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Fuzzy Prediction of Transmembrane Protein Topology ⋆

by Shiyu Chen A, Xinyang Deng A, Chuan Cui A, Yong Deng A B
"... The prediction of the topology of transmembrane proteins is one of the open issues in bioinformatics. There are many methods proposed to predict transmembrane protein topology. However, these methods have some shortcomings to correctly predict on the boundary of the transmembrane region. In this pap ..."
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The prediction of the topology of transmembrane proteins is one of the open issues in bioinformatics. There are many methods proposed to predict transmembrane protein topology. However, these methods have some shortcomings to correctly predict on the boundary of the transmembrane region

Predicting Transmembrane Protein Topology with a Hidden Markov Model: Application to Complete Genomes

by Anders Krogh, Björn Larsson, Gunnar von Heijne, Erik L. L. Sonnhammer - J. MOL. BIOL , 2001
"... ..."
Abstract - Cited by 899 (17 self) - Add to MetaCart
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Methods for Transmembrane Protein Topology and Alpha Helix Prediction

by Kristen Carnohan , 2012
"... Alpha-helical transmembrane proteins are essential to many biological processes, such as transport, signaling, intracellular communication, cell recognition, and adhesion 1. These proteins also comprise the majority of drug targets. However, because experimentally determining the structures of these ..."
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Alpha-helical transmembrane proteins are essential to many biological processes, such as transport, signaling, intracellular communication, cell recognition, and adhesion 1. These proteins also comprise the majority of drug targets. However, because experimentally determining the structures

Multiple State Hidden Markov Model to Predict Transmembrane Protein Topology1)

by unknown authors
"... This paper describes a new modeling method for the prediction of transmembrane protein topology. The structural regions of the transmembrane protein have been modeled by means of a multiple state hidden Markov model that has provided for the detailed modeling of the heterogeneous amino acid distribu ..."
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This paper describes a new modeling method for the prediction of transmembrane protein topology. The structural regions of the transmembrane protein have been modeled by means of a multiple state hidden Markov model that has provided for the detailed modeling of the heterogeneous amino acid

D: The Use of Functional Domains to Improve Transmembrane Protein Topology Prediction

by Emily W. Xu, Daniel G. Brown, Paul Kearney - J Bioinform Comput Biol , 2006
"... Transmembrane proteins affect vital cellular functions and diseases, and are a focus of drug design. It is difficult to obtain diffraction quality crystals to study transmembrane protein structure. Computational tools for transmembrane protein topology prediction fill in the gap between the abundanc ..."
Abstract - Cited by 5 (1 self) - Add to MetaCart
Transmembrane proteins affect vital cellular functions and diseases, and are a focus of drug design. It is difficult to obtain diffraction quality crystals to study transmembrane protein structure. Computational tools for transmembrane protein topology prediction fill in the gap between

1 THE USE OF FUNCTIONAL DOMAINS TO IMPROVE TRANSMEMBRANE PROTEIN TOPOLOGY PREDICTION

by Emily W. Xu, Ab Tn N, Daniel G. Brown, Paul Kearney
"... Transmembrane proteins affect vital cellular functions and diseases, and are a focus of drug design. It is difficult to obtain diffraction quality crystals to study transmembrane protein structure. Computational tools for transmembrane protein topology prediction fill in the gap between the abundanc ..."
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Transmembrane proteins affect vital cellular functions and diseases, and are a focus of drug design. It is difficult to obtain diffraction quality crystals to study transmembrane protein structure. Computational tools for transmembrane protein topology prediction fill in the gap between

The Use of Internal and External Functional Domains to Improve Transmembrane Protein Topology Prediction

by Emily Wei Xu, Emily Wei Xu
"... I hereby declare that I am the sole author of this thesis. This is a true copy of the thesis, including any required final revisions, as accepted by my examiners. I understand that my thesis may be made electronically available to the public. ii Membrane proteins are involved in vital cellular funct ..."
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functions and have important implications in disease processes, drug design and therapy. However, it is difficult to obtain diffraction quality crystals to study transmembrane protein structure. Transmembrane protein topology prediction tools try to fill in the gap between abundant number of transmembrane

HMM_RA: An Improved Method for Alpha-Helical Transmembrane Protein Topology Prediction

by Jing Hu, Changhui Yan , 2008
"... α-helical transmembrane (TM) proteins play important and diverse functional roles in cells. The ability to predict the topology of these proteins is important for identifying functional sites and inferring function of membrane proteins. This paper presents a Hidden Markov Model (referred to as HMM_ ..."
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α-helical transmembrane (TM) proteins play important and diverse functional roles in cells. The ability to predict the topology of these proteins is important for identifying functional sites and inferring function of membrane proteins. This paper presents a Hidden Markov Model (referred to as HMM

A hidden Markov model for predicting transmembrane helices in protein sequences

by Erik L. L. Sonnhammer - In Proceedings of the 6th International Conference on Intelligent Systems for Molecular Biology (ISMB , 1998
"... A novel method to model and predict the location and orientation of alpha helices in membrane- spanning proteins is presented. It is based on a hidden Markov model (HMM) with an architecture that corresponds closely to the biological system. The model is cyclic with 7 types of states for helix core, ..."
Abstract - Cited by 373 (9 self) - Add to MetaCart
and constraints involved. Models were estimated both by maximum likelihood and a discriminative method, and a method for reassignment of the membrane helix boundaries were developed. In a cross validated test on single sequences, our transmembrane HMM, TMHMM, correctly predicts the entire topology for 77

The SWISS-MODEL Workspace: A web-based environment for protein structure homology modelling

by Konstantin Arnold, Lorenza Bordoli, Torsten Schwede, et al. - BIOINFORMATICS , 2005
"... Motivation: Homology models of proteins are of great interest for planning and analyzing biological experiments when no experimental three-dimensional structures are available. Building homology models requires specialized programs and up-to-date sequence and structural databases. Integrating all re ..."
Abstract - Cited by 575 (5 self) - Add to MetaCart
Motivation: Homology models of proteins are of great interest for planning and analyzing biological experiments when no experimental three-dimensional structures are available. Building homology models requires specialized programs and up-to-date sequence and structural databases. Integrating all
Results 1 - 10 of 8,092