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Results 1 - 10
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24,726
Folding of a Small Helical Protein Using Hydrogen Bonds and Hydrophobicity Forces
, 2002
"... : A reduced protein model with ve to six atoms per amino acid and ve amino acid types is developed and tested on a three-helix-bundle protein, a 46-amino acid fragment from staphylococcal protein A. The model does not rely on the widely used Go approximation where non-native interactions are ignore ..."
Abstract
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Cited by 10 (7 self)
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: A reduced protein model with ve to six atoms per amino acid and ve amino acid types is developed and tested on a three-helix-bundle protein, a 46-amino acid fragment from staphylococcal protein A. The model does not rely on the widely used Go approximation where non-native interactions
Folding of a Small Helical Protein Using Hydrogen Bonds and
, 2001
"... A reduced protein model with five to six atoms per amino acid and five amino acid types is developed and tested on a three-helix-bundle protein, a 46-amino acid fragment from staphylococcal protein A. The model does not rely on the widely used Gō approximation where non-native interactions are ignor ..."
Abstract
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A reduced protein model with five to six atoms per amino acid and five amino acid types is developed and tested on a three-helix-bundle protein, a 46-amino acid fragment from staphylococcal protein A. The model does not rely on the widely used Gō approximation where non-native interactions
Distance Geometry Generates Native-Like Folds for Small Helical Proteins Using the Consensus Distances of Predicted Protein Structures
, 1998
"... For successful ab initio protein structure prediction, a method is needed to identify native-like structures from a set containing both native and non-native protein-like conformations. In this regard, the use of distance geometry has shown promise when accurate inter-residue distances are available ..."
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Cited by 14 (8 self)
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are available. We describe a method by which distance geometry restraints are culled from sets of 500 protein-like conformations for four small helical proteins generated by the method of Simons et al. (1997). A consensus-based approach was applied in which every inter-Calpha distance was measured, and the most
Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features
, 1983
"... For a successful analysis of the relation between amino acid sequence and protein structure, an unambiguous and physically meaningful definition of secondary structure is essential. We have developed a set of simple and physically motivated criteria for secondary structure, programmed as a pattern-r ..."
Abstract
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Cited by 2096 (5 self)
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For a successful analysis of the relation between amino acid sequence and protein structure, an unambiguous and physically meaningful definition of secondary structure is essential. We have developed a set of simple and physically motivated criteria for secondary structure, programmed as a pattern
Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions
- J. MOL. BIOL
, 1997
"... We explore the ability of a simple simulated annealing procedure to assemble native-like structures from fragments of unrelated protein structures with similar local sequences using Bayesian scoring functions. Environment and residue pair specific contributions to the scoring functions appear as the ..."
Abstract
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Cited by 393 (70 self)
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annealing procedure rapidly and frequently generates native-like structures for small helical proteins and better than random structures for small b sheet containing proteins. Most of the simulated structures have native-like solvent accessibility and secondary structure patterns, and thus ensembles
Modeling and simulation of genetic regulatory systems: A literature review
- JOURNAL OF COMPUTATIONAL BIOLOGY
, 2002
"... In order to understand the functioning of organisms on the molecular level, we need to know which genes are expressed, when and where in the organism, and to which extent. The regulation of gene expression is achieved through genetic regulatory systems structured by networks of interactions between ..."
Abstract
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Cited by 738 (14 self)
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DNA, RNA, proteins, and small molecules. As most genetic regulatory networks of interest involve many components connected through interlocking positive and negative feedback loops, an intuitive understanding of their dynamics is hard to obtain. As a consequence, formal methods and computer tools
Rho GTPases and the actin cytoskeleton
- Science
, 1998
"... The actin cytoskeleton mediates a variety of essential biological functions in all eukaryotic cells. In addition to providing a structural framework around which cell shape and polarity are defined, its dynamic properties provide the driving force for cells to move and to divide. Understanding the b ..."
Abstract
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Cited by 615 (4 self)
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their interaction with multiple target proteins, they ensure coordinated control of other cellular activities such as gene transcription and adhesion. The story begins back in the early 1990s with the analysis of Rho, then a newly described member of the Ras superfamily of small guanosine triphosphatases (GTPases
A hidden Markov model for predicting transmembrane helices in protein sequences
- 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
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Cited by 373 (9 self)
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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
Asymmetry in the assembly of the RNAi enzyme complex. Cell 115
, 2003
"... A key step in RNA interference (RNAi) is assembly of the RISC, the protein-siRNA complex that mediates target RNA cleavage. Here, we show that the two strands of an siRNA duplex are not equally eligible for assembly into RISC. Rather, both the absolute and relative stabilities of the base pairs at t ..."
Abstract
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Cited by 405 (6 self)
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A key step in RNA interference (RNAi) is assembly of the RISC, the protein-siRNA complex that mediates target RNA cleavage. Here, we show that the two strands of an siRNA duplex are not equally eligible for assembly into RISC. Rather, both the absolute and relative stabilities of the base pairs
Crystal structure of rhodopsin: a G protein-coupled receptor
- LeTrong I, Teller DC, Okada T, Stenkamp RE et
, 2000
"... Heterotrimeric guanine nucleotideÐbinding protein (G protein)Ðcoupled recep-tors (GPCRs) respond to a variety of different external stimuli and activate G proteins. GPCRs share many structural features, including a bundle of seven transmembrane a helices connected by six loops of varying lengths. We ..."
Abstract
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Cited by 376 (4 self)
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Heterotrimeric guanine nucleotideÐbinding protein (G protein)Ðcoupled recep-tors (GPCRs) respond to a variety of different external stimuli and activate G proteins. GPCRs share many structural features, including a bundle of seven transmembrane a helices connected by six loops of varying lengths
Results 1 - 10
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24,726
