Biblio
] Exploring The Conformational Landscape Of Bioactive Small Molecules,
, Journal of Chemical Theory and Computation, 08/2020, (2020)
Bioactive Conformational Ensemble Server And Database. A Public Framework To Speed Up In Silico Drug Discovery,
, Journal of Chemical Theory and Computation, 08/2020, (2020)
Breathing, bubbling, and bending: DNA flexibility from multimicrosecond simulations,
, Physical Review E, Volume 86, Number 2, p.021903, (2012)
X-Pol Potential: An Electronic Structure-Based Force Field for Molecular Dynamics Simulation of a Solvated Protein in Water.,
, J Chem Theory Comput, 2009 Feb 17, Volume 5, p.459-467, (2009)
Interoperability with Moby 1.0–it’s better than sharing your toothbrush!,
, Brief Bioinform, 2008 May, Volume 9, p.220-31, (2008)
Molywood: streamlining the design and rendering of molecular movies,
, Bioinformatics, 06/2020, (2020)
Pre-exascale HPC approaches for molecular dynamics simulations. Covid-19 research: A use case,
, WIREs Computational Molecular Science, 05/2022, Volume In Press, p.e1622, (2022)
Omicron mutations increase interdomain interactions and reduce epitope exposure in the SARS-CoV-2 spike,
, iScience, 02/2023, Volume 26, Issue 2, p.105981, (2023)
Differential stability of 2’F-ANA*RNA and ANA*RNA hybrid duplexes: roles of structure, pseudohydrogen bonding, hydration, ion uptake and flexibility.,
, Nucleic Acids Res, 2010 Apr, Volume 38, p.2498-511, (2010)
A multi-modal coarse grained model of DNA flexibility mappable to the atomistic level,
, Nucleic Acids Research, 01/2020, (2020)
A DNA methylation map of human cancer at single base-pair resolution,
, Oncogene, 06/2017, p.1-10, (2017)
Comparison of molecular dynamics and superfamily spaces of protein domain deformation.,
, BMC Struct Biol, 2009, Volume 9, p.6, (2009)
Ab initio study of the structural, tautomeric, pairing, and electronic properties of seleno-derivatives of thymine.,
, J Phys Chem B, 2009 Oct 29, Volume 113, p.14465-72, (2009)
Ab initio study of naphtho-homologated DNA bases.,
, J Phys Chem B, 2008 Feb 21, Volume 112, p.2179-86, (2008)
Alternative splicing mechanisms for the modulation of protein function: conservation between human and other species.,
, J Mol Biol, 2004 Jan 9, Volume 335, p.495-502, (2004)
Contribution of engineered electrostatic interactions to the stability of cytosolic malate dehydrogenase.,
, Protein Eng, 2001 Nov, Volume 14, p.911-7, (2001)
Sequential amino acid exchange across b(0,+)-like system in chicken brush border jejunum.,
, J Membr Biol, 2001 Apr 1, Volume 180, p.213-20, (2001)
Rational design of novel N-alkyl-N capped biostable RNA nanostructures for efficient long-term inhibition of gene expression,
, Nucleic Acids Research, 11/2016, Volume 44, p.4354-4367, (2016)
A multifunctional toolkit for target-directed cancer therapy,
, Chemical Communications, 2019, Volume 55, Issue 6, p.802 - 805, (2019)
Functionalization of the 3’-ends of DNA and RNA strands with N-ethyl-N-coupled nucleosides: a promising approach to avoid 3’-exonuclease-catalyzed hydrolysis of therapeutic oligonucleotides.,
, Chembiochem, 2013 Mar 4, Volume 14, p.510-20, (2013)
The Origins and the Biological Consequences of the Pur/Pyr DNA·RNA Asymmetry,
, Chem, 04/2019, (2019)
Enabling HMMER for the Grid with COMP Superscalar,
, Procedia Computer Science, Volume 1, p.2629–2638, (2010)
Structural analysis of the Candida albicans mitochondrial DNA maintenance factor Gcf1p reveals a dynamic DNA-bridging mechanism,
, Nucleic Acids Research, 05/2023, p.gkad397, (2023)
A fast method for the determination of fractional contributions to solvation in proteins.,
, Protein Sci, 2006 Nov, Volume 15, p.2525-33, (2006)
The (in)dependence of alternative splicing and gene duplication.,
, PLoS Comput Biol, 2007 Mar 2, Volume 3, p.e33, (2007)
A procedure for identifying homologous alternative splicing events.,
, BMC Bioinformatics, 2007, Volume 8, p.260, (2007)
Alternative splicing of transcription factors’ genes: beyond the increase of proteome diversity.,
, Comp Funct Genomics, 2009, p.905894, (2009)
Geometrical and electronic structure variability of the sugar-phosphate backbone in nucleic acids.,
, J Phys Chem B, 2008 Jul 10, Volume 112, p.8188-97, (2008)
High-Throughput Prediction of the Impact of Genetic Variability on Drug Sensitivity and Resistance Patterns for Clinically Relevant Epidermal Growth Factor Receptor Mutations from Atomistic Simulations,
, Journal of Chemical Information and Modeling, 12/2022, Volume In press, (2022)
Enzyme-directed mutasynthesis: a combined experimental and theoretical approach to substrate recognition of a polyketide synthase.,
, ACS Chem Biol, 2013 Feb 15, Volume 8, p.443-50, (2013)
Unconventional interactions between water and heterocyclic nitrogens in protein structures.,
, Proteins, 2004 Oct 1, Volume 57, p.1-8, (2004)
A systematic study of the energetics involved in structural changes upon association and connectivity in protein interaction networks.,
, Structure, 2011 Jun 8, Volume 19, p.881-9, (2011)
Emergence of chromatin hierarchical loops from protein disorder and nucleosome asymmetry,
, Proceedings of the National Academy of Sciences, 03/2020, Volume 117, Issue 13, p.7216, (2020)
Nature of base stacking: reference quantum-chemical stacking energies in ten unique B-DNA base-pair steps.,
, Chemistry, 2006 Mar 20, Volume 12, p.2854-65, (2006)
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)
Performance of the IEF-MST solvation continuum model in the SAMPL2 blind test prediction of hydration and tautomerization free energies.,
, J Comput Aided Mol Des, 2010 Apr, Volume 24, p.281-91, (2010)
Performance of the IEF-MST solvation continuum model in a blind test prediction of hydration free energies.,
, J Phys Chem B, 2009 Jul 9, Volume 113, p.9330-4, (2009)
Induction effects in metal cation-benzene complexes.,
, Phys Chem Chem Phys, 2008 May 21, Volume 10, p.2616-24, (2008)
Structure-directed reversion in the pi-facial stereoselective alkylation of chiral bicyclic lactams.,
, J Org Chem, 2008 Oct 3, Volume 73, p.7756-63, (2008)
On the origin of the stereoselectivity in the alkylation of oxazolopiperidone enolates.,
, J Am Chem Soc, 2006 May 24, Volume 128, p.6581-8, (2006)
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)
Solution structure of a DNA duplex with a chiral alkyl phosphonate moiety,
, Nucleic Acids Research, Volume 29, p.2973-2985, (2001)
Dissection of the recognition properties of p38 MAP kinase. Determination of the binding mode of a new pyridinyl-heterocycle inhibitor family.,
, J Med Chem, 2007 Jan 25, Volume 50, p.283-93, (2007)
DNA-triplex stabilizing properties of 8-aminoguanine,
, Nucleic Acids Research, Volume 28, p.4531-4539, (2000)
Making Canonical Workflow Building Blocks Interoperable across Workflow Languages,
, Data Intelligence, 2022, p.1 - 16, (2022)
Connecting proline and γ-aminobutyric acid in stressed plants through non-enzymatic reactions.,
, PLoS One, 2015, Volume 10, p.e0115349, (2015)
pyPcazip: A PCA-based toolkit for compression and analysis of molecular simulation data,
, SoftwareX, 12/2016, Volume 5, p.44 - 50, (2016)
Residues Coevolution Guides the Systematic Identification of Alternative Functional Conformations in Proteins,
, Structure, Volume 24, p.116 - 126, (2016)
Finding Conformational Transition Pathways from Discrete Molecular Dynamics Simulations,
, Journal of Chemical Theory and Computation, 2012/11/13, Volume 8, p.4707 - 4718, (2012)
Exploration of conformational transition pathways from coarse-grained simulations.,
, Bioinformatics, 2013 Aug 15, Volume 29, p.1980-6, (2013)