, Always put native as the second structure, by which TM-score * is normalized. * 2, The returned (x1(i),y1(i),z1(i)) are the rotated structure after * TM-score superposition. ************************************************************************* ************************************************************************* *** dis<8, simplified search engine subroutine TMscore8_search(dx,L1,x1,y1,z1,n1,L2,x2,y2,z2,n2, & TM,Rcomm,Lcomm) PARAMETER(nmax=5000) common/stru/xt(nmax),yt(nmax),zt(nmax),xb(nmax),yb(nmax),zb(nmax) common/nres/nresA(nmax),nresB(nmax),nseqA,nseqB common/para/d,d0 common/d0min/d0_min common/align/n_ali,iA(nmax),iB(nmax) common/nscore/i_ali(nmax),n_cut ![1,n_ali],align residues for the score dimension k_ali(nmax),k_ali0(nmax) dimension L_ini(100),iq(nmax) common/scores/score double precision score,score_max dimension xa(nmax),ya(nmax),za(nmax) dimension iL0(nmax) dimension x1(nmax),y1(nmax),z1(nmax),n1(nmax) dimension x2(nmax),y2(nmax),z2(nmax),n2(nmax) ccc RMSD: double precision r_1(3,nmax),r_2(3,nmax),r_3(3,nmax),w(nmax) double precision u(3,3),t(3),rms,drms !armsd is real data w /nmax*1.0/ ccc ********* convert input data *************************** * because L1=L2 in this special case----------> nseqA=L1 nseqB=L2 do i=1,nseqA xa(i)=x1(i) ya(i)=y1(i) za(i)=z1(i) nresA(i)=n1(i) xb(i)=x2(i) yb(i)=y2(i) zb(i)=z2(i) nresB(i)=n2(i) iA(i)=i iB(i)=i enddo n_ali=L1 !number of aligned residues Lcomm=L1 ************///// * parameters: ***************** *** d0-------------> d0=dx if(d0.lt.d0_min)d0=d0_min *** d0_search -----> d0_search=d0 if(d0_search.gt.8)d0_search=8 if(d0_search.lt.4.5)d0_search=4.5 *** iterative parameters -----> n_it=20 !maximum number of iterations d_output=5 !for output alignment n_init_max=6 !maximum number of L_init n_init=0 L_ini_min=4 if(n_ali.lt.4)L_ini_min=n_ali do i=1,n_init_max-1 n_init=n_init+1 L_ini(n_init)=n_ali/2**(n_init-1) if(L_ini(n_init).le.L_ini_min)then L_ini(n_init)=L_ini_min goto 402 endif enddo n_init=n_init+1 L_ini(n_init)=L_ini_min 402 continue ****************************************************************** * find the maximum score starting from local structures superposition ****************************************************************** score_max=-1 !TM-score do 333 i_init=1,n_init L_init=L_ini(i_init) iL_max=n_ali-L_init+1 k=0 do i=1,iL_max,40 !this is the simplification! k=k+1 iL0(k)=i enddo if(iL0(k).lt.iL_max)then k=k+1 iL0(k)=iL_max endif n_shift=k do 300 i_shift=1,n_shift iL=iL0(i_shift) LL=0 ka=0 do i=1,L_init k=iL+i-1 ![1,n_ali] common aligned r_1(1,i)=xa(iA(k)) r_1(2,i)=ya(iA(k)) r_1(3,i)=za(iA(k)) r_2(1,i)=xb(iB(k)) r_2(2,i)=yb(iB(k)) r_2(3,i)=zb(iB(k)) LL=LL+1 ka=ka+1 k_ali(ka)=k enddo call u3b(w,r_1,r_2,LL,1,rms,u,t,ier) !u rotate r_1 to r_2 if(i_init.eq.1)then !global superposition armsd=dsqrt(rms/LL) Rcomm=armsd endif do j=1,nseqA xt(j)=t(1)+u(1,1)*xa(j)+u(1,2)*ya(j)+u(1,3)*za(j) yt(j)=t(2)+u(2,1)*xa(j)+u(2,2)*ya(j)+u(2,3)*za(j) zt(j)=t(3)+u(3,1)*xa(j)+u(3,2)*ya(j)+u(3,3)*za(j) enddo d=d0_search-1 call score_fun8 !init, get scores, n_cut+i_ali(i) for iteration if(score_max.lt.score)then score_max=score ka0=ka do i=1,ka0 k_ali0(i)=k_ali(i) enddo endif *** iteration for extending ----------------------------------> d=d0_search+1 do 301 it=1,n_it LL=0 ka=0 do i=1,n_cut m=i_ali(i) ![1,n_ali] r_1(1,i)=xa(iA(m)) r_1(2,i)=ya(iA(m)) r_1(3,i)=za(iA(m)) r_2(1,i)=xb(iB(m)) r_2(2,i)=yb(iB(m)) r_2(3,i)=zb(iB(m)) ka=ka+1 k_ali(ka)=m LL=LL+1 enddo call u3b(w,r_1,r_2,LL,1,rms,u,t,ier) !u rotate r_1 to r_2 do j=1,nseqA xt(j)=t(1)+u(1,1)*xa(j)+u(1,2)*ya(j)+u(1,3)*za(j) yt(j)=t(2)+u(2,1)*xa(j)+u(2,2)*ya(j)+u(2,3)*za(j) zt(j)=t(3)+u(3,1)*xa(j)+u(3,2)*ya(j)+u(3,3)*za(j) enddo call score_fun8 !get scores, n_cut+i_ali(i) for iteration if(score_max.lt.score)then score_max=score ka0=ka do i=1,ka k_ali0(i)=k_ali(i) enddo endif if(it.eq.n_it)goto 302 if(n_cut.eq.ka)then neq=0 do i=1,n_cut if(i_ali(i).eq.k_ali(i))neq=neq+1 enddo if(n_cut.eq.neq)goto 302 endif 301 continue !for iteration 302 continue 300 continue !for shift 333 continue !for initial length, L_ali/M ******** return the final rotation **************** LL=0 do i=1,ka0 m=k_ali0(i) !record of the best alignment r_1(1,i)=xa(iA(m)) r_1(2,i)=ya(iA(m)) r_1(3,i)=za(iA(m)) r_2(1,i)=xb(iB(m)) r_2(2,i)=yb(iB(m)) r_2(3,i)=zb(iB(m)) LL=LL+1 enddo call u3b(w,r_1,r_2,LL,1,rms,u,t,ier) !u rotate r_1 to r_2 do j=1,nseqA x1(j)=t(1)+u(1,1)*xa(j)+u(1,2)*ya(j)+u(1,3)*za(j) y1(j)=t(2)+u(2,1)*xa(j)+u(2,2)*ya(j)+u(2,3)*za(j) z1(j)=t(3)+u(3,1)*xa(j)+u(3,2)*ya(j)+u(3,3)*za(j) enddo TM=score_max c^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ return END ************************************************************************* ************************************************************************* * This is a subroutine to compare two structures and find the * superposition that has the maximum TM-score. * * L1--Length of the first structure * (x1(i),y1(i),z1(i))--coordinates of i'th residue at the first structure * n1(i)--Residue sequence number of i'th residue at the first structure * L2--Length of the second structure * (x2(i),y2(i),z2(i))--coordinates of i'th residue at the second structure * n2(i)--Residue sequence number of i'th residue at the second structure * TM--TM-score of the comparison * Rcomm--RMSD of two structures in the common aligned residues * Lcomm--Length of the common aligned regions * * Note: * 1, Always put native as the second structure, by which TM-score * is normalized. * 2, The returned (x1(i),y1(i),z1(i)) are the rotated structure after * TM-score superposition. ************************************************************************* ************************************************************************* *** dis<8, but same search engine subroutine TMscore8(dx,L1,x1,y1,z1,n1,L2,x2,y2,z2,n2, & TM,Rcomm,Lcomm) PARAMETER(nmax=5000) common/stru/xt(nmax),yt(nmax),zt(nmax),xb(nmax),yb(nmax),zb(nmax) common/nres/nresA(nmax),nresB(nmax),nseqA,nseqB common/para/d,d0 common/d0min/d0_min common/align/n_ali,iA(nmax),iB(nmax) common/nscore/i_ali(nmax),n_cut ![1,n_ali],align residues for the score dimension k_ali(nmax),k_ali0(nmax) dimension L_ini(100),iq(nmax) common/scores/score double precision score,score_max dimension xa(nmax),ya(nmax),za(nmax) dimension x1(nmax),y1(nmax),z1(nmax),n1(nmax) dimension x2(nmax),y2(nmax),z2(nmax),n2(nmax) ccc RMSD: double precision r_1(3,nmax),r_2(3,nmax),r_3(3,nmax),w(nmax) double precision u(3,3),t(3),rms,drms !armsd is real data w /nmax*1.0/ ccc ********* convert input data *************************** * because L1=L2 in this special case----------> nseqA=L1 nseqB=L2 do i=1,nseqA xa(i)=x1(i) ya(i)=y1(i) za(i)=z1(i) nresA(i)=n1(i) xb(i)=x2(i) yb(i)=y2(i) zb(i)=z2(i) nresB(i)=n2(i) iA(i)=i iB(i)=i enddo n_ali=L1 !number of aligned residues Lcomm=L1 ************///// * parameters: ***************** *** d0-------------> d0=dx if(d0.lt.d0_min)d0=d0_min *** d0_search -----> d0_search=d0 if(d0_search.gt.8)d0_search=8 if(d0_search.lt.4.5)d0_search=4.5 *** iterative parameters -----> n_it=20 !maximum number of iterations d_output=5 !for output alignment n_init_max=6 !maximum number of L_init n_init=0 L_ini_min=4 if(n_ali.lt.4)L_ini_min=n_ali do i=1,n_init_max-1 n_init=n_init+1 L_ini(n_init)=n_ali/2**(n_init-1) if(L_ini(n_init).le.L_ini_min)then L_ini(n_init)=L_ini_min goto 402 endif enddo n_init=n_init+1 L_ini(n_init)=L_ini_min 402 continue ****************************************************************** * find the maximum score starting from local structures superposition ****************************************************************** score_max=-1 !TM-score do 333 i_init=1,n_init L_init=L_ini(i_init) iL_max=n_ali-L_init+1 do 300 iL=1,iL_max !on aligned residues, [1,nseqA] LL=0 ka=0 do i=1,L_init k=iL+i-1 ![1,n_ali] common aligned r_1(1,i)=xa(iA(k)) r_1(2,i)=ya(iA(k)) r_1(3,i)=za(iA(k)) r_2(1,i)=xb(iB(k)) r_2(2,i)=yb(iB(k)) r_2(3,i)=zb(iB(k)) LL=LL+1 ka=ka+1 k_ali(ka)=k enddo call u3b(w,r_1,r_2,LL,1,rms,u,t,ier) !u rotate r_1 to r_2 if(i_init.eq.1)then !global superposition armsd=dsqrt(rms/LL) Rcomm=armsd endif do j=1,nseqA xt(j)=t(1)+u(1,1)*xa(j)+u(1,2)*ya(j)+u(1,3)*za(j) yt(j)=t(2)+u(2,1)*xa(j)+u(2,2)*ya(j)+u(2,3)*za(j) zt(j)=t(3)+u(3,1)*xa(j)+u(3,2)*ya(j)+u(3,3)*za(j) enddo d=d0_search-1 call score_fun8 !init, get scores, n_cut+i_ali(i) for iteration if(score_max.lt.score)then score_max=score ka0=ka do i=1,ka0 k_ali0(i)=k_ali(i) enddo endif *** iteration for extending ----------------------------------> d=d0_search+1 do 301 it=1,n_it LL=0 ka=0 do i=1,n_cut m=i_ali(i) ![1,n_ali] r_1(1,i)=xa(iA(m)) r_1(2,i)=ya(iA(m)) r_1(3,i)=za(iA(m)) r_2(1,i)=xb(iB(m)) r_2(2,i)=yb(iB(m)) r_2(3,i)=zb(iB(m)) ka=ka+1 k_ali(ka)=m LL=LL+1 enddo call u3b(w,r_1,r_2,LL,1,rms,u,t,ier) !u rotate r_1 to r_2 do j=1,nseqA xt(j)=t(1)+u(1,1)*xa(j)+u(1,2)*ya(j)+u(1,3)*za(j) yt(j)=t(2)+u(2,1)*xa(j)+u(2,2)*ya(j)+u(2,3)*za(j) zt(j)=t(3)+u(3,1)*xa(j)+u(3,2)*ya(j)+u(3,3)*za(j) enddo call score_fun8 !get scores, n_cut+i_ali(i) for iteration if(score_max.lt.score)then score_max=score ka0=ka do i=1,ka k_ali0(i)=k_ali(i) enddo endif if(it.eq.n_it)goto 302 if(n_cut.eq.ka)then neq=0 do i=1,n_cut if(i_ali(i).eq.k_ali(i))neq=neq+1 enddo if(n_cut.eq.neq)goto 302 endif 301 continue !for iteration 302 continue 300 continue !for shift 333 continue !for initial length, L_ali/M ******** return the final rotation **************** LL=0 do i=1,ka0 m=k_ali0(i) !record of the best alignment r_1(1,i)=xa(iA(m)) r_1(2,i)=ya(iA(m)) r_1(3,i)=za(iA(m)) r_2(1,i)=xb(iB(m)) r_2(2,i)=yb(iB(m)) r_2(3,i)=zb(iB(m)) LL=LL+1 enddo call u3b(w,r_1,r_2,LL,1,rms,u,t,ier) !u rotate r_1 to r_2 do j=1,nseqA x1(j)=t(1)+u(1,1)*xa(j)+u(1,2)*ya(j)+u(1,3)*za(j) y1(j)=t(2)+u(2,1)*xa(j)+u(2,2)*ya(j)+u(2,3)*za(j) z1(j)=t(3)+u(3,1)*xa(j)+u(3,2)*ya(j)+u(3,3)*za(j) enddo TM=score_max c^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ return END ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc c 1, collect those residues with dis nseqA=L1 nseqB=L2 do i=1,nseqA xa(i)=x1(i) ya(i)=y1(i) za(i)=z1(i) nresA(i)=n1(i) xb(i)=x2(i) yb(i)=y2(i) zb(i)=z2(i) nresB(i)=n2(i) iA(i)=i iB(i)=i enddo n_ali=L1 !number of aligned residues Lcomm=L1 ************///// * parameters: ***************** *** d0-------------> c d0=1.24*(nseqB-15)**(1.0/3.0)-1.8 d0=dx if(d0.lt.d0_min)d0=d0_min *** d0_search -----> d0_search=d0 if(d0_search.gt.8)d0_search=8 if(d0_search.lt.4.5)d0_search=4.5 *** iterative parameters -----> n_it=20 !maximum number of iterations d_output=5 !for output alignment n_init_max=6 !maximum number of L_init n_init=0 L_ini_min=4 if(n_ali.lt.4)L_ini_min=n_ali do i=1,n_init_max-1 n_init=n_init+1 L_ini(n_init)=n_ali/2**(n_init-1) if(L_ini(n_init).le.L_ini_min)then L_ini(n_init)=L_ini_min goto 402 endif enddo n_init=n_init+1 L_ini(n_init)=L_ini_min 402 continue ****************************************************************** * find the maximum score starting from local structures superposition ****************************************************************** score_max=-1 !TM-score do 333 i_init=1,n_init L_init=L_ini(i_init) iL_max=n_ali-L_init+1 do 300 iL=1,iL_max !on aligned residues, [1,nseqA] LL=0 ka=0 do i=1,L_init k=iL+i-1 ![1,n_ali] common aligned r_1(1,i)=xa(iA(k)) r_1(2,i)=ya(iA(k)) r_1(3,i)=za(iA(k)) r_2(1,i)=xb(iB(k)) r_2(2,i)=yb(iB(k)) r_2(3,i)=zb(iB(k)) LL=LL+1 ka=ka+1 k_ali(ka)=k enddo call u3b(w,r_1,r_2,LL,1,rms,u,t,ier) !u rotate r_1 to r_2 if(i_init.eq.1)then !global superposition armsd=dsqrt(rms/LL) Rcomm=armsd endif do j=1,nseqA xt(j)=t(1)+u(1,1)*xa(j)+u(1,2)*ya(j)+u(1,3)*za(j) yt(j)=t(2)+u(2,1)*xa(j)+u(2,2)*ya(j)+u(2,3)*za(j) zt(j)=t(3)+u(3,1)*xa(j)+u(3,2)*ya(j)+u(3,3)*za(j) enddo d=d0_search-1 call score_fun !init, get scores, n_cut+i_ali(i) for iteration if(score_max.lt.score)then score_max=score ka0=ka do i=1,ka0 k_ali0(i)=k_ali(i) enddo endif *** iteration for extending ----------------------------------> d=d0_search+1 do 301 it=1,n_it LL=0 ka=0 do i=1,n_cut m=i_ali(i) ![1,n_ali] r_1(1,i)=xa(iA(m)) r_1(2,i)=ya(iA(m)) r_1(3,i)=za(iA(m)) r_2(1,i)=xb(iB(m)) r_2(2,i)=yb(iB(m)) r_2(3,i)=zb(iB(m)) ka=ka+1 k_ali(ka)=m LL=LL+1 enddo call u3b(w,r_1,r_2,LL,1,rms,u,t,ier) !u rotate r_1 to r_2 do j=1,nseqA xt(j)=t(1)+u(1,1)*xa(j)+u(1,2)*ya(j)+u(1,3)*za(j) yt(j)=t(2)+u(2,1)*xa(j)+u(2,2)*ya(j)+u(2,3)*za(j) zt(j)=t(3)+u(3,1)*xa(j)+u(3,2)*ya(j)+u(3,3)*za(j) enddo call score_fun !get scores, n_cut+i_ali(i) for iteration if(score_max.lt.score)then score_max=score ka0=ka do i=1,ka k_ali0(i)=k_ali(i) enddo endif if(it.eq.n_it)goto 302 if(n_cut.eq.ka)then neq=0 do i=1,n_cut if(i_ali(i).eq.k_ali(i))neq=neq+1 enddo if(n_cut.eq.neq)goto 302 endif 301 continue !for iteration 302 continue 300 continue !for shift 333 continue !for initial length, L_ali/M ******** return the final rotation **************** LL=0 do i=1,ka0 m=k_ali0(i) !record of the best alignment r_1(1,i)=xa(iA(m)) r_1(2,i)=ya(iA(m)) r_1(3,i)=za(iA(m)) r_2(1,i)=xb(iB(m)) r_2(2,i)=yb(iB(m)) r_2(3,i)=zb(iB(m)) LL=LL+1 enddo call u3b(w,r_1,r_2,LL,1,rms,u,t,ier) !u rotate r_1 to r_2 do j=1,nseqA x1(j)=t(1)+u(1,1)*xa(j)+u(1,2)*ya(j)+u(1,3)*za(j) y1(j)=t(2)+u(2,1)*xa(j)+u(2,2)*ya(j)+u(2,3)*za(j) z1(j)=t(3)+u(3,1)*xa(j)+u(3,2)*ya(j)+u(3,3)*za(j) enddo TM=score_max c^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ return END ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc c 1, collect those residues with dis