Biblio
] MoDEL (Molecular Dynamics Extended Library): a database of atomistic molecular dynamics trajectories.,
, Structure, 2010 Nov 10, Volume 18, p.1399-409, (2010)
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)
Dramatic effect of furanose C2’ substitution on structure and stability: directing the folding of the human telomeric quadruplex with a single fluorine atom.,
, J Am Chem Soc, 2013 Apr 10, Volume 135, p.5344-7, (2013)
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)
COCO: a simple tool to enrich the representation of conformational variability in NMR structures.,
, Proteins, 2009 Apr, Volume 75, p.206-16, (2009)
Role of Pre-A motif in nitric oxide scavenging by truncated hemoglobin, HbN, of Mycobacterium tuberculosis.,
, J Biol Chem, 2009 May 22, Volume 284, p.14457-68, (2009)
Molecular basis of substrate-induced permeation by an amino acid antiporter.,
, Proc Natl Acad Sci U S A, 2011 Mar 8, Volume 108, p.3935-40, (2011)
On the performance of continuum solvation methods. A comment on "Universal approaches to solvation modeling".,
, Acc Chem Res, 2009 Apr 21, Volume 42, p.489-92; discussion 493-7, (2009)
Theoretical study of the mechanisms of substrate recognition by catalase.,
, J Am Chem Soc, 2001 Oct 3, Volume 123, p.9665-72, (2001)
DNAlive: a tool for the physical analysis of DNA at the genomic scale.,
, Bioinformatics, 2008 Aug 1, Volume 24, p.1731-2, (2008)
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)
A computational and experimental study of O-glycosylation. Catalysis by human UDP-GalNAc polypeptide:GalNAc transferase-T2.,
, Org Biomol Chem, 2014 May 7, Volume 12, p.2645-55, (2014)
Retaining glycosyltransferase mechanism studied by QM/MM methods: lipopolysaccharyl-α-1,4-galactosyltransferase C transfers α-galactose via an oxocarbenium ion-like transition state.,
, J Am Chem Soc, 2012 Mar 14, Volume 134, p.4743-52, (2012)
Substrate-assisted and nucleophilically assisted catalysis in bovine α1,3-galactosyltransferase. Mechanistic implications for retaining glycosyltransferases.,
, J Am Chem Soc, 2013 May 8, Volume 135, p.7053-63, (2013)
Classical molecular interaction potentials: improved setup procedure in molecular dynamics simulations of proteins.,
, Proteins, 2001 Dec 1, Volume 45, p.428-37, (2001)
Theoretical characterization of the dynamical behavior and transport properties of alpha,gamma-peptide nanotubes in solution.,
, J Am Chem Soc, 2009 Nov 4, Volume 131, p.15678-86, (2009)
Defining the nature of thermal intermediate in 3 state folding proteins: apoflavodoxin, a study case.,
, PLoS Comput Biol, 2012, Volume 8, p.e1002647, (2012)
Ligand-induced changes in the binding sites of proteins.,
, Bioinformatics, 2002 Jul, Volume 18, p.939-48, (2002)
Extension of the MST continuum solvation model to the RM1 semiempirical Hamiltonian.,
, J Comput Chem, 2008 Mar, Volume 29, p.578-87, (2008)
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)
PMUT: a web-based tool for the annotation of pathological mutations on proteins.,
, Bioinformatics, 2005 Jul 15, Volume 21, p.3176-8, (2005)
Characterization of compensated mutations in terms of structural and physico-chemical properties.,
, J Mol Biol, 2007 Jan 5, Volume 365, p.249-56, (2007)
Functional and structural conservation of CBS domains from CLC chloride channels.,
, J Physiol, 2004 Jun 1, Volume 557, p.363-78, (2004)
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)
Exploring the suitability of coarse-grained techniques for the representation of protein dynamics.,
, Biophys J, 2008 Sep, Volume 95, p.2127-38, (2008)
Effects of local electric fields on the redox free energy of single stranded DNA.,
, Chem Commun (Camb), 2011 Mar 7, Volume 47, p.2646-8, (2011)
Evidence for transcript networks composed of chimeric RNAs in human cells.,
, PLoS One, 2012, Volume 7, p.e28213, (2012)
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)
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)
Direct measurement of the dielectric polarization properties of DNA.,
, Proc Natl Acad Sci U S A, 2014 Sep 2, Volume 111, p.E3624-30, (2014)
Theoretical study of a new DNA structure: the antiparallel Hoogsteen duplex.,
, J Am Chem Soc, 2003 Nov 26, Volume 125, p.14603-12, (2003)
Theoretical study of the Hoogsteen-Watson-Crick junctions in DNA.,
, Biophys J, 2006 Feb 1, Volume 90, p.1000-8, (2006)
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)
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)
GRID-MD-A tool for massive simulation of protein channels.,
, Proteins, 2008 Feb 15, Volume 70, p.892-9, (2008)
Unveiling case-control relationships in designing a simple and powerful method for detecting gene-gene interactions.,
, Genet Epidemiol, 2012 Nov, Volume 36, p.710-6, (2012)
Exploring the dynamics of calix[4]pyrrole: effect of solvent and fluorine substitution.,
, Chemistry, 2007, Volume 13, p.1108-16, (2007)
Structural, dynamical, and electronic transport properties of modified DNA duplexes containing size-expanded nucleobases.,
, J Phys Chem A, 2011 Oct 20, Volume 115, p.11344-54, (2011)
Unique tautomeric properties of isoguanine.,
, J Am Chem Soc, 2004 Jan 14, Volume 126, p.154-64, (2004)
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)
Ligand-induced dynamical regulation of NO conversion in Mycobacterium tuberculosis truncated hemoglobin-N.,
, Proteins, 2006 Aug 1, Volume 64, p.457-64, (2006)
Structural mechanics of DNA wrapping in the nucleosome.,
, J Mol Biol, 2010 Feb 19, Volume 396, p.264-79, (2010)
Structural analysis of an equilibrium folding intermediate in the apoflavodoxin native ensemble by small-angle X-ray scattering.,
, J Mol Biol, 2011 Mar 4, Volume 406, p.604-19, (2011)
Properties of triple helices formed by parallel-stranded hairpins containing 8-aminopurines.,
, Nucleic Acids Res, 2002 Jun 15, Volume 30, p.2609-19, (2002)
Antiparallel triple helices. Structural characteristics and stabilization by 8-amino derivatives.,
, J Am Chem Soc, 2003 Dec 24, Volume 125, p.16127-38, (2003)
A Native Ternary Complex Trapped in a Crystal Reveals the Catalytic Mechanism of a Retaining Glycosyltransferase.,
, Angew Chem Int Ed Engl, 2015 Aug 17, Volume 54, p.9898-902, (2015)