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pro vyhledávání: '"Stephen H. Bryant"'
Publikováno v:
Analytica Chimica Acta. 909:41-50
Identification of drug-target interactions (DTI) is a central task in drug discovery processes. In this work, a simple but effective regularized least squares integrating with nonlinear kernel fusion (RLS-KF) algorithm is proposed to perform DTI pred
While novel technologies such as high-throughput screening have advanced together with significant investment by pharmaceutical companies during the past decades, the success rate for drug development has not yet been improved prompting researchers l
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::0b20b2a7041a66c8e42633897084b981
https://europepmc.org/articles/PMC6781586/
https://europepmc.org/articles/PMC6781586/
Publikováno v:
Analytica Chimica Acta. 806:117-127
It is common that imbalanced datasets are often generated from high-throughput screening (HTS). For a given dataset without taking into account the imbalanced nature, most classification methods tend to produce high predictive accuracy for the majori
Autor:
Stephen H. Bryant, Anna R. Panchenko
Publikováno v:
Protein Science. 11:361-370
Sequence comparison methods based on position-specific score matrices (PSSMs) have proven a useful tool for recognition of the divergent members of a protein family and for annotation of functional sites. Here we investigate one of the factors that a
Publikováno v:
Nucleic Acids Research
The sequencing of complete genomes has created a pressing need for automated annotation of gene function. Because domains are the basic units of protein function and evolution, a gene can be annotated from a domain database by aligning domains to the
Publikováno v:
Journal of Molecular Biology. 296:1319-1331
Using a benchmark set of structurally similar proteins, we conduct a series of threading experiments intended to identify a scoring function with an optimal combination of contact-potential and sequence-profile terms. The benchmark set is selected to
Autor:
Aron Marchler-Bauer, Stephen H. Bryant
Publikováno v:
Proteins: Structure, Function, and Genetics. 37:218-225
We present a retrospective analysis of CASP3 threading predictions, applying evaluation and assessment criteria used at CASP2. Our purpose is twofold. First, we wish to ask whether measures of model accuracy are comparable between CASP3 and CASP2, ev
Autor:
Stephen H. Bryant, Aron Marchler-Bauer
Publikováno v:
Trends in Biochemical Sciences. 22:236-240
Prediction of protein structure by fold recognition, or threading, was recently put to the test in a ‘blind’ structure prediction experiment, CASP2. Thirty-two teams from around the world participated, preparing predictions for 22 different ‘ta
Autor:
Stephen H. Bryant, Aron Marchler-Bauer
Publikováno v:
Proteins: Structure, Function, and Genetics. 29:74-82
Threading predictions for CASP2 target proteins were compared to their true structures using a series of precisely defined measures of agreement, calculated in a fully automatic way. Fold recognition specificity was calculated as the proportion of a
Autor:
Stephen H. Bryant
Publikováno v:
Proteins: Structure, Function, and Genetics. 26:172-185
Threading experiments with proteins from the globin family provide an indication of the nature of the structural similarity required for successful fold recognition and accurate sequence-structure alignment. Threading scores are found to rise above t