Sequence—evolution—function: computational approaches in comparative genomics
E Koonin, MY Galperin - 2002 - books.google.com
Sequence-Evolution-Function is an introduction to the computational approaches that play a
critical role in the emerging new branch of biology known as functional genomics. The book …
critical role in the emerging new branch of biology known as functional genomics. The book …
Protein secondary structure prediction
W Pirovano, J Heringa - Data Mining Techniques for the Life Sciences, 2010 - Springer
While the prediction of a native protein structure from sequence continues to remain a
challenging problem, over the past decades computational methods have become quite …
challenging problem, over the past decades computational methods have become quite …
Protein secondary structure prediction based on position-specific scoring matrices
DT Jones - Journal of molecular biology, 1999 - Elsevier
A two-stage neural network has been used to predict protein secondary structure based on
the position specific scoring matrices generated by PSI-BLAST. Despite the simplicity and …
the position specific scoring matrices generated by PSI-BLAST. Despite the simplicity and …
Regulation of chromatin structure by site-specific histone H3 methyltransferases
The organization of chromatin into higher-order structures influences chromosome function
and epigenetic gene regulation. Higher-order chromatin has been proposed to be nucleated …
and epigenetic gene regulation. Higher-order chromatin has been proposed to be nucleated …
VEGA–an open platform to develop chemo-bio-informatics applications, using plug-in architecture and script programming
A Pedretti, L Villa, G Vistoli - Journal of computer-aided molecular design, 2004 - Springer
In this paper we present the expandability and flexibility features of the VEGA program
(downloadable free of charge at http://www. ddl. unimi. it), for the development of custom …
(downloadable free of charge at http://www. ddl. unimi. it), for the development of custom …
Evaluation and improvement of multiple sequence methods for protein secondary structure prediction
A new dataset of 396 protein domains is developed and used to evaluate the performance of
the protein secondary structure prediction algorithms DSC, PHD, NNSSP, and PREDATOR …
the protein secondary structure prediction algorithms DSC, PHD, NNSSP, and PREDATOR …
JPred: a consensus secondary structure prediction server.
An interactive protein secondary structure prediction Internet server is presented. The server
allows a single sequence or multiple alignment to be submitted, and returns predictions from …
allows a single sequence or multiple alignment to be submitted, and returns predictions from …
PRALINE: a multiple sequence alignment toolbox that integrates homology-extended and secondary structure information
VA Simossis, J Heringa - Nucleic acids research, 2005 - academic.oup.com
PRofile ALIgNEment (PRALINE) is a fully customizable multiple sequence alignment
application. In addition to a number of available alignment strategies, PRALINE can …
application. In addition to a number of available alignment strategies, PRALINE can …
Molecular signature of hypersaline adaptation: insights from genome and proteome composition of halophilic prokaryotes
Background Halophilic prokaryotes are adapted to thrive in extreme conditions of salinity.
Identification and analysis of distinct macromolecular characteristics of halophiles provide …
Identification and analysis of distinct macromolecular characteristics of halophiles provide …
Predicting drug-target interaction networks based on functional groups and biological features
Background Study of drug-target interaction networks is an important topic for drug
development. It is both time-consuming and costly to determine compound-protein …
development. It is both time-consuming and costly to determine compound-protein …