Biblio
Exploring the dynamics of calix[4]pyrrole: effect of solvent and fluorine substitution.,
, Chemistry, 2007, Volume 13, p.1108-16, (2007)
Functional and structural characterization of the first prokaryotic member of the L-amino acid transporter (LAT) family: a model for APC transporters.,
, J Biol Chem, 2007 May 4, Volume 282, p.13270-81, (2007)
A hydrophobic similarity analysis of solvation effects on nucleic acid bases.,
, J Mol Model, 2007 Feb, Volume 13, p.357-65, (2007)
The (in)dependence of alternative splicing and gene duplication.,
, PLoS Comput Biol, 2007 Mar 2, Volume 3, p.e33, (2007)
Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers.,
, Biophys J, 2007 Jun 1, Volume 92, p.3817-29, (2007)
The structure of human 4F2hc ectodomain provides a model for homodimerization and electrostatic interaction with plasma membrane.,
, J Biol Chem, 2007 Oct 26, Volume 282, p.31444-52, (2007)
Theoretical study of large conformational transitions in DNA: the B<–>A conformational change in water and ethanol/water.,
, Nucleic Acids Res, 2007, Volume 35, p.3330-8, (2007)
Thorough validation of protein normal mode analysis: a comparative study with essential dynamics.,
, Structure, 2007 May, Volume 15, p.565-75, (2007)
Data mining of molecular dynamics trajectories of nucleic acids.,
, J Biomol Struct Dyn, 2006 Feb, Volume 23, p.447-56, (2006)
Dispersion and repulsion contributions to the solvation free energy: comparison of quantum mechanical and classical approaches in the polarizable continuum model.,
, J Comput Chem, 2006 Nov 30, Volume 27, p.1769-80, (2006)
A fast method for the determination of fractional contributions to solvation in proteins.,
, Protein Sci, 2006 Nov, Volume 15, p.2525-33, (2006)
G-quadruplexes can maintain their structure in the gas phase.,
, J Am Chem Soc, 2006 Mar 22, Volume 128, p.3608-19, (2006)
Ligand-induced dynamical regulation of NO conversion in Mycobacterium tuberculosis truncated hemoglobin-N.,
, Proteins, 2006 Aug 1, Volume 64, p.457-64, (2006)
Theoretical study of the Hoogsteen-Watson-Crick junctions in DNA.,
, Biophys J, 2006 Feb 1, Volume 90, p.1000-8, (2006)
Design, synthesis, and biological evaluation of dual binding site acetylcholinesterase inhibitors: new disease-modifying agents for Alzheimer’s disease.,
, J Med Chem, 2005 Nov 17, Volume 48, p.7223-33, (2005)
MST continuum study of the hydration free energies of monovalent ionic species.,
, J Phys Chem B, 2005 Mar 3, Volume 109, p.3565-74, (2005)
Partition of protein solvation into group contributions from molecular dynamics simulations.,
, Proteins, 2005 Jan 1, Volume 58, p.101-9, (2005)
PMUT: a web-based tool for the annotation of pathological mutations on proteins.,
, Bioinformatics, 2005 Jul 15, Volume 21, p.3176-8, (2005)
SAR and 3D-QSAR studies on thiadiazolidinone derivatives: exploration of structural requirements for glycogen synthase kinase 3 inhibitors.,
, J Med Chem, 2005 Nov 17, Volume 48, p.7103-12, (2005)
Structure, recognition properties, and flexibility of the DNA.RNA hybrid.,
, J Am Chem Soc, 2005 Apr 6, Volume 127, p.4910-20, (2005)
Theoretical study of the truncated hemoglobin HbN: exploring the molecular basis of the NO detoxification mechanism.,
, J Am Chem Soc, 2005 Mar 30, Volume 127, p.4433-44, (2005)
Effect of bulky lesions on DNA: solution structure of a DNA duplex containing a cholesterol adduct.,
, J Biol Chem, 2004 Jun 4, Volume 279, p.24552-60, (2004)
Exploring the binding mode of semicarbazide-sensitive amine oxidase/VAP-1: identification of novel substrates with insulin-like activity.,
, J Med Chem, 2004 Sep 23, Volume 47, p.4865-74, (2004)
Exploring the counterion atmosphere around DNA: what can be learned from molecular dynamics simulations?,
, Biophys J, 2004 Aug, Volume 87, p.800-11, (2004)
Functional and structural conservation of CBS domains from CLC chloride channels.,
, J Physiol, 2004 Jun 1, Volume 557, p.363-78, (2004)
Linear response theory: an alternative to PB and GB methods for the analysis of molecular dynamics trajectories?,
, Proteins, 2004 Nov 15, Volume 57, p.458-67, (2004)
Molecular modelling approaches to the design of acetylcholinesterase inhibitors: new challenges for the treatment of Alzheimer’s disease.,
, Curr Pharm Des, 2004, Volume 10, p.3131-40, (2004)
Relative flexibility of DNA and RNA: a molecular dynamics study.,
, J Mol Biol, 2004 Oct 22, Volume 343, p.627-38, (2004)
Theoretical study of the guanine –> 6-thioguanine substitution in duplexes, triplexes, and tetraplexes.,
, J Am Chem Soc, 2004 Nov 10, Volume 126, p.14642-50, (2004)
Unique tautomeric properties of isoguanine.,
, J Am Chem Soc, 2004 Jan 14, Volume 126, p.154-64, (2004)
Antiparallel triple helices. Structural characteristics and stabilization by 8-amino derivatives.,
, J Am Chem Soc, 2003 Dec 24, Volume 125, p.16127-38, (2003)
Continuum and discrete calculation of fractional contributions to solvation free energy.,
, J Comput Chem, 2003 Oct, Volume 24, p.1610-23, (2003)
Four-stranded DNA structure stabilized by a novel G:C:A:T tetrad.,
, J Am Chem Soc, 2003 May 14, Volume 125, p.5654-62, (2003)
The structure and dynamics of DNA in the gas phase.,
, J Am Chem Soc, 2003 Jul 2, Volume 125, p.8007-14, (2003)
Theoretical methods for the simulation of nucleic acids.,
, Chem Soc Rev, 2003 Nov, Volume 32, p.350-64, (2003)
Theoretical studies on the inhibition mechanism of cyclooxygenase-2. Is there a unique recognition site?,
, J Med Chem, 2003 Apr 10, Volume 46, p.1372-82, (2003)
Theoretical study of a new DNA structure: the antiparallel Hoogsteen duplex.,
, J Am Chem Soc, 2003 Nov 26, Volume 125, p.14603-12, (2003)
Fast estimation of hydrogen-bonding donor and acceptor propensities: a GMIPp study.,
, J Comput Aided Mol Des, 2002 Aug-Sep, Volume 16, p.569-83, (2002)
Hoogsteen-based parallel-stranded duplexes of DNA. Effect of 8-amino-purine derivatives.,
, J Am Chem Soc, 2002 Mar 27, Volume 124, p.3133-42, (2002)
Hydrophobic similarity between molecules: a MST-based hydrophobic similarity index.,
, J Comput Chem, 2002 Apr 15, Volume 23, p.554-63, (2002)
Ligand-induced changes in the binding sites of proteins.,
, Bioinformatics, 2002 Jul, Volume 18, p.939-48, (2002)
Properties of triple helices formed by parallel-stranded hairpins containing 8-aminopurines.,
, Nucleic Acids Res, 2002 Jun 15, Volume 30, p.2609-19, (2002)
Theoretical study of anion binding to calix[4]pyrrole: the effects of solvent, fluorine substitution, cosolute, and water traces.,
, J Am Chem Soc, 2002 Oct 30, Volume 124, p.12796-805, (2002)
Classical molecular interaction potentials: improved setup procedure in molecular dynamics simulations of proteins.,
, Proteins, 2001 Dec 1, Volume 45, p.428-37, (2001)
Contribution of engineered electrostatic interactions to the stability of cytosolic malate dehydrogenase.,
, Protein Eng, 2001 Nov, Volume 14, p.911-7, (2001)
Theoretical study of the mechanisms of substrate recognition by catalase.,
, J Am Chem Soc, 2001 Oct 3, Volume 123, p.9665-72, (2001)