Published in Nucleic Acids Res on January 01, 2006
Protonate3D: assignment of ionization states and hydrogen coordinates to macromolecular structures. Proteins (2009) 1.81
MCCE2: improving protein pKa calculations with extensive side chain rotamer sampling. J Comput Chem (2009) 1.55
Benchmarking pK(a) prediction. BMC Biochem (2006) 1.47
A fast and accurate computational approach to protein ionization. Protein Sci (2008) 1.07
Analysis of the electrochemistry of hemes with E(m)s spanning 800 mV. Proteins (2009) 0.93
Developing hybrid approaches to predict pKa values of ionizable groups. Proteins (2011) 0.84
IPC - Isoelectric Point Calculator. Biol Direct (2016) 0.83
On the development of protein pKa calculation algorithms. Proteins (2011) 0.83
Capturing, sharing and analysing biophysical data from protein engineering and protein characterization studies. Nucleic Acids Res (2010) 0.81
pKa predictions for proteins, RNAs, and DNAs with the Gaussian dielectric function using DelPhi pKa. Proteins (2015) 0.80
Calculating pKa values in the cAMP-dependent protein kinase: the effect of conformational change and ligand binding. Protein Sci (2010) 0.78
Gut pH as a limiting factor for digestive proteolysis in cultured juveniles of the gilthead sea bream (Sparus aurata). Fish Physiol Biochem (2011) 0.78
Proteome-pI: proteome isoelectric point database. Nucleic Acids Res (2016) 0.75
aKMT Catalyzes Extensive Protein Lysine Methylation in the Hyperthermophilic Archaeon Sulfolobus islandicus but is Dispensable for the Growth of the Organism. Mol Cell Proteomics (2016) 0.75
Highly perturbed pKa values in the unfolded state of hen egg white lysozyme. Biophys J (2012) 0.75
A collaborative environment for developing and validating predictive tools for protein biophysical characteristics. J Comput Aided Mol Des (2012) 0.75
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31
The Protein Data Bank. Nucleic Acids Res (2000) 187.10
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res (2003) 52.80
Classical electrostatics in biology and chemistry. Science (1995) 17.26
Prediction of pH-dependent properties of proteins. J Mol Biol (1994) 4.99
Electrostatic calculations of the pKa values of ionizable groups in bacteriorhodopsin. J Mol Biol (1992) 3.92
The determinants of pKas in proteins. Biochemistry (1996) 3.45
Combining conformational flexibility and continuum electrostatics for calculating pK(a)s in proteins. Biophys J (2002) 3.44
Energetics of enzyme catalysis. Proc Natl Acad Sci U S A (1978) 3.34
Calculations of enzymatic reactions: calculations of pKa, proton transfer reactions, and general acid catalysis reactions in enzymes. Biochemistry (1981) 2.20
Variability in the pKa of histidine side-chains correlates with burial within proteins. Proteins (2002) 1.54
Empirical relationships between protein structure and carboxyl pKa values in proteins. Proteins (2002) 1.42
Electrostatic contributions to protein-protein interactions: fast energetic filters for docking and their physical basis. Protein Sci (2001) 1.29
Improved pKa calculations through flexibility based sampling of a water-dominated interaction scheme. Protein Sci (2004) 1.26
Calculating pKa values in enzyme active sites. Protein Sci (2003) 1.21
On the evaluation and optimization of protein X-ray structures for pKa calculations. Protein Sci (2003) 1.17
Insensitivity of perturbed carboxyl pK(a) values in the ovomucoid third domain to charge replacement at a neighboring residue. Biochemistry (2000) 1.01
NMPdb: Database of Nuclear Matrix Proteins. Nucleic Acids Res (2005) 0.98
Mechanistic roles of Thr134, Tyr160, and Lys 164 in the reaction catalyzed by dTDP-glucose 4,6-dehydratase. Biochemistry (2001) 0.95
Continuum electrostatic analysis of irregular ionization and proton allocation in proteins. Proteins (2002) 0.93
The ionization of a buried glutamic acid is thermodynamically linked to the stability of Leishmania mexicana triose phosphate isomerase. Eur J Biochem (2000) 0.91
siRNAdb: a database of siRNA sequences. Nucleic Acids Res (2005) 0.91
Analysis of the pH-dependent folding and stability of histidine point mutants allows characterization of the denatured state and transition state for protein folding. J Mol Biol (2005) 0.90
The pKa of His-24 in the folding transition state of apomyoglobin. Proc Natl Acad Sci U S A (2001) 0.88
Ionization properties of titratable groups in ribonuclease T1. II. Electrostatic analysis. Eur Biophys J (2001) 0.82
Ionization properties of titratable groups in ribonuclease T1. I. pKa values in the native state determined by two-dimensional heteronuclear NMR spectroscopy. Eur Biophys J (2001) 0.81
The role of Tyr41 and His155 in the functional properties of superoxide dismutase from the archaeon Sulfolobus solfataricus. Biochemistry (2004) 0.78
Determinants of human immunodeficiency virus type 1 escape from the primary CD8+ cytotoxic T lymphocyte response. J Exp Med (2004) 3.48
Allelic skewing of DNA methylation is widespread across the genome. Am J Hum Genet (2010) 3.17
Benchmarking B cell epitope prediction: underperformance of existing methods. Protein Sci (2004) 2.70
VaxiJen: a server for prediction of protective antigens, tumour antigens and subunit vaccines. BMC Bioinformatics (2007) 2.10
JenPep: a database of quantitative functional peptide data for immunology. Bioinformatics (2002) 1.75
Identifiying human MHC supertypes using bioinformatic methods. J Immunol (2004) 1.72
JenPep: a novel computational information resource for immunobiology and vaccinology. J Chem Inf Comput Sci (2003) 1.64
Analysis of peptide-protein binding using amino acid descriptors: prediction and experimental verification for human histocompatibility complex HLA-A0201. J Med Chem (2005) 1.62
SVRMHC prediction server for MHC-binding peptides. BMC Bioinformatics (2006) 1.59
In silico identification of supertypes for class II MHCs. J Immunol (2005) 1.52
MHCPred: A server for quantitative prediction of peptide-MHC binding. Nucleic Acids Res (2003) 1.48
Benchmarking pK(a) prediction. BMC Biochem (2006) 1.47
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
Gene expression changes with age in skin, adipose tissue, blood and brain. Genome Biol (2013) 1.34
EpiJen: a server for multistep T cell epitope prediction. BMC Bioinformatics (2006) 1.26
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
Harnessing bioinformatics to discover new vaccines. Drug Discov Today (2007) 1.22
MHCPred: bringing a quantitative dimension to the online prediction of MHC binding. Appl Bioinformatics (2003) 1.19
Bacterial bioinformatics: pathogenesis and the genome. J Mol Microbiol Biotechnol (2002) 1.18
AntigenDB: an immunoinformatics database of pathogen antigens. Nucleic Acids Res (2009) 1.18
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
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
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
On the hierarchical classification of G protein-coupled receptors. Bioinformatics (2007) 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
Quantitative online prediction of peptide binding to the major histocompatibility complex. J Mol Graph Model (2004) 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
HLA-A3 supermotif defined by quantitative structure-activity relationship analysis. Protein Eng (2003) 0.97
On the hydrophobicity of peptides: Comparing empirical predictions of peptide log P values. Bioinformation (2006) 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
Computer aided selection of candidate vaccine antigens. Immunome Res (2010) 0.95
Evolutionary dynamics of hepatitis C virus envelope genes during chronic infection. J Gen Virol (2005) 0.95
Proteomic applications of automated GPCR classification. Proteomics (2007) 0.95
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
Synthesis, structural and biological studies of ubiquitin mutants containing (2S, 4S)-5-fluoroleucine residues strategically placed in the hydrophobic core. Chembiochem (2003) 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
MHCPred 2.0: an updated quantitative T-cell epitope prediction server. Appl Bioinformatics (2006) 0.90
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
Hypermethylation in the ZBTB20 gene is associated with major depressive disorder. Genome Biol (2014) 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
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
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
Class I T-cell epitope prediction: improvements using a combination of proteasome cleavage, TAP affinity, and MHC binding. Mol Immunol (2006) 0.86
Peptide binding to the HLA-DRB1 supertype: a proteochemometrics analysis. Eur J Med Chem (2009) 0.86
Toward bacterial protein sub-cellular location prediction: single-class discrimminant models for all gram- and gram+ compartments. Bioinformation (2006) 0.85
In silico prediction of peptide-MHC binding affinity using SVRMHC. Methods Mol Biol (2007) 0.85
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
Multi-class subcellular location prediction for bacterial proteins. Bioinformation (2006) 0.84
Optimizing amino acid groupings for GPCR classification. Bioinformatics (2008) 0.84
Computational vaccinology: quantitative approaches. Novartis Found Symp (2003) 0.83
EpiTOP--a proteochemometric tool for MHC class II binding prediction. Bioinformatics (2010) 0.83
Statistical deconvolution of enthalpic energetic contributions to MHC-peptide binding affinity. BMC Struct Biol (2006) 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
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
Quantitative approaches to computational vaccinology. Immunol Cell Biol (2002) 0.82
Immunoinformatic evaluation of multiple epitope ensembles as vaccine candidates: E coli 536. Bioinformation (2012) 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
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
An update on the functional molecular immunology (FIMM) database. Appl Bioinformatics (2005) 0.81
Quantitative structure-activity relationships and the prediction of MHC supermotifs. Methods (2004) 0.80
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
A comparative molecular similarity indices (CoMSIA) study of peptide binding to the HLA-A3 superfamily. Bioorg Med Chem (2003) 0.79
Receptor-ligand binding sites and virtual screening. Curr Med Chem (2006) 0.79
Novel perforin mutation in a patient with hemophagocytic lymphohistiocytosis and CD45 abnormal splicing. Am J Med Genet A (2003) 0.79
Lipocalins in bioscience: the first family gathering. Bioessays (2004) 0.79
From 'perfect mix' to 'potion magique'-- regulatory T cells and anti-inflammatory cytokines as adjuvant targets. Nat Rev Microbiol (2008) 0.79
Combining algorithms to predict bacterial protein sub-cellular location: Parallel versus concurrent implementations. Bioinformation (2006) 0.79
Beta barrel trans-membrane proteins: Enhanced prediction using a Bayesian approach. Bioinformation (2006) 0.78
MHC Class II Binding Prediction-A Little Help from a Friend. J Biomed Biotechnol (2010) 0.78
Using databases and data mining in vaccinology. Expert Opin Drug Discov (2007) 0.78
Empirical prediction of peptide octanol-water partition coefficients. Bioinformation (2006) 0.78
Static energy analysis of MHC class I and class II peptide-binding affinity. Methods Mol Biol (2007) 0.77
Molecular dynamics simulations: bring biomolecular structures alive on a computer. Methods Mol Biol (2007) 0.76
HLA-DP2 binding prediction by molecular dynamics simulations. Protein Sci (2011) 0.76
EpiDOCK: a molecular docking-based tool for MHC class II binding prediction. Protein Eng Des Sel (2013) 0.76
Histidine hydrogen bonding in MHC at pH 5 and pH 7 modeled by molecular docking and molecular dynamics simulations. Curr Comput Aided Drug Des (2014) 0.76
AllerTOP v.2--a server for in silico prediction of allergens. J Mol Model (2014) 0.76
In silico identification of novel G protein coupled receptors. Methods Mol Biol (2009) 0.76
Present perspectives on the automated classification of the G-protein coupled receptors (GPCRs) at the protein sequence level. Curr Top Med Chem (2011) 0.76
DSD--an integrated, web-accessible database of Dehydrogenase Enzyme Stereospecificities. BMC Bioinformatics (2005) 0.75