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Disulfide bonds prediction using ILP

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Disulfide bonds prediction using ILP

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  1. Abstract We address the issue of predicting disulfide bonds in protein sequences. We propose to tackle with this problem in the framework of Inductive Logic Programming (ILP). Our goal is to infer characteristic patterns on physico-chemical properties of amino acids around cystines involved in disulfide bonds. The physico-chemical properties include hydrophobicity, charge, size, and sub-classes like aromatic, aliphatic, ... In our experiments we used the Progol’s algorithm[2]. Due to the huge size of the hypothesis space, we ran this algorithm with a two level search. The first level aimed at discovering a relevant subspace of the Herbrand universe, i.e the interesting properties, by sampling a restricted subset of hypotheses. The second level aims at discovering prediction rules, using this time the restricted Herbrand universe and the whole hypothesis space. The hypothesis space is described and organized in the background knowledge. We used a window of length 14 (7 amino acids on each side of the cysteine) and subsequences of properties were enumerated on sub-windows of size 4. We used 2 data bases in our experiments, one for the learning phase and the other for the test. Results show that only 13 rules are needed to cover more than 90% of the 2 data bases, which is a very good result with respect to the simplicity of the characterization. Keywords Disulfide bonds, Inductive Logic Programming. Ionic link Hydrogen link Hydrophobic effect Disulfide bond >/Pdb/Entries/pdb1e0f.ent Chaine=K IRFGMGKVPCPDGEVGYTCDCGEKICLYGQSCNDGQCSGDPKPSS ILP Knowledge [1] properties(a,[hydrophobic, small, tiny])… type(-7,far). type(-7,left). … pattern(quatuor(A,B,C,D),[LA,LB,LC,LD]):- property(A,LA),property(B,LB),property(C,LC), property(D,LD)… BackgroundKnowledge [1] :-modeh(1,example(+context))? :-modeb(*,pattern1(+context,#properties)? … :-set(noise,5)? … prune(_,(pattern1(_,_),pattern1(_,_)))… properties(a,[hydrophobic, small, tiny]). type(-7,far). type(-7,left). … pattern(quatuor(A,B,C,D),[LA,LB,LC,LD]):- property(A,LA),property(B,LB),property(C,LC), property(D,LD)… example(context([I,t,p,v,n,a,t, a,I,r,h,p,c,h]))… :-example(context([s,d,k,v,g,q,a, c,r,p,v,a,f,d]))… • Results [1] • Example(A):- • pattern3(A,quatuor(s,p,s,not(s))), • pattern2(A,quatuor1(not(p),s,h),close), • pattern1(A,pair(h,h,p,p)). • Example(A):- • pattern2(A,quatuor(s,p,not(c),h),close), • pattern1(A,quatuor(h,h(o),not(p),not(s))). PROGOL [2] Positive [1] example(context([I,t,p,v,n,a,t, a,I,r,h,p,c,h])). example(context([t,c,a,I,r,h,p, h,g,n,l,m,n,q]))… Negative [1] :-example(context([s,d,k,v,g,q,a, c,r,p,v,a,f,d])). :-example(context([s,h,m,e,e,d,p, e,c,k,s,I,v,k]))… H2 H1 H3 I L P I L P I L P BK4 BK1 BK2 BK3 Disulfide bonds prediction using ILP IRISA – INRIA Symbiose project Campus de Beaulieu 35042 Rennes cedex France Jacques Nicolas Ingrid Jacquemin • References • I.Jacquemin, J.Nicolas. Modélisation de cystéines oxydées à l’aide de la programmation logique inductive. JOBIM, 2005. • S.Muggleton Progol, http://www.doc.ic.ac.uk/~shm/progol.html 1998 For more information contact Ingrid Jacquemin Campus de Beaulieu 35042 Rennes France tel.: +33(0)2 99 84 74 51 ingrid.jacquemin@irisa.fr

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