Published in Biotechnol J on January 01, 2007
Ligand docking and binding site analysis with PyMOL and Autodock/Vina. J Comput Aided Mol Des (2010) 2.67
CAVER 3.0: a tool for the analysis of transport pathways in dynamic protein structures. PLoS Comput Biol (2012) 2.64
Mechanism of recognition of compounds of diverse structures by the multidrug efflux pump AcrB of Escherichia coli. Proc Natl Acad Sci U S A (2010) 1.54
MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels. Nucleic Acids Res (2012) 1.34
Detecting pore-lining regions in transmembrane protein sequences. BMC Bioinformatics (2012) 1.22
Structural differences between soluble and membrane bound cytochrome P450s. J Inorg Biochem (2011) 1.04
Why boys will be boys: two pathways of fetal testicular androgen biosynthesis are needed for male sexual differentiation. Am J Hum Genet (2011) 1.00
Finding and characterizing tunnels in macromolecules with application to ion channels and pores. Biophys J (2009) 0.97
A substrate channel in the nitrogenase MoFe protein. J Biol Inorg Chem (2009) 0.96
The structure of neuroglobin at high Xe and Kr pressure reveals partial conservation of globin internal cavities. Biophys J (2009) 0.94
A single mutation in a tunnel to the active site changes the mechanism and kinetics of product release in haloalkane dehalogenase LinB. J Biol Chem (2012) 0.87
Molecular basis of reduced glucosylceramidase activity in the most common Gaucher disease mutant, N370S. J Biol Chem (2010) 0.84
Different functions of MdtB and MdtC subunits in the heterotrimeric efflux transporter MdtB(2)C complex of Escherichia coli. Biochemistry (2012) 0.82
Evidence for a bicarbonate "escort" site in Haemophilus influenzae beta-carbonic anhydrase . Biochemistry (2010) 0.79
Structural and kinetic isotope effect studies of nicotinamidase (Pnc1) from Saccharomyces cerevisiae. Biochemistry (2011) 0.78
Finding molecular dioxygen tunnels in homoprotocatechuate 2,3-dioxygenase: implications for different reactivity of identical subunits. Eur Biophys J (2009) 0.77
Analysis of water channels by molecular dynamics simulation of heterotetrameric sarcosine oxidase. Biophys Physicobiol (2015) 0.75
Ligand-based virtual screening interface between PyMOL and LiSiCA. J Cheminform (2016) 0.75
Enzyme discovery beyond homology: a unique hydroxynitrile lyase in the Bet v1 superfamily. Sci Rep (2017) 0.75
Interactions of cations with RNA loop-loop complexes. Biophys J (2011) 0.75
CAVER: a new tool to explore routes from protein clefts, pockets and cavities. BMC Bioinformatics (2006) 4.11
Functionalization of graphene: covalent and non-covalent approaches, derivatives and applications. Chem Rev (2012) 3.19
MOLE: a Voronoi diagram-based explorer of molecular channels, pores, and tunnels. Structure (2007) 2.49
Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles. J Chem Theory Comput (2011) 2.12
Protein profiles of bronchoalveolar lavage fluid from patients with pulmonary sarcoidosis. Am J Respir Crit Care Med (2006) 1.61
A novel sarcoidosis risk locus for Europeans on chromosome 11q13.1. Am J Respir Crit Care Med (2012) 1.56
Genome-wide association analysis reveals 12q13.3-q14.1 as new risk locus for sarcoidosis. Eur Respir J (2012) 1.47
Molecular dynamics and quantum mechanics of RNA: conformational and chemical change we can believe in. Acc Chem Res (2010) 1.40
Redesigning dehalogenase access tunnels as a strategy for degrading an anthropogenic substrate. Nat Chem Biol (2009) 1.39
Association of interleukin-1 receptor antagonist and interleukin-6 polymorphisms with osteolysis after total hip arthroplasty: comment on the article by Gordon et al. Arthritis Rheum (2009) 1.39
MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels. Nucleic Acids Res (2012) 1.34
MOLE 2.0: advanced approach for analysis of biomacromolecular channels. J Cheminform (2013) 1.26
Interleukin-1 gene cluster polymorphisms in sarcoidosis and idiopathic pulmonary fibrosis. Am J Respir Crit Care Med (2002) 1.22
Membrane position of ibuprofen agrees with suggested access path entrance to cytochrome P450 2C9 active site. J Phys Chem A (2011) 1.21
Crystal structure of haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26 at 0.95 A resolution: dynamics of catalytic residues. Biochemistry (2004) 1.19
Involvement of microRNAs in physiological and pathological processes in the lung. Respir Res (2010) 1.17
Flexibility of human cytochromes P450: molecular dynamics reveals differences between CYPs 3A4, 2C9, and 2A6, which correlate with their substrate preferences. J Phys Chem B (2008) 1.16
Environmental applications of chemically pure natural ferrihydrite. Environ Sci Technol (2007) 1.15
Interleukin 1alpha single-nucleotide polymorphism associated with systemic sclerosis. J Rheumatol (2004) 1.13
Protonation states of the key active site residues and structural dynamics of the glmS riboswitch as revealed by molecular dynamics. J Phys Chem B (2010) 1.11
Reference simulations of noncanonical nucleic acids with different χ variants of the AMBER force field: quadruplex DNA, quadruplex RNA and Z-DNA. J Chem Theory Comput (2012) 1.09
Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters. J Chem Theory Comput (2013) 1.09
Extensive molecular dynamics simulations showing that canonical G8 and protonated A38H+ forms are most consistent with crystal structures of hairpin ribozyme. J Phys Chem B (2010) 1.07
Activation and inhibition of cyclin-dependent kinase-2 by phosphorylation; a molecular dynamics study reveals the functional importance of the glycine-rich loop. Protein Sci (2004) 1.04
Adsorption of small organic molecules on graphene. J Am Chem Soc (2013) 1.04
PSMB2 and RPL32 are suitable denominators to normalize gene expression profiles in bronchoalveolar cells. BMC Mol Biol (2008) 1.04
Simultaneous up-regulation of matrix metalloproteinases 1, 2, 3, 7, 8, 9 and tissue inhibitors of metalloproteinases 1, 4 in serum of patients with chronic obstructive pulmonary disease. Respirology (2012) 1.04
Dynamics and hydration of the active sites of mammalian cytochromes P450 probed by molecular dynamics simulations. Curr Drug Metab (2012) 1.02
Dependence of A-RNA simulations on the choice of the force field and salt strength. Phys Chem Chem Phys (2009) 1.01
Variation in cytokine genes can contribute to severity of acetabular osteolysis and risk for revision in patients with ABG 1 total hip arthroplasty: a genetic association study. BMC Med Genet (2009) 1.00
Force-field dependence of chignolin folding and misfolding: comparison with experiment and redesign. Biophys J (2012) 0.97
Simulations of A-RNA duplexes. The effect of sequence, solute force field, water model, and salt concentration. J Phys Chem B (2012) 0.96
General base catalysis for cleavage by the active-site cytosine of the hepatitis delta virus ribozyme: QM/MM calculations establish chemical feasibility. J Phys Chem B (2008) 0.96
Theoretical studies of RNA catalysis: hybrid QM/MM methods and their comparison with MD and QM. Methods (2009) 0.95
The mechanism of inhibition of the cyclin-dependent kinase-2 as revealed by the molecular dynamics study on the complex CDK2 with the peptide substrate HHASPRK. Protein Sci (2005) 0.94
Mechanism of enhanced conversion of 1,2,3-trichloropropane by mutant haloalkane dehalogenase revealed by molecular modeling. J Comput Aided Mol Des (2006) 0.94
How to understand quantum chemical computations on DNA and RNA systems? A practical guide for non-specialists. Methods (2013) 0.92
Large-scale compensation of errors in pairwise-additive empirical force fields: comparison of AMBER intermolecular terms with rigorous DFT-SAPT calculations. Phys Chem Chem Phys (2010) 0.90
Transferable scoring function based on semiempirical quantum mechanical PM6-DH2 method: CDK2 with 15 structurally diverse inhibitors. J Comput Aided Mol Des (2011) 0.90
Molecular mechanism of preQ1 riboswitch action: a molecular dynamics study. J Phys Chem B (2012) 0.90
Effect of guanine to inosine substitution on stability of canonical DNA and RNA duplexes: molecular dynamics thermodynamics integration study. J Phys Chem B (2013) 0.89
Graphene fluoride: a stable stoichiometric graphene derivative and its chemical conversion to graphene. Small (2010) 0.89
Expression of macrophage inflammatory protein-3 beta/CCL19 in pulmonary sarcoidosis. Am J Respir Crit Care Med (2003) 0.88
The DNA and RNA sugar-phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies. Phys Chem Chem Phys (2012) 0.87
Positioning of antioxidant quercetin and its metabolites in lipid bilayer membranes: implication for their lipid-peroxidation inhibition. J Phys Chem B (2012) 0.87
Functional flexibility of human cyclin-dependent kinase-2 and its evolutionary conservation. Protein Sci (2007) 0.87
Glycine-rich loop of mitochondrial processing peptidase alpha-subunit is responsible for substrate recognition by a mechanism analogous to mitochondrial receptor Tom20. J Mol Biol (2010) 0.87
The Nature of the Binding of Au, Ag, and Pd to Benzene, Coronene, and Graphene: From Benchmark CCSD(T) Calculations to Plane-Wave DFT Calculations. J Chem Theory Comput (2011) 0.86
Convergence of Free Energy Profile of Coumarin in Lipid Bilayer. J Chem Theory Comput (2012) 0.86
Interaction energies for the purine inhibitor roscovitine with cyclin-dependent kinase 2: correlated ab initio quantum-chemical, DFT and empirical calculations. Chemistry (2006) 0.86
QM/MM studies of hairpin ribozyme self-cleavage suggest the feasibility of multiple competing reaction mechanisms. J Phys Chem B (2011) 0.86
Quantification of the interaction forces between metals and graphene by quantum chemical calculations and dynamic force measurements under ambient conditions. ACS Nano (2013) 0.86
Expression of the chemokine PARC mRNA in bronchoalveolar cells of patients with sarcoidosis. Immunol Lett (2002) 0.86
Behavior of human cytochromes P450 on lipid membranes. J Phys Chem B (2013) 0.86
Chemical nature of boron and nitrogen dopant atoms in graphene strongly influences its electronic properties. Phys Chem Chem Phys (2014) 0.86
The MCP-1-2518 (A to G) single nucleotide polymorphism in Czech patients with pulmonary sarcoidosis: association with Löfgren's syndrome. Sarcoidosis Vasc Diffuse Lung Dis (2007) 0.86
CC chemokine receptor (CCR)2 polymorphism in Czech patients with myocardial infarction. Immunol Lett (2003) 0.85
Monocyte chemoattractant protein-1 in patients with peripheral arterial disease. Mediators Inflamm (2004) 0.84
Noncanonical hydrogen bonding in nucleic acids. Benchmark evaluation of key base-phosphate interactions in folded RNA molecules using quantum-chemical calculations and molecular dynamics simulations. J Phys Chem A (2011) 0.84
The macrophage migration inhibitory factor (MIF) gene polymorphism in Czech and Russian patients with myocardial infarction. Clin Chim Acta (2009) 0.84
Association of C1QB gene polymorphism with schizophrenia in Armenian population. BMC Med Genet (2011) 0.84
Functional characterization of the complement receptor type 1 and its circulating ligands in patients with schizophrenia. BMC Clin Pathol (2011) 0.84
Flexibility of human cytochrome P450 enzymes: molecular dynamics and spectroscopy reveal important function-related variations. Biochim Biophys Acta (2010) 0.84
Functional genetic polymorphisms of monocyte chemoattractant protein 1 and C-C chemokine receptor type 2 in ischemic stroke. J Interferon Cytokine Res (2013) 0.83
Thiofluorographene-hydrophilic graphene derivative with semiconducting and genosensing properties. Adv Mater (2015) 0.83
Molecular dynamics study of Pseudomonas aeruginosa lectin-II complexed with monosaccharides. Proteins (2008) 0.83
Second step of hydrolytic dehalogenation in haloalkane dehalogenase investigated by QM/MM methods. Proteins (2008) 0.83
ATP and magnesium drive conformational changes of the Na+/K+-ATPase cytoplasmic headpiece. Biochim Biophys Acta (2009) 0.83
Nature and magnitude of aromatic base stacking in DNA and RNA: Quantum chemistry, molecular mechanics, and experiment. Biopolymers (2013) 0.83
A cancer-derived mutation in the PSTAIRE helix of cyclin-dependent kinase 2 alters the stability of cyclin binding. Biochim Biophys Acta (2010) 0.82
A computational study of the glycine-rich loop of mitochondrial processing peptidase. PLoS One (2013) 0.82
Possible impact of MADCAM1 gene single nucleotide polymorphisms to the outcome of allogeneic hematopoietic stem cell transplantation. Hum Immunol (2009) 0.82
Band gaps and structural properties of graphene halides and their derivates: a hybrid functional study with localized orbital basis sets. J Chem Phys (2012) 0.82
Density-functional, density-functional tight-binding, and wave function calculations on biomolecular systems. J Phys Chem A (2007) 0.82
Association of chronic stable angina pectoris with MCP-1-2518 A/G single nucleotide polymorphism in the Slovak population. Clin Chim Acta (2008) 0.82
Halogenated graphenes: rapidly growing family of graphene derivatives. ACS Nano (2013) 0.82
Modelling of graphene functionalization. Phys Chem Chem Phys (2015) 0.82
Characterization of p40 and IL-10 in the BALF of patients with pulmonary sarcoidosis. J Interferon Cytokine Res (2003) 0.81
Regulatory phosphorylation of cyclin-dependent kinase 2: insights from molecular dynamics simulations. J Mol Model (2008) 0.81
Variation in the IL1B, TNF and IL6 genes and individual susceptibility to prosthetic joint infection. BMC Immunol (2012) 0.80
Amphiphilic drug-like molecules accumulate in a membrane below the head group region. J Phys Chem B (2014) 0.80
Semiempirical quantum mechanical method PM6-DH2X describes the geometry and energetics of CK2-inhibitor complexes involving halogen bonds well, while the empirical potential fails. J Phys Chem B (2011) 0.80
Activated phenotype of circulating neutrophils in familial Mediterranean fever. Immunobiology (2012) 0.80
Analysis of CDK2 active-site hydration: a method to design new inhibitors. Proteins (2004) 0.80
The role of an active site Mg(2+) in HDV ribozyme self-cleavage: insights from QM/MM calculations. Phys Chem Chem Phys (2015) 0.79
Molecular insight into affinities of drugs and their metabolites to lipid bilayers. J Phys Chem B (2013) 0.79
Benchmark quantum-chemical calculations on a complete set of rotameric families of the DNA sugar-phosphate backbone and their comparison with modern density functional theory. Phys Chem Chem Phys (2013) 0.79
Two C-terminal ankyrin repeats form the minimal stable unit of the ankyrin repeat protein p18INK4c. J Mol Model (2008) 0.79
Binding of quinidine radically increases the stability and decreases the flexibility of the cytochrome P450 2D6 active site. J Inorg Biochem (2012) 0.79
CCL5/RANTES gene polymorphisms in Slavonic patients with myocardial infarction. Mediators Inflamm (2011) 0.79
Association study in Romanians confirms IL23A gene haplotype block rs2066808/rs11171806 as conferring risk to psoriatic arthritis. Cytokine (2013) 0.79
Monocyte chemoattractant protein-1 in schizophrenia: -2518A/G genetic variant and protein levels in Armenian population. Cytokine (2012) 0.78
Polymorphisms of the immune response genes: selected biological, methodical and medical aspects. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub (2009) 0.78
Coarse-grain simulations of skin ceramide NS with newly derived parameters clarify structure of melted phase. J Phys Chem B (2015) 0.78
Genetic variation in key molecules of the Th-17 immune response is not associated with risk for prosthetic joint infection in a Czech population. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub (2012) 0.78