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Randomized Algorithms for Three Dimensional Protein Structures
Randomized Algorithms for Three Dimensional. Protein ... compare protein structures and measure the de- ... of intra and inter-molecular atomic distances [1, .
[ 2005-0722-JCIS-3DPSC.pdf - Read/Download File

Tools and Algorithms for Refined Comparison of Protein Structures
The three dimensional structure of proteins is ... (3). , A. 1. 2 = B means BB = A , and o denotes the zero vector. Thus, d(P, Q), R and a can be computed in. O(n) time [12]. .... spread n probes uniformly on the sphere at random in details.
[ 0705-MINO-StrcCmp.pdf - Read/Download File

Comparisons of Semi-local Alignment Algorithms for Protein Structures
son and alignment of protein structures represents .... or vector x, let (x)i(i = 1, 2, 3 ) denote the i-th ..... Randomized algorithms for three dimensional protein.
[ 0c96052b51d63d5656000000.pdf - Read/Download File

Protein Structures Alignment Algorithms by Parametric Searching
compare protein structures and measure the de- .... 2 A−1,. (2) where the matrix A = (Aij) i, j = 1, 2, 3 is given by. Aij = n. ∑ k=1. (pk)i(qk)j, ... is generally a randomized algorithm and a variable ..... three dimensional protein structures alignment.
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Protein Structure Comparison: Algorithms and Applications - Brown
1. Dipartimento Elettronica e Informatica, Via Gradenigo 6/A, Padova,[email protected] ... on algorithms and applications for protein fold (structure) comparison. The following are ... By their nature, three-dimensional computational problems are inherently ..... ing, Randomized Algorithms and various Metaheuristics.
[ Lancia-2003-PSC.pdf - Read/Download File

Protein Structure Alignment Using a Graph Matching Technique
alignment is, given two three-dimensional protein structures, to nd spatially equivalent ... comparison with a previous alignment algorithm. ... random sampling technique is used in RAND, while a fragment based searching method is used ... 1 p. 2 p. 5 p. 4 p. 3 p. 6 p. 7 q. 2 q. 4 q. 5 q. 3 q. 1 q. 6 q. 7. P. Q. Figure 1 : Example of ...
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Fast Algorithms for Determining Protein Structure Similarity - ETH TIK
algorithmic techniques such as randomization, and/or an approximate matching scheme ... in the number of atoms in the proteins being compared, making the ... approximation algorithm for the three-dimensional case was given in [1], which ...
[ protein.pdf - Read/Download File

Why similar protein sequences encode similar three-dimensional
Our results indicate that three-dimensional protein structure is evolutionarily more .... The design procedure started from a randomized sequence having a given composition. ... We used this algorithm for designing pseudohomologs, i.e., sequences ... Table 1. Comparison of knowledge-based potentials of template proteins ...
[ 300nu34v4862r135.pdf - Read/Download File

Efficient Protein Tertiary Structure Retrievals and Classifications
Using Content Based Comparison Algorithms. A Dissertation ... 1.1.1 A Need for Fast Protein Three-Dimensional Structure Retrieval 1. 1.1.2 A Need for .... using three sets of representative protein substructures generated by a random order.
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Protein Sectors: Evolutionary Units of Three-Dimensional Structure
Najeeb Halabi,1,4 Olivier Rivoire,2,4 Stanislas Leibler,2,3 and Rama Ranganathan1,*. 1The Green ... the sectors are features of protein structures than reflect the evolutionary ... randomized versions of the data; significant patterns of correla- tions are ... also permits a quantitative comparison of the degree of indepen- dence ...
[ halabi al_09.pdf - Read/Download File

The Evolutionary Capacity of Protein Structures - Department of
develop randomized algorithms that perform approximate enu- ... termines the protein's three-dimensional shape under physio- .... lows for comparison with this related work. ... description of the THOM2 function.1 The sequence distribu-.
[ recomb04-count.pdf - Read/Download File

protein structure comparison via contact map alignment - RI Ufla
5.2 Comparison of the GRASP-PR heuristic with other algorithms . . . . . 37 .... Greedy Random Adaptive Search Procedure com Path-relinking para o Maximum. Contact Map ... 1 PROTEIN STRUCTURES AND CONTACT MAPS. Proteins ... Three-dimensional structure of proteins can be represented by their distance maps.
[ DISSERTAÇÃO_Protein structure comparison via contact map alignment.pdf - Read/Download File

programming Protein structure comparison using iterated double
May 7, 1996 ... three-dimensional superposition of the structural coordinate sets, but often the .... optimality of the score was to add a random component into the ... 1. Double dynamic programming algorithm. Two protein structures A.
[ download?doi=10.1.1.133.4624&rep=rep1&type=pdf - Read/Download File

Evaluation and improvements in the automatic alignment of protein
of the three-dimensional structures are used as a standard ... Automatic sequence comparisons (e.g. Needleman and Wunsch,. 1970 ... gramming algorithms such as those originally applied in ... ing homology against a background of randomized sequences, ... simplest form this may indicate a score of 1 for identity and 0.
[ Evaluation_and_improvements_in_the_automatic_alignment_of_protein_sequences_1987.pdf - Read/Download File

Comparing Graph Representations of Protein Structure for Mining
to graph representations of protein three-dimensional structure. .... Section 3 presents the data structure and the algorithm for subgraph mining, and Section 4 .... 1. A graph database G of three labeled graphs. The mappings q1 → p2, q2 → p1, and q3 → p3 ..... Randomized pharmacophore identification for drug design.
[ jcb05.pdf - Read/Download File

Structure Based Protein Multiple Sequence Alignment Algorithm on
The comparison of 3D (three dimensional) protein structure involves ... 1 An algorithm that Combine sequence and structure of Protein. 2 A new toolkit for protein ...
[ 86-A680.pdf - Read/Download File

Can three-dimensional contacts in protein structures be predicted by
algorithms. In conclusion, we ... of functional mutants after random mutagenesis and analysis of correlated ... the three—dimensional structure of a protein ( Epstein er aL, 1963;. Anfinsen, 1981 .... _ 1, if a mutation occurred on branch k at position l 3 gl" _ 0 ..... is relatively small compared to the set of all observed contacts.
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GEOMETRIC AND TOPOLOGICAL METHODS IN PROTEIN
is made possible by the diversity of their three-dimensional structures, which are capable ... algorithm to find promising initial relative placements of the proteins. ... xii. List of Figures xiii. 1 Introduction. 1. 1.1 Protein Structure and Geometric Models . ..... 3.7 Comparisons between DP and GreedyFrechetSimp algorithms . . . 55.
[ yusu_phdthesis.pdf - Read/Download File

STATISTICAL GEOMETRY ANALYSIS OF PROTEINS: IMPLICA
protein structures is studied using a statistical geometry approach. ... several tested native proteins score the highest among 100,000 random ... Accurate prediction of protein three-dimensional (3D) structure from its primary ... comparison, alignment, and classification of known protein structures. ... incremental algorithm.
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Handbook of - School of Systems Biology
3.5 Protein Structure Comparison and Classification ......................... .. ... tional data . Accurate prediction of protein three-dimensional structure from its ... algorithm is a variation of the randomized, incremental algorithm of Clarkson. Statistical ..... {3, 1} decreases with the increase of the content of class {4] simplices. According.
[ hcs04-vaisman-sc.pdf - Read/Download File

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