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» Computing with Evolving Proteins
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ISMB
1993
14 years 11 months ago
Probabilistic Structure Calculations: A Three-Dimensional tRNA Structure from Sequence Correlation Data
Algorithmsbasedonprobability theorycanaddressissues of uncertainty directly throughtheir representational frameworkandtheir theoryfor data combination.In this paper, wediscuss the...
Russ B. Altman
78
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BIB
2006
141views more  BIB 2006»
14 years 10 months ago
Statistical significance in biological sequence analysis
One of the major goals of computational sequence analysis is to find sequence similarities, which could serve as evidence of structural and functional conservation, as well as of ...
Alexander Yu. Mitrophanov, Mark Borodovsky
106
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BMCBI
2006
129views more  BMCBI 2006»
14 years 10 months ago
Fast index based algorithms and software for matching position specific scoring matrices
Background: In biological sequence analysis, position specific scoring matrices (PSSMs) are widely used to represent sequence motifs in nucleotide as well as amino acid sequences....
Michael Beckstette, Robert Homann, Robert Giegeric...
JCB
2006
79views more  JCB 2006»
14 years 10 months ago
A Stability Boundary Based Method for Finding Saddle Points on Potential Energy Surfaces
The task of finding saddle points on potential energy surfaces plays a crucial role in understanding the dynamics of a micromolecule as well as in studying the folding pathways of...
Chandan K. Reddy, Hsiao-Dong Chiang
95
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JCC
2006
103views more  JCC 2006»
14 years 10 months ago
Flooding in GROMACS: Accelerated barrier crossings in molecular dynamics
: The major bottleneck of today's atomistic molecular dynamics (MD) simulations is that because of the enormous computational effort involved, only processes at nanoseconds to...
Oliver F. Lange, Lars V. Schäfer, Helmut Grub...