Published in Protein Sci on December 01, 2009
A structure-based benchmark for protein-protein binding affinity. Protein Sci (2011) 1.81
On the binding affinity of macromolecular interactions: daring to ask why proteins interact. J R Soc Interface (2012) 1.16
Prediction of protein-protein binding free energies. Protein Sci (2012) 1.01
Potentials of mean force for protein structure prediction vindicated, formalized and generalized. PLoS One (2010) 0.93
DECK: Distance and environment-dependent, coarse-grained, knowledge-based potentials for protein-protein docking. BMC Bioinformatics (2011) 0.93
Kinetic rate constant prediction supports the conformational selection mechanism of protein binding. PLoS Comput Biol (2012) 0.89
Contacts-based prediction of binding affinity in protein-protein complexes. Elife (2015) 0.87
A functional feature analysis on diverse protein-protein interactions: application for the prediction of binding affinity. J Comput Aided Mol Des (2014) 0.84
Optimizing scoring function of protein-nucleic acid interactions with both affinity and specificity. PLoS One (2013) 0.81
How structure defines affinity in protein-protein interactions. PLoS One (2014) 0.77
Incorporating specificity into optimization: evaluation of SPA using CSAR 2014 and CASF 2013 benchmarks. J Comput Aided Mol Des (2016) 0.76
ROTAS: a rotamer-dependent, atomic statistical potential for assessment and prediction of protein structures. BMC Bioinformatics (2014) 0.75
Characterizing informative sequence descriptors and predicting binding affinities of heterodimeric protein complexes. BMC Bioinformatics (2015) 0.75
The Protein Data Bank. Nucleic Acids Res (2000) 187.10
Statistical potential for assessment and prediction of protein structures. Protein Sci (2006) 8.98
Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Protein Sci (2002) 7.40
Calculation of protein-ligand binding affinities. Annu Rev Biophys Biomol Struct (2007) 6.12
Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins. J Mol Biol (1990) 6.08
Knowledge-based potentials for proteins. Curr Opin Struct Biol (1995) 3.94
Determination of atomic desolvation energies from the structures of crystallized proteins. J Mol Biol (1997) 3.49
Boltzmann's principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structures. J Comput Aided Mol Des (1993) 3.06
Calculation of the free energy of association for protein complexes. Protein Sci (1992) 3.03
A general and fast scoring function for protein-ligand interactions: a simplified potential approach. J Med Chem (1999) 2.98
Effective energy functions for protein structure prediction. Curr Opin Struct Biol (2000) 2.92
Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors. Angew Chem Int Ed Engl (2002) 2.75
Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation. J Mol Biol (1997) 2.20
Structure-derived potentials and protein simulations. Curr Opin Struct Biol (1996) 2.11
Novel knowledge-based mean force potential at atomic level. J Mol Biol (1997) 1.98
A knowledge-based energy function for protein-ligand, protein-protein, and protein-DNA complexes. J Med Chem (2005) 1.76
Computational methods to predict binding free energy in ligand-receptor complexes. J Med Chem (1995) 1.72
Empirical potentials and functions for protein folding and binding. Curr Opin Struct Biol (1997) 1.66
Comparison of database potentials and molecular mechanics force fields. Curr Opin Struct Biol (1997) 1.53
Potential energy functions for threading. Curr Opin Struct Biol (1996) 1.39
In quest of an empirical potential for protein structure prediction. Curr Opin Struct Biol (2006) 1.38
Development of novel statistical potentials for protein fold recognition. Curr Opin Struct Biol (2004) 1.33
Potential of mean force for protein-protein interaction studies. Proteins (2002) 1.24
A preference-based free-energy parameterization of enzyme-inhibitor binding. Applications to HIV-1-protease inhibitor design. Protein Sci (1995) 1.21
Stability scale and atomic solvation parameters extracted from 1023 mutation experiments. Proteins (2002) 1.08
Statistical potentials and scoring functions applied to protein-ligand binding. Curr Opin Struct Biol (2001) 1.03
Prediction of protein thermostability with a direction- and distance-dependent knowledge-based potential. Protein Sci (2005) 0.90
A mesenchymal-to-epithelial transition initiates and is required for the nuclear reprogramming of mouse fibroblasts. Cell Stem Cell (2010) 7.94
Vitamin C enhances the generation of mouse and human induced pluripotent stem cells. Cell Stem Cell (2009) 5.49
Draft genome of the filarial nematode parasite Brugia malayi. Science (2007) 5.28
Incorporation of aminoacyl-tRNA into the ribosome as seen by cryo-electron microscopy. Nat Struct Biol (2003) 3.77
Dot1a-AF9 complex mediates histone H3 Lys-79 hypermethylation and repression of ENaCalpha in an aldosterone-sensitive manner. J Biol Chem (2006) 2.59
Presenilin couples the paired phosphorylation of beta-catenin independent of axin: implications for beta-catenin activation in tumorigenesis. Cell (2002) 2.37
The fragile X protein controls microtubule-associated protein 1B translation and microtubule stability in brain neuron development. Proc Natl Acad Sci U S A (2004) 2.34
Presenilin-1 mutations of leucine 166 equally affect the generation of the Notch and APP intracellular domains independent of their effect on Abeta 42 production. Proc Natl Acad Sci U S A (2002) 2.29
Generation of induced pluripotent stem cell lines from Tibetan miniature pig. J Biol Chem (2009) 2.17
Risk factors for ERCP-related complications: a prospective multicenter study. Am J Gastroenterol (2009) 2.12
Glucocorticoids promote hepatic cholestasis in mice by inhibiting the transcriptional activity of the farnesoid X receptor. Gastroenterology (2012) 2.05
RelB, a new partner of aryl hydrocarbon receptor-mediated transcription. Mol Endocrinol (2007) 1.95
Age-accelerated atherosclerosis correlates with failure to upregulate antioxidant genes. Circ Res (2009) 1.88
MicroRNA-21 regulates vascular smooth muscle cell function via targeting tropomyosin 1 in arteriosclerosis obliterans of lower extremities. Arterioscler Thromb Vasc Biol (2011) 1.80
TAp63 is a master transcriptional regulator of lipid and glucose metabolism. Cell Metab (2012) 1.77
Impaired glial glutamate transport in a mouse tuberous sclerosis epilepsy model. Ann Neurol (2003) 1.72
Involvement of PI3K/PTEN/AKT/mTOR pathway in invasion and metastasis in hepatocellular carcinoma: Association with MMP-9. Hepatol Res (2009) 1.70
Aldosterone-induced Sgk1 relieves Dot1a-Af9-mediated transcriptional repression of epithelial Na+ channel alpha. J Clin Invest (2007) 1.69
Yin Yang 1 promotes hepatic steatosis through repression of farnesoid X receptor in obese mice. Gut (2013) 1.59
Mechanism for the disassembly of the posttermination complex inferred from cryo-EM studies. Mol Cell (2005) 1.58
A highly homozygous and parthenogenetic human embryonic stem cell line derived from a one-pronuclear oocyte following in vitro fertilization procedure. Cell Res (2007) 1.58
Aldosterone-sensitive repression of ENaCalpha transcription by a histone H3 lysine-79 methyltransferase. Am J Physiol Cell Physiol (2005) 1.56
Accelerated plaque accumulation, associative learning deficits, and up-regulation of alpha 7 nicotinic receptor protein in transgenic mice co-expressing mutant human presenilin 1 and amyloid precursor proteins. J Biol Chem (2002) 1.54
An approach to identify over-represented cis-elements in related sequences. Nucleic Acids Res (2003) 1.53
Oncofetal long noncoding RNA PVT1 promotes proliferation and stem cell-like property of hepatocellular carcinoma cells by stabilizing NOP2. Hepatology (2014) 1.53
The role of tRNA as a molecular spring in decoding, accommodation, and peptidyl transfer. FEBS Lett (2005) 1.52
ULK1 translocates to mitochondria and phosphorylates FUNDC1 to regulate mitophagy. EMBO Rep (2014) 1.49
Sequential introduction of reprogramming factors reveals a time-sensitive requirement for individual factors and a sequential EMT-MET mechanism for optimal reprogramming. Nat Cell Biol (2013) 1.47
Loss of tuberous sclerosis complex 1 (Tsc1) expression results in increased Rheb/S6K pathway signaling important for astrocyte cell size regulation. Glia (2004) 1.47
Over-expression of AEG-1 significantly associates with tumour aggressiveness and poor prognosis in human non-small cell lung cancer. J Pathol (2009) 1.43
DBSubLoc: database of protein subcellular localization. Nucleic Acids Res (2004) 1.43
Bead-based microarray analysis of microRNA expression in hepatocellular carcinoma: miR-338 is downregulated. Hepatol Res (2009) 1.42
Generation of human induced pluripotent stem cells from umbilical cord matrix and amniotic membrane mesenchymal cells. J Biol Chem (2010) 1.41
Real-time measurement of solute transport within the lacunar-canalicular system of mechanically loaded bone: direct evidence for load-induced fluid flow. J Bone Miner Res (2011) 1.40
A novel method for protein secondary structure prediction using dual-layer SVM and profiles. Proteins (2004) 1.38
miR-124 inhibits cell proliferation in gastric cancer through down-regulation of SPHK1. J Pathol (2012) 1.38
Bier spots: six case reports. J Am Acad Dermatol (2009) 1.37
In silico identification of the key components and steps in IFN-gamma induced JAK-STAT signaling pathway. FEBS Lett (2005) 1.37
Intracellular ATP levels are a pivotal determinant of chemoresistance in colon cancer cells. Cancer Res (2011) 1.31
Glioma formation in neurofibromatosis 1 reflects preferential activation of K-RAS in astrocytes. Cancer Res (2005) 1.30
Apoptotic cells protect mice against lipopolysaccharide-induced shock. J Immunol (2008) 1.29
Characteristics of organic phosphorus fractions in different trophic sediments of lakes from the middle and lower reaches of Yangtze River region and Southwestern Plateau, China. Environ Pollut (2007) 1.29
Lamina propria CD4+ T lymphocytes synergize with murine intestinal epithelial cells to enhance proinflammatory response against an intracellular pathogen. J Immunol (2002) 1.27
MicroRNA-9 reduces cell invasion and E-cadherin secretion in SK-Hep-1 cell. Med Oncol (2009) 1.26
Developmentally-programmed FMRP expression in oligodendrocytes: a potential role of FMRP in regulating translation in oligodendroglia progenitors. Hum Mol Genet (2003) 1.26
Interleukin-8 modulates growth and invasiveness of estrogen receptor-negative breast cancer cells. Int J Cancer (2007) 1.26
In situ measurement of transport between subchondral bone and articular cartilage. J Orthop Res (2009) 1.25
Cryo-EM visualization of transfer messenger RNA with two SmpBs in a stalled ribosome. Proc Natl Acad Sci U S A (2006) 1.24
Funneled landscape leads to robustness of cell networks: yeast cell cycle. PLoS Comput Biol (2006) 1.21
Rescue of ATP7B function in hepatocyte-like cells from Wilson's disease induced pluripotent stem cells using gene therapy or the chaperone drug curcumin. Hum Mol Genet (2011) 1.20
Retracted Funneled landscape leads to robustness of cellular networks: MAPK signal transduction. Biophys J (2006) 1.20
Primary tracheobronchial amyloidosis in China: analysis of 64 cases and a review of literature. J Huazhong Univ Sci Technolog Med Sci (2010) 1.19
Direct evidence of Parkinson pathology spread from the gastrointestinal tract to the brain in rats. Acta Neuropathol (2014) 1.18
Droplet motion on designed microtextured superhydrophobic surfaces with tunable wettability. Langmuir (2008) 1.18
Modulation of the chemokines KC and MCP-1 by 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) in mice. Arch Biochem Biophys (2007) 1.18
Genome-wide association analysis of meat quality traits in a porcine Large White × Minzhu intercross population. Int J Biol Sci (2012) 1.17
Expression profiling in tuberous sclerosis complex (TSC) knockout mouse astrocytes to characterize human TSC brain pathology. Glia (2004) 1.16
Two new lactones and one new aryl-8-oxa-bicyclo[3,2,1]oct-3-en-2-one from Descurainia sophia. Chem Pharm Bull (Tokyo) (2004) 1.14
Vascular endothelial growth factor C promotes cervical cancer metastasis via up-regulation and activation of RhoA/ROCK-2/moesin cascade. BMC Cancer (2010) 1.14
Myosin light chain kinase is necessary for tonic airway smooth muscle contraction. J Biol Chem (2009) 1.14
NBA-Palm: prediction of palmitoylation site implemented in Naïve Bayes algorithm. BMC Bioinformatics (2006) 1.12
A new phenotype of asthma: chest tightness as the sole presenting manifestation. Ann Allergy Asthma Immunol (2013) 1.11
Dynamic association of the fragile X mental retardation protein as a messenger ribonucleoprotein between microtubules and polyribosomes. Mol Biol Cell (2007) 1.10
Elevated cross-talk between subchondral bone and cartilage in osteoarthritic joints. Bone (2011) 1.10
Electronic and magnetic properties of Ni nanoparticles embedded in various organic semiconductor matrices. J Phys Chem B (2009) 1.09
MeMo: a web tool for prediction of protein methylation modifications. Nucleic Acids Res (2006) 1.09
Linc2GO: a human LincRNA function annotation resource based on ceRNA hypothesis. Bioinformatics (2013) 1.09
Induced pluripotent stem cells can be used to model the genomic imprinting disorder Prader-Willi syndrome. J Biol Chem (2010) 1.07
Scaffolding as an organizing principle in trans-translation. The roles of small protein B and ribosomal protein S1. J Biol Chem (2006) 1.07
FAK is involved in invasion and metastasis of hepatocellular carcinoma. Clin Exp Metastasis (2010) 1.07
Pathogenesis of aryl hydrocarbon receptor-mediated development of lymphoma is associated with increased cyclooxygenase-2 expression. Am J Pathol (2007) 1.06
Mouse meningiocytes express Sox2 and yield high efficiency of chimeras after nuclear reprogramming with exogenous factors. J Biol Chem (2008) 1.05
Cryo-EM structure of the mammalian eukaryotic release factor eRF1-eRF3-associated termination complex. Proc Natl Acad Sci U S A (2012) 1.05
Do all threats work the same way? Divergent effects of fear and disgust on sensory perception and attention. J Neurosci (2011) 1.05
miR-145 suppresses cell invasion in hepatocellular carcinoma cells: miR-145 targets ADAM17. Hepatol Res (2013) 1.04
Expression and prognostic impact of PRL-3 in lymph node metastasis of gastric cancer: its molecular mechanism was investigated using artificial microRNA interference. Int J Cancer (2008) 1.04
Preferential duplication in the sparse part of yeast protein interaction network. Mol Biol Evol (2006) 1.04
Development of highly polymorphic simple sequence repeat markers using genome-wide microsatellite variant analysis in Foxtail millet [Setaria italica (L.) P. Beauv]. BMC Genomics (2014) 1.04
Rab23 is a potential biological target for treating hepatocellular carcinoma. World J Gastroenterol (2007) 1.03
Lipopolysaccharide induces lung fibroblast proliferation through Toll-like receptor 4 signaling and the phosphoinositide3-kinase-Akt pathway. PLoS One (2012) 1.02
Inferring functional linkages between proteins from evolutionary scenarios. J Mol Biol (2006) 1.02
DBMLoc: a Database of proteins with multiple subcellular localizations. BMC Bioinformatics (2008) 1.02
Characterization of proliferating cells from newborn mouse cochleae. Neuroreport (2006) 1.02
Monodisperse Hsp16.3 nonamer exhibits dynamic dissociation and reassociation, with the nonamer dissociation prerequisite for chaperone-like activity. J Mol Biol (2002) 1.01
The IRAK-1-BCL10-MALT1-TRAF6-TAK1 cascade mediates signaling to NF-kappaB from Toll-like receptor 4. J Biol Chem (2006) 1.01
Helicobacter pylori infection synergizes with three inflammation-related genetic variants in the GWASs to increase risk of gastric cancer in a Chinese population. PLoS One (2013) 1.01
Clinical significance of miR-221 and its inverse correlation with p27Kip¹ in hepatocellular carcinoma. Mol Biol Rep (2010) 1.01
NSC 74859-mediated inhibition of STAT3 enhances the anti-proliferative activity of cetuximab in hepatocellular carcinoma. Liver Int (2011) 1.00
When the sense of smell meets emotion: anxiety-state-dependent olfactory processing and neural circuitry adaptation. J Neurosci (2013) 1.00
A new nor-lignan from the seeds of Descurainia sophia. Nat Prod Res (2006) 1.00
Individualizing antimetabolic treatment strategies for head and neck squamous cell carcinoma based on TP53 mutational status. Cancer (2011) 1.00
MicroRNA-362 induces cell proliferation and apoptosis resistance in gastric cancer by activation of NF-κB signaling. J Transl Med (2014) 1.00
Molecular recollision interferometry in high harmonic generation. Phys Rev Lett (2008) 0.99
Secretin activation of the apical Na+-dependent bile acid transporter is associated with cholehepatic shunting in rats. Hepatology (2005) 0.98