Published in Proteins on December 01, 2004
Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently. Chem Soc Rev (2015) 1.74
Structure-based predictive models for allosteric hot spots. PLoS Comput Biol (2009) 0.98
Bioinformatic method for protein thermal stabilization by structural entropy optimization. Proc Natl Acad Sci U S A (2008) 0.95
PROTS: a fragment based protein thermo-stability potential. Proteins (2011) 0.86
Structure and biochemical characterization of an adenylate kinase originating from the psychrophilic organism Marinibacillus marinus. Acta Crystallogr Sect F Struct Biol Cryst Commun (2009) 0.86
Protein thermostability prediction within homologous families using temperature-dependent statistical potentials. PLoS One (2014) 0.84
Interconversion of functional motions between mesophilic and thermophilic adenylate kinases. PLoS Comput Biol (2011) 0.83
Protein thermal stability enhancement by designing salt bridges: a combined computational and experimental study. PLoS One (2014) 0.83
Boosting prediction performance of protein-protein interaction hot spots by using structural neighborhood properties. J Comput Biol (2013) 0.82
Insight into the structure, dynamics and the unfolding property of amylosucrases: implications of rational engineering on thermostability. PLoS One (2012) 0.81
PROTS-RF: a robust model for predicting mutation-induced protein stability changes. PLoS One (2012) 0.81
PredHS: a web server for predicting protein-protein interaction hot spots by using structural neighborhood properties. Nucleic Acids Res (2014) 0.80
Stability curve prediction of homologous proteins using temperature-dependent statistical potentials. PLoS Comput Biol (2014) 0.78
Optimal design of thermally stable proteins. Bioinformatics (2008) 0.76
PredPhos: an ensemble framework for structure-based prediction of phosphorylation sites. J Biol Res (Thessalon) (2016) 0.76
Distance-dependent statistical potentials for discriminating thermophilic and mesophilic proteins. Biochem Biophys Res Commun (2010) 0.76
Is it possible to stabilize a thermophilic protein further using sequences and structures of mesophilic proteins: a theoretical case study concerning DgAS. Theor Biol Med Model (2013) 0.75
Determinants of Thermostability in Serine Hydroxymethyltransferase Identified by Principal Component Analysis. Sci Rep (2017) 0.75
Accurate prediction of functional effects for variants by combining gradient tree boosting with optimal neighborhood properties. PLoS One (2017) 0.75
Detection and characterisation of mutations responsible for allele-specific protein thermostabilities at the Mn-superoxide dismutase gene in the deep-sea hydrothermal vent polychaete Alvinella pompejana. J Mol Evol (2013) 0.75
Prediction of protein subcellular localization. Proteins (2006) 4.46
Three-dimensional reconstruction of brain-wide wiring networks in Drosophila at single-cell resolution. Curr Biol (2010) 4.04
Predicting subcellular localization of proteins for Gram-negative bacteria by support vector machines based on n-peptide compositions. Protein Sci (2004) 3.02
KinasePhos 2.0: a web server for identifying protein kinase-specific phosphorylation sites based on sequences and coupling patterns. Nucleic Acids Res (2007) 2.69
Hubba: hub objects analyzer--a framework of interactome hubs identification for network biology. Nucleic Acids Res (2008) 1.65
(PS)2: protein structure prediction server. Nucleic Acids Res (2006) 1.59
DSAP: deep-sequencing small RNA analysis pipeline. Nucleic Acids Res (2010) 1.41
Predicting RNA-binding sites of proteins using support vector machines and evolutionary information. BMC Bioinformatics (2008) 1.39
Trypsin-induced proteome alteration during cell subculture in mammalian cells. J Biomed Sci (2010) 1.29
Antiviral treatment for hepatitis C virus infection is associated with improved renal and cardiovascular outcomes in diabetic patients. Hepatology (2014) 1.27
Protein subcellular localization prediction based on compartment-specific features and structure conservation. BMC Bioinformatics (2007) 1.25
Proportion of solvent-exposed amino acids in a protein and rate of protein evolution. Mol Biol Evol (2007) 1.23
Deriving protein dynamical properties from weighted protein contact number. Proteins (2008) 1.23
Cloning, purification, crystallization and preliminary X-ray crystallographic analysis of XC847, a 3'-5' oligoribonuclease from Xanthomonas campestris. Acta Crystallogr Sect F Struct Biol Cryst Commun (2005) 1.19
Prediction of the bonding states of cysteines using the support vector machines based on multiple feature vectors and cysteine state sequences. Proteins (2004) 1.19
(PS)2-v2: template-based protein structure prediction server. BMC Bioinformatics (2009) 1.15
PGTdb: a database providing growth temperatures of prokaryotes. Bioinformatics (2004) 1.12
Solution structure of plant nonspecific lipid transfer protein-2 from rice (Oryza sativa). J Biol Chem (2002) 1.12
Predicting helix-helix interactions from residue contacts in membrane proteins. Bioinformatics (2009) 1.11
pKNOT: the protein KNOT web server. Nucleic Acids Res (2007) 1.08
Relationship between protein structures and disulfide-bonding patterns. Proteins (2003) 1.07
Identification of MYO18A as a novel interacting partner of the PAK2/betaPIX/GIT1 complex and its potential function in modulating epithelial cell migration. Mol Biol Cell (2009) 1.07
Site-specific structural constraints on protein sequence evolutionary divergence: local packing density versus solvent exposure. Mol Biol Evol (2013) 1.07
A mechanistic stress model of protein evolution accounts for site-specific evolutionary rates and their relationship with packing density and flexibility. BMC Evol Biol (2014) 1.07
CPDB: a database of circular permutation in proteins. Nucleic Acids Res (2008) 1.05
Aloe-emodin is an interferon-inducing agent with antiviral activity against Japanese encephalitis virus and enterovirus 71. Int J Antimicrob Agents (2008) 1.05
Protein structural similarity search by Ramachandran codes. BMC Bioinformatics (2007) 1.04
CPSARST: an efficient circular permutation search tool applied to the detection of novel protein structural relationships. Genome Biol (2008) 1.03
Computational analysis of KRAS mutations: implications for different effects on the KRAS p.G12D and p.G13D mutations. PLoS One (2013) 1.00
Construction and analysis of a plant non-specific lipid transfer protein database (nsLTPDB). BMC Genomics (2012) 1.00
Evolutionary information hidden in a single protein structure. Proteins (2012) 0.99
Proteomics study of oxidative stress and Src kinase inhibition in H9C2 cardiomyocytes: a cell model of heart ischemia-reperfusion injury and treatment. Free Radic Biol Med (2010) 0.99
Binding mechanism of nonspecific lipid transfer proteins and their role in plant defense. Biochemistry (2004) 0.99
A hub-attachment based method to detect functional modules from confidence-scored protein interactions and expression profiles. BMC Bioinformatics (2010) 0.98
Functional proteomic and structural insights into molecular targets related to the growth inhibitory effect of tanshinone IIA on HeLa cells. Proteomics (2010) 0.96
GI-POP: a combinational annotation and genomic island prediction pipeline for ongoing microbial genome projects. Gene (2013) 0.96
Fine-grained protein fold assignment by support vector machines using generalized npeptide coding schemes and jury voting from multiple-parameter sets. Proteins (2003) 0.95
Prediction of disulfide connectivity from protein sequences. Proteins (2005) 0.94
Mitochondrial proteomics analysis of tumorigenic and metastatic breast cancer markers. Funct Integr Genomics (2011) 0.94
Structure-based protein engineering for alpha-amylase inhibitory activity of plant defensin. Proteins (2007) 0.92
Enhanced membrane protein topology prediction using a hierarchical classification method and a new scoring function. J Proteome Res (2008) 0.92
Amino acid coupling patterns in thermophilic proteins. Proteins (2005) 0.92
Human pancreatitis-associated protein forms fibrillar aggregates with a native-like conformation. J Biol Chem (2006) 0.91
Solution structure of the plant defensin VrD1 from mung bean and its possible role in insecticidal activity against bruchids. Proteins (2006) 0.90
Structure-stability-activity relationship in covalently cross-linked N-carbamoyl D-amino acid amidohydrolase and N-acylamino acid racemase. J Mol Biol (2006) 0.90
Identification of putative miRNAs from the deep-branching unicellular flagellates. Genomics (2011) 0.90
Lipid binding in rice nonspecific lipid transfer protein-1 complexes from Oryza sativa. Protein Sci (2004) 0.90
On the relationship between the protein structure and protein dynamics. Proteins (2008) 0.90
A comparison of different electrostatic potentials on prediction accuracy in CoMFA and CoMSIA studies. Eur J Med Chem (2010) 0.89
pKNOT v.2: the protein KNOT web server. Nucleic Acids Res (2012) 0.89
Proteomic analysis of gemcitabine-induced drug resistance in pancreatic cancer cells. Mol Biosyst (2011) 0.89
iSARST: an integrated SARST web server for rapid protein structural similarity searches. Nucleic Acids Res (2009) 0.89
The effect of different electrostatic potentials on docking accuracy: a case study using DOCK5.4. Bioorg Med Chem Lett (2008) 0.89
Codon-usage bias versus gene conversion in the evolution of yeast duplicate genes. Proc Natl Acad Sci U S A (2006) 0.88
cytoHubba: identifying hub objects and sub-networks from complex interactome. BMC Syst Biol (2014) 0.88
Crystal structure of the dopamine N-acetyltransferase-acetyl-CoA complex provides insights into the catalytic mechanism. Biochem J (2012) 0.87
GEM: a Gaussian Evolutionary Method for predicting protein side-chain conformations. Protein Sci (2002) 0.87
Crystal structure of Helicobacter pylori formamidase AmiF reveals a cysteine-glutamate-lysine catalytic triad. J Biol Chem (2007) 0.86
NMR structure note--solution structure of a bacterial BolA-like protein XC975 from a plant pathogen Xanthomonas campestris pv. campestris. J Biomol NMR (2005) 0.86
Prazosin displays anticancer activity against human prostate cancers: targeting DNA and cell cycle. Neoplasia (2007) 0.86
Predicting disulfide connectivity patterns. Proteins (2007) 0.86
Human RegIV protein adopts a typical C-type lectin fold but binds mannan with two calcium-independent sites. J Mol Biol (2010) 0.86
Characterization and structural analyses of nonspecific lipid transfer protein 1 from mung bean. Biochemistry (2005) 0.85
Deciphering the preference and predicting the viability of circular permutations in proteins. PLoS One (2012) 0.85
Biosynthesis of fluorescent allophycocyanin alpha-subunits by autocatalytic bilin attachment. Biochemistry (2006) 0.85
Mutagenesis study of rice nonspecific lipid transfer protein 2 reveals residues that contribute to structure and ligand binding. Proteins (2008) 0.84
Proteomic and redox-proteomic analysis of berberine-induced cytotoxicity in breast cancer cells. J Proteomics (2012) 0.84
Solution structure of family 21 carbohydrate-binding module from Rhizopus oryzae glucoamylase. Biochem J (2007) 0.84
Anti-atherogenic effect of berberine on LXRalpha-ABCA1-dependent cholesterol efflux in macrophages. J Cell Biochem (2010) 0.84
Protein complexity, gene duplicability and gene dispensability in the yeast genome. Gene (2006) 0.84
Preparation, crystallization and preliminary X-ray analysis of XC2382, an ApaG protein of unknown structure from Xanthomonas campestris. Acta Crystallogr Sect F Struct Biol Cryst Commun (2005) 0.83
Design and synthesis of alpha-ketoamides as cathepsin S inhibitors with potential applications against tumor invasion and angiogenesis. J Med Chem (2010) 0.83
Structural basis for the improved potency of peroxisome proliferator-activated receptor (PPAR) agonists. ChemMedChem (2010) 0.83
On the relationship between catalytic residues and their protein contact number. Curr Protein Pept Sci (2011) 0.83
Protein kinase inhibitor design by targeting the Asp-Phe-Gly (DFG) motif: the role of the DFG motif in the design of epidermal growth factor receptor inhibitors. J Med Chem (2013) 0.83
Computational analysis of a novel mutation in ETFDH gene highlights its long-range effects on the FAD-binding motif. BMC Struct Biol (2011) 0.82
On the relationship between the sequence conservation and the packing density profiles of the protein complexes. Proteins (2013) 0.82
Purification and characterization of a novel 7-kDa non-specific lipid transfer protein-2 from rice (Oryza sativa). Biochem Biophys Res Commun (2002) 0.82
A simple way to compute protein dynamics without a mechanical model. Proteins (2007) 0.82
WRC-213, an l-methionine-conjugated mitoxantrone derivative, displays anticancer activity with reduced cardiotoxicity and drug resistance: identification of topoisomerase II inhibition and apoptotic machinery in prostate cancers. Biochem Pharmacol (2007) 0.81
Crystal structure of HP0242, a hypothetical protein from Helicobacter pylori with a novel fold. Proteins (2006) 0.81
Comparative analysis of the folding dynamics and kinetics of an engineered knotted protein and its variants derived from HP0242 of Helicobacter pylori. J Phys Condens Matter (2015) 0.81
Detection and alignment of 3D domain swapping proteins using angle-distance image-based secondary structural matching techniques. PLoS One (2010) 0.81
Plasma proteomic analysis of the critical limb ischemia markers in diabetic patients with hemodialysis. Mol Biosyst (2011) 0.81
Reconstructing phylogeny from metabolic substrate-product relationships. BMC Bioinformatics (2011) 0.81
Nuclear localization of orphan receptor protein kinase (Ror1) is mediated through the juxtamembrane domain. BMC Cell Biol (2010) 0.81
Cytoskeleton network and cellular migration modulated by nuclear-localized receptor tyrosine kinase ROR1. Anticancer Res (2011) 0.81
Proteomic analysis of proteins responsible for the development of doxorubicin resistance in human uterine cancer cells. J Proteomics (2012) 0.80
Proteomic analysis of a drosophila IBMPFD model reveals potential pathogenic mechanisms. Mol Biosyst (2012) 0.80
Generation of ligand-based pharmacophore model and virtual screening for identification of novel tubulin inhibitors with potent anticancer activity. J Med Chem (2009) 0.80
Anti-phosphopeptide antibody, P-STM as a novel tool for detecting mitotic phosphoproteins: identification of lamins A and C as two major targets. J Cell Biochem (2005) 0.80
Indol-1-yl acetic acids as peroxisome proliferator-activated receptor agonists: design, synthesis, structural biology, and molecular docking studies. J Med Chem (2006) 0.80