Protein recognition by sequence-to-structure fitness Bridging efficiency and capacity of threading models
➤ Gửi thông báo lỗi ⚠️ Báo cáo tài liệu vi phạmNội dung chi tiết: Protein recognition by sequence-to-structure fitness Bridging efficiency and capacity of threading models
Protein recognition by sequence-to-structure fitness Bridging efficiency and capacity of threading models
Protein recognition by sequence-to-structure fitness:Bridging efficiency and capacity of threading models.Jaroslaw Meller12 and Ron Elber1*’Department Protein recognition by sequence-to-structure fitness Bridging efficiency and capacity of threading modelst of Computer ScienceUpson Hall 4130Cornell UniversityIthaca NY 148532Department of Computer Methods,Nicholas Copernicus University,87-100 Tonin, Poland* Corresponding authorPhone (607)255-7416Fax (607)255-4428e-mail nmiii}cs£0ii]dL£duRunning title: “Efficient threading model”Keywords: Linear Progra Protein recognition by sequence-to-structure fitness Bridging efficiency and capacity of threading modelsmming, Potential Optimization, Lennard Jones, Decoy structures, threading, gaps and deletions1Abstract“Threading*’ is a technique to match a sequenceProtein recognition by sequence-to-structure fitness Bridging efficiency and capacity of threading models
with a protein shape. Compatibility between a sequence and known protein folds is evaluated according to a scoring function and the best matching struProtein recognition by sequence-to-structure fitness:Bridging efficiency and capacity of threading models.Jaroslaw Meller12 and Ron Elber1*’Department Protein recognition by sequence-to-structure fitness Bridging efficiency and capacity of threading modelsom non-native shapes with a limited computational cost, is an active field of research. We revisit here two widely used families of threading potentials, namely the pairwise and profile models.To design optimal scoring functions we use linear programming. We show that pair potentials have larger pre Protein recognition by sequence-to-structure fitness Bridging efficiency and capacity of threading modelsdiction capacity compared to profile energies. However, alignments with gaps are more efficient to compute when profile potentials are used. We therefProtein recognition by sequence-to-structure fitness Bridging efficiency and capacity of threading models
ore search and propose a new profile model with comparable prediction capacity to contact potentials. Linear programming is also used to determine optProtein recognition by sequence-to-structure fitness:Bridging efficiency and capacity of threading models.Jaroslaw Meller12 and Ron Elber1*’Department Protein recognition by sequence-to-structure fitness Bridging efficiency and capacity of threading modelses that suggest clear guidelines how to avoid false positives. Extensive tests of the new protocol are presented. The new model provides an efficient alternative to pair energies for threading approach, maintaining comparable accuracy.2I. IntroductionThe threading approach [1-8] to protein recogniti Protein recognition by sequence-to-structure fitness Bridging efficiency and capacity of threading modelson is a generalization of the sequence-to-sequence alignment. Rather than matching the unknown sequence S; to another sequence Sj (one dimensional matProtein recognition by sequence-to-structure fitness Bridging efficiency and capacity of threading models
ching) we match the sequence s. to a shape X; (three dimensional matching). Experiments found a limited set of folds compared to a large diversity of Protein recognition by sequence-to-structure fitness:Bridging efficiency and capacity of threading models.Jaroslaw Meller12 and Ron Elber1*’Department Protein recognition by sequence-to-structure fitness Bridging efficiency and capacity of threading modelsrities between proteins. Hence, the determination of overall folds is reduced to tests of sequence fitness into known and limited number of shapes.The sequence-structure compatibility is commonly evaluated using reduced representations of protein structures. Assuming that each amino acid residue is Protein recognition by sequence-to-structure fitness Bridging efficiency and capacity of threading modelsrepresented by a point in 3D space one may define an effective energy of a protein as a sum of inter-residue interactions. The effective pair energiesProtein recognition by sequence-to-structure fitness Bridging efficiency and capacity of threading models
can be derived from the analysis of contacts in known structures. Knowledge-based painvise potentials proved to be very successful in fold recognitioProtein recognition by sequence-to-structure fitness:Bridging efficiency and capacity of threading models.Jaroslaw Meller12 and Ron Elber1*’Department Protein recognition by sequence-to-structure fitness Bridging efficiency and capacity of threading modelsonn of a sum of individual site contributions, depending on the structural environment (e.g. the solvatron.'burial state or the secondary structure) of a site, rhe above distinction is motivated by computational difficulties OÍ finding optimal alignments with gaps when employing pairwise models.3Con Protein recognition by sequence-to-structure fitness Bridging efficiency and capacity of threading modelssider the alignment of a sequence s = of length n, where Of is one of the twenty amino acids, into a structure X = (Xj,x2,...,xm) with tn sites, whereProtein recognition by sequence-to-structure fitness Bridging efficiency and capacity of threading models
x; is an approximate spatial location of an amino acid (taken here to be the geometric center of the side chain). We wish to place each of the amino Protein recognition by sequence-to-structure fitness:Bridging efficiency and capacity of threading models.Jaroslaw Meller12 and Ron Elber1*’Department Protein recognition by sequence-to-structure fitness Bridging efficiency and capacity of threading models to consider deletions and insertions into the aligned sequence. For that purpose we introduce an “extended” sequence, s , which may include gap “residues” (spaces, or empty structural sites) and deletions (removal of an amino acid, or an amino acid corresponding to a virtual structural site).Our go Protein recognition by sequence-to-structure fitness Bridging efficiency and capacity of threading modelsal is to identify the matching structure x; with the extended sequence s,. The process of aligning a sequence s into a structure X provides an optimalProtein recognition by sequence-to-structure fitness Bridging efficiency and capacity of threading models
score and the extended sequence s. This double achievement can be obtained using dynamic programming (DP) algorithm [16-19]. In DP the computational Protein recognition by sequence-to-structure fitness:Bridging efficiency and capacity of threading models.Jaroslaw Meller12 and Ron Elber1*’Department Protein recognition by sequence-to-structure fitness Bridging efficiency and capacity of threading modelsgnments.In contrast to profile models, however, the potentials based on identifiable pair interactions do not lead to alignments with dynamic programming. A number of heuristic algorithms providing approximate alignments have been proposed [20], however they cannot guarantee an optimal solution with Protein recognition by sequence-to-structure fitness Bridging efficiency and capacity of threading models less than exponential number of operations [21]. Another common approach is to approximate the energy by a profile model (the so-called frozen enviroProtein recognition by sequence-to-structure fitness Bridging efficiency and capacity of threading models
nment approximation) and to perform the alignment using DP [22]. In4this work, we are aiming at deriving systematic approximations to pair energies thProtein recognition by sequence-to-structure fitness:Bridging efficiency and capacity of threading models.Jaroslaw Meller12 and Ron Elber1*’Department Protein recognition by sequence-to-structure fitness Bridging efficiency and capacity of threading modelsite sensitive to variations in shapes [23]. Therefore, painvise potentials are often employed in conjunction with various complementary “signals", such as sequence similarity, secondary structures or family profiles [9-11,24-28], which enhance the recognition when the tertiary contacts are significa Protein recognition by sequence-to-structure fitness Bridging efficiency and capacity of threading modelsntly altered. In GenTHREADER [9], for example, sequence alignment methods are employed as the primary detection tools. A pairwise threading potentialProtein recognition by sequence-to-structure fitness Bridging efficiency and capacity of threading models
is then employed to evaluate consistency of the sequence alignments with the underlying structures. Bryant et. a), use, in turn, an energy function whProtein recognition by sequence-to-structure fitness:Bridging efficiency and capacity of threading models.Jaroslaw Meller12 and Ron Elber1*’Department Protein recognition by sequence-to-structure fitness Bridging efficiency and capacity of threading modelsss sensitive to variations in shapes than simple contact models, in which inter-residues interactions are assumed to be constant up to a certain cutoff distance and are set to zero if the inter-residue distance is larger than cutoff distance. A number of distance dependent pairwise potentials have b Protein recognition by sequence-to-structure fitness Bridging efficiency and capacity of threading modelseen proposed in the past [29,30]. We consider both: simple contact models, as well as distance dependent, power law potentials, and compare their perfProtein recognition by sequence-to-structure fitness Bridging efficiency and capacity of threading models
ormance with that of novel profile models.Protein recognition by sequence-to-structure fitness:Bridging efficiency and capacity of threading models.Jaroslaw Meller12 and Ron Elber1*’DepartmentProtein recognition by sequence-to-structure fitness:Bridging efficiency and capacity of threading models.Jaroslaw Meller12 and Ron Elber1*’DepartmentGọi ngay
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