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Results 1 - 10
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13,958
Improved prediction of signal peptides -- SignalP 3.0
- J. MOL. BIOL.
, 2004
"... We describe improvements of the currently most popular method for prediction of classically secreted proteins, SignalP. SignalP consists of two different predictors based on neural network and hidden Markov model algorithms, where both components have been updated. Motivated by the idea that the cle ..."
Abstract
-
Cited by 654 (7 self)
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We describe improvements of the currently most popular method for prediction of classically secreted proteins, SignalP. SignalP consists of two different predictors based on neural network and hidden Markov model algorithms, where both components have been updated. Motivated by the idea
Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. sect
- A
, 1991
"... Map interpretation remains a critical step in solving the structure of a macromolecule. Errors introduced at this early stage may persist throughout crystallo-graphic refinement and result in an incorrect struc-ture. The normally quoted crystallographic residual is often a poor description for the q ..."
Abstract
-
Cited by 1051 (9 self)
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for the quality of the model. Strategies and tools are described that help to alleviate this problem. These simplify the model-building process, quantify the goodness of fit of the model on a per-residue basis and locate possible errors in pep-tide and side-chain conformations.
A combined transmembrane topology and signal peptide prediction method
- J. Mol. Biol
, 2004
"... Hidden Markov models (HMMs) have been successfully applied to the tasks of transmembrane protein topology prediction and signal peptide prediction. In this paper we expand upon this work by making use of the more powerful class of dynamic Bayesian networks (DBNs). Our model, Philius, is inspired by ..."
Abstract
-
Cited by 233 (10 self)
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Hidden Markov models (HMMs) have been successfully applied to the tasks of transmembrane protein topology prediction and signal peptide prediction. In this paper we expand upon this work by making use of the more powerful class of dynamic Bayesian networks (DBNs). Our model, Philius, is inspired
A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase QM calculations
- J. Comput. Chem
, 2003
"... Abstract: Molecular mechanics models have been applied extensively to study the dynamics of proteins and nucleic acids. Here we report the development of a third-generation point-charge all-atom force field for proteins. Following the earlier approach of Cornell et al., the charge set was obtained b ..."
Abstract
-
Cited by 229 (6 self)
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Abstract: Molecular mechanics models have been applied extensively to study the dynamics of proteins and nucleic acids. Here we report the development of a third-generation point-charge all-atom force field for proteins. Following the earlier approach of Cornell et al., the charge set was obtained
Antigen
, 2011
"... to trim a vast variety of antigenic peptide precursors to generate mature epitopes for binding to major histocompatibility class I molecules. We report here the first structure of ERAP2 determined at 3.08 Å by X-ray crystallography. On the basis of residual electron density, a lysine residue has bee ..."
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to trim a vast variety of antigenic peptide precursors to generate mature epitopes for binding to major histocompatibility class I molecules. We report here the first structure of ERAP2 determined at 3.08 Å by X-ray crystallography. On the basis of residual electron density, a lysine residue has
Prediction of signal peptides and signal anchors by a hidden Markov model
- Proc. Int. Conf. Intell. Syst. Mol. Biol
, 1998
"... A hidden Markov model of signal peptides has been developed. It contains submodels for the N-terminal part, the hydrophobic region, and the region around the cleavage site. For known signal peptides, the model can be used to assign objective boundaries between these three regions. Applied to our dat ..."
Abstract
-
Cited by 157 (10 self)
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A hidden Markov model of signal peptides has been developed. It contains submodels for the N-terminal part, the hydrophobic region, and the region around the cleavage site. For known signal peptides, the model can be used to assign objective boundaries between these three regions. Applied to our
Characterization of monoclonal antibody directed against mouse macrophage and lymphocyte Fc receptors.J. Exp. Med
, 1979
"... Fc receptors 1 (FcR) recognize the Fc domain of IgG and are found on macrophages, lymphocytes, and polymorphonuclear leukocytes (for reviews see Kerbel and Davies [1] and Dickler[2]). These receptors enable the effector cells to recognize foreign antigens to which antibodies are bound and may also p ..."
Abstract
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Cited by 183 (7 self)
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Fc receptors 1 (FcR) recognize the Fc domain of IgG and are found on macrophages, lymphocytes, and polymorphonuclear leukocytes (for reviews see Kerbel and Davies [1] and Dickler[2]). These receptors enable the effector cells to recognize foreign antigens to which antibodies are bound and may also
Antigen presentation by chemically modified splenocytes induces antigen-specific T cell unresponsiveness
- in vitro and in vivo .J Exp Med. 165 :302
, 1987
"... Despite a large body of evidence concerning the phenomenon of immune tolerance at the T cell level, the actual mechanism of unresponsiveness is not understood. Experimentally, T cell unresponsiveness can be induced in adults by the intravenous injection of high doses of soluble antigen (1) or of ant ..."
Abstract
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Cited by 114 (2 self)
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) or of antigen coupled to syngeneic splenocytes (reviewed in references 2-6). Two major hypotheses have been proposed (3-6) to explain unresponsiveness: regulation by suppressor T cells or direct inactivation of responding T cells by antigen. The suppression model of unresponsiveness states that a complex
Conversion of Peripheral CD4 � CD25 � Naive T Cells to CD4 � CD25 � Regulatory T Cells by TGF- � Induction of Transcription Factor Foxp3
"... CD4�CD25 � regulatory T cells (Treg) are instrumental in the maintenance of immunological tolerance. One critical question is whether Treg can only be generated in the thymus or can differentiate from peripheral CD4�CD25 � naive T cells. In this paper, we present novel evidence that conversion of na ..."
Abstract
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Cited by 149 (0 self)
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. These converted anergic/suppressor cells are not only unresponsive to TCR stimulation and produce neither T helper cell 1 nor T helper cell 2 cytokines but they also express TGF- � and inhibit normal T cell proliferation in vitro. More importantly, in an ovalbumin peptide TCR transgenic adoptive transfer model
Oxidative stress can alter the antigenicity of immunodominant peptides
- J Leukoc Biol
, 2010
"... peptides ..."
Results 1 - 10
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13,958
