Published in BMC Biochem on June 02, 2006
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A fast and accurate computational approach to protein ionization. Protein Sci (2008) 1.07
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Calculating pKa values in the cAMP-dependent protein kinase: the effect of conformational change and ligand binding. Protein Sci (2010) 0.78
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A self-consistent, microenvironment modulated screened coulomb potential approximation to calculate pH-dependent electrostatic effects in proteins. Biophys J (1999) 1.44
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pH, ionic strength, and temperature dependences of ionization equilibria for the carboxyl groups in turkey ovomucoid third domain. Biochemistry (1995) 1.33
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Individual ionization constants of all the carboxyl groups in ribonuclease HI from Escherichia coli determined by NMR. Biochemistry (1994) 1.19
An empirical model for electrostatic interactions in proteins incorporating multiple geometry-dependent dielectric constants. Proteins (2003) 1.17
The determinants of carboxyl pKa values in turkey ovomucoid third domain. Proteins (2004) 1.17
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pKa calculations for class A beta-lactamases: influence of substrate binding. Protein Sci (1999) 1.09
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Clostridium perfringens epsilon-toxin shows structural similarity to the pore-forming toxin aerolysin. Nat Struct Mol Biol (2004) 1.55
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Predicting Class II MHC-Peptide binding: a kernel based approach using similarity scores. BMC Bioinformatics (2006) 1.41
Identifying candidate subunit vaccines using an alignment-independent method based on principal amino acid properties. Vaccine (2006) 1.37
In silico identified CCR4 antagonists target regulatory T cells and exert adjuvant activity in vaccination. Proc Natl Acad Sci U S A (2008) 1.34
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Additive method for the prediction of protein-peptide binding affinity. Application to the MHC class I molecule HLA-A*0201. J Proteome Res (2003) 1.23
Quantitative prediction of mouse class I MHC peptide binding affinity using support vector machine regression (SVR) models. BMC Bioinformatics (2006) 1.22
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ImmunoGrid: towards agent-based simulations of the human immune system at a natural scale. Philos Trans A Math Phys Eng Sci (2010) 1.16
Computer-aided biotechnology: from immuno-informatics to reverse vaccinology. Trends Biotechnol (2008) 1.13
Towards the chemometric dissection of peptide--HLA-A*0201 binding affinity: comparison of local and global QSAR models. J Comput Aided Mol Des (2005) 1.11
PPD v1.0--an integrated, web-accessible database of experimentally determined protein pKa values. Nucleic Acids Res (2006) 1.10
Mycobacterium tuberculosis peptides presented by HLA-E molecules are targets for human CD8 T-cells with cytotoxic as well as regulatory activity. PLoS Pathog (2010) 1.06
FIMM, a database of functional molecular immunology: update 2002. Nucleic Acids Res (2002) 1.06
Clostridium absonum alpha-toxin: new insights into clostridial phospholipase C substrate binding and specificity. J Mol Biol (2003) 1.05
Transporter associated with antigen processing preselection of peptides binding to the MHC: a bioinformatic evaluation. J Immunol (2004) 1.04
BPROMPT: A consensus server for membrane protein prediction. Nucleic Acids Res (2003) 1.03
Structure of the food-poisoning Clostridium perfringens enterotoxin reveals similarity to the aerolysin-like pore-forming toxins. J Mol Biol (2011) 1.02
On the hierarchical classification of G protein-coupled receptors. Bioinformatics (2007) 1.01
Quantitative online prediction of peptide binding to the major histocompatibility complex. J Mol Graph Model (2004) 1.01
Toward an atomistic understanding of the immune synapse: large-scale molecular dynamics simulation of a membrane-embedded TCR-pMHC-CD4 complex. Mol Immunol (2007) 1.01
LIPPRED: A web server for accurate prediction of lipoprotein signal sequences and cleavage sites. Bioinformation (2006) 1.01
Physicochemical explanation of peptide binding to HLA-A*0201 major histocompatibility complex: a three-dimensional quantitative structure-activity relationship study. Proteins (2002) 1.00
MHC class I bound to an immunodominant Theileria parva epitope demonstrates unconventional presentation to T cell receptors. PLoS Pathog (2010) 0.99
Greater CD8+ TCR heterogeneity and functional flexibility in HIV-2 compared to HIV-1 infection. J Immunol (2003) 0.99
On the hydrophobicity of peptides: Comparing empirical predictions of peptide log P values. Bioinformation (2006) 0.97
Molecular architecture and functional analysis of NetB, a pore-forming toxin from Clostridium perfringens. J Biol Chem (2012) 0.97
HLA-A3 supermotif defined by quantitative structure-activity relationship analysis. Protein Eng (2003) 0.97
Coupling in silico and in vitro analysis of peptide-MHC binding: a bioinformatic approach enabling prediction of superbinding peptides and anchorless epitopes. J Immunol (2004) 0.97
Molecular basis of peptide recognition by the TCR: affinity differences calculated using large scale computing. J Immunol (2005) 0.96
Proteomic applications of automated GPCR classification. Proteomics (2007) 0.95
Evolutionary dynamics of hepatitis C virus envelope genes during chronic infection. J Gen Virol (2005) 0.95
A computational analysis of the antigenic properties of haemagglutinin in influenza A H3N2. Bioinformatics (2010) 0.93
Visualizing helicases unwinding DNA at the single molecule level. Nucleic Acids Res (2010) 0.93
New horizons in mouse immunoinformatics: reliable in silico prediction of mouse class I histocompatibility major complex peptide binding affinity. Org Biomol Chem (2004) 0.92
Toward prediction of class II mouse major histocompatibility complex peptide binding affinity: in silico bioinformatic evaluation using partial least squares, a robust multivariate statistical technique. J Chem Inf Model (2006) 0.91
Peptide binding prediction for the human class II MHC allele HLA-DP2: a molecular docking approach. BMC Struct Biol (2011) 0.91
A comparative molecular similarity index analysis (CoMSIA) study identifies an HLA-A2 binding supermotif. J Comput Aided Mol Des (2003) 0.90
Immunoinformatics. Predicting immunogenicity in silico. Preface. Methods Mol Biol (2007) 0.90
MHCPred 2.0: an updated quantitative T-cell epitope prediction server. Appl Bioinformatics (2006) 0.90
In silico prediction of peptide binding affinity to class I mouse major histocompatibility complexes: a comparative molecular similarity index analysis (CoMSIA) study. J Chem Inf Model (2005) 0.88
Large-scale molecular dynamics simulations of HLA-A*0201 complexed with a tumor-specific antigenic peptide: can the alpha3 and beta2m domains be neglected? J Comput Chem (2004) 0.88
Peptide length significantly influences in vitro affinity for MHC class II molecules. Immunome Res (2008) 0.88
Peptide recognition by the T cell receptor: comparison of binding free energies from thermodynamic integration, Poisson-Boltzmann and linear interaction energy approximations. Philos Trans A Math Phys Eng Sci (2005) 0.87
Toward the discovery of vaccine adjuvants: coupling in silico screening and in vitro analysis of antagonist binding to human and mouse CCR4 receptors. PLoS One (2009) 0.86
Peptide binding to the HLA-DRB1 supertype: a proteochemometrics analysis. Eur J Med Chem (2009) 0.86
Class I T-cell epitope prediction: improvements using a combination of proteasome cleavage, TAP affinity, and MHC binding. Mol Immunol (2006) 0.86
In silico prediction of peptide-MHC binding affinity using SVRMHC. Methods Mol Biol (2007) 0.85
Clostridium perfringens epsilon toxin H149A mutant as a platform for receptor binding studies. Protein Sci (2013) 0.85
Toward bacterial protein sub-cellular location prediction: single-class discrimminant models for all gram- and gram+ compartments. Bioinformation (2006) 0.85
Multi-class subcellular location prediction for bacterial proteins. Bioinformation (2006) 0.84
Analysis of antigenically important residues in human influenza A virus in terms of B-cell epitopes. J Virol (2011) 0.84
Optimizing amino acid groupings for GPCR classification. Bioinformatics (2008) 0.84
Toward the atomistic simulation of T cell epitopes automated construction of MHC: peptide structures for free energy calculations. J Mol Graph Model (2007) 0.84
The first strain of Clostridium perfringens isolated from an avian source has an alpha-toxin with divergent structural and kinetic properties. Biochemistry (2002) 0.84
Crystal structure of the C. perfringens alpha-toxin with the active site closed by a flexible loop region. J Mol Biol (2002) 0.84
Monomeric PcrA helicase processively unwinds plasmid lengths of DNA in the presence of the initiator protein RepD. Nucleic Acids Res (2013) 0.83
Statistical deconvolution of enthalpic energetic contributions to MHC-peptide binding affinity. BMC Struct Biol (2006) 0.83
EpiTOP--a proteochemometric tool for MHC class II binding prediction. Bioinformatics (2010) 0.83
Predicting class I major histocompatibility complex (MHC) binders using multivariate statistics: comparison of discriminant analysis and multiple linear regression. J Chem Inf Model (2007) 0.83
Integrating in silico and in vitro analysis of peptide binding affinity to HLA-Cw*0102: a bioinformatic approach to the prediction of new epitopes. PLoS One (2009) 0.83
A novel predictive technique for the MHC class II peptide-binding interaction. Mol Med (2004) 0.83
Modeling the peptide-T cell receptor interaction by the comparative molecular similarity indices analysis-soft independent modeling of class analogy technique. J Med Chem (2006) 0.83
Immunoinformatic evaluation of multiple epitope ensembles as vaccine candidates: E coli 536. Bioinformation (2012) 0.82
Quantitative approaches to computational vaccinology. Immunol Cell Biol (2002) 0.82
GPCRTree: online hierarchical classification of GPCR function. BMC Res Notes (2008) 0.82
AllerTOP--a server for in silico prediction of allergens. BMC Bioinformatics (2013) 0.82
An update on the functional molecular immunology (FIMM) database. Appl Bioinformatics (2005) 0.81
Identification of the HLA-DM/HLA-DR interface. Mol Immunol (2007) 0.81
TATPred: a Bayesian method for the identification of twin arginine translocation pathway signal sequences. Bioinformation (2006) 0.81
Cloning, expression, and characterization of a novel molecular motor, Leishmania myosin-XXI. J Biol Chem (2012) 0.81
Are bacterial vaccine antigens T-cell epitope depleted? Trends Immunol (2008) 0.81
A computational Grid framework for immunological applications. Philos Trans A Math Phys Eng Sci (2009) 0.81
Quantitative structure-activity relationships and the prediction of MHC supermotifs. Methods (2004) 0.80
A single-molecule approach to visualize the unwinding activity of DNA helicases. Methods Mol Biol (2011) 0.80
Visualisation of variable binding pockets on protein surfaces by probabilistic analysis of related structure sets. BMC Bioinformatics (2012) 0.80
Lipocalins in bioscience: the first family gathering. Bioessays (2004) 0.79
Toward the prediction of class I and II mouse major histocompatibility complex-peptide-binding affinity: in silico bioinformatic step-by-step guide using quantitative structure-activity relationships. Methods Mol Biol (2007) 0.79
From 'perfect mix' to 'potion magique'-- regulatory T cells and anti-inflammatory cytokines as adjuvant targets. Nat Rev Microbiol (2008) 0.79