Biblio
] On the nature of DNA hyperchromic effect.,
, J Phys Chem B, 2013 Jul 25, Volume 117, p.8697-704, (2013)
The BioExcel methodology for developing dynamic, scalable, reliable and portable computational biomolecular workflows,
, 2022 IEEE 18th International Conference on e-Science (e-Science), 12/2022, (2022)
i-Motif folding intermediates with zero-nucleotide loops are trapped by 2′-fluoroarabinocytidine via F···H and O···H hydrogen bonds,
, Communications Chemistry, 02/2023, Volume 6, Issue 1, p.31, (2023)
Exploring the suitability of coarse-grained techniques for the representation of protein dynamics.,
, Biophys J, 2008 Sep, Volume 95, p.2127-38, (2008)
Discrete Molecular Dynamics Approach to the Study of Disordered and Aggregating Proteins,
, Journal of Chemical Theory and Computation, 03/2017, Volume 13, Issue 3, p.1454 - 1461, (2017)
Protein flexibility from discrete molecular dynamics simulations using quasi-physical potentials.,
, Proteins, 2010 Jan, Volume 78, p.83-94, (2010)
Efficient relaxation of protein-protein interfaces by discrete molecular dynamics simulations,
, Journal of Chemical Theory and Computation, Volume 9, p.1222-1229, (2013)
PACSAB: Coarse-Grained Force Field for the Study of Protein-Protein Interactions and Conformational Sampling in Multiprotein Systems.,
, J Chem Theory Comput, 2015 Dec 8, Volume 11, p.5929-38, (2015)
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)
Side chain to main chain hydrogen bonds stabilize a polyglutamine helix in a transcription factor,
, Nature Communication, 05/2019, Volume 10, Issue 1, p.2034, (2019)
Functional and structural conservation of CBS domains from CLC chloride channels.,
, J Physiol, 2004 Jun 1, Volume 557, p.363-78, (2004)
Developments and applications of the OPTIMADE API for materials discovery, design, and data exchange,
, Digital Discovery, 04/2024, p. - , (2024)
Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing Nucleic Acids Force Fields,
, Journal of Chemical Theory and Computation, 2009/09/08, Volume 5, Issue 9, p.2514 - 2530, (2009)
Unique tautomeric and recognition properties of thioketothymines?,
, J Am Chem Soc, 2009 Sep 9, Volume 131, p.12845-53, (2009)
The DNA-forming properties of 6-selenoguanine,
, Phys. Chem. Chem. Phys., Volume 16, p.1101-1110, (2014)
Toward a consensus view of duplex RNA flexibility.,
, Biophys J, 2010 Sep 22, Volume 99, p.1876-85, (2010)
SEABED: Small molEcule activity scanner weB servicE baseD.,
, Bioinformatics, 2015 Mar 1, Volume 31, p.773-5, (2015)
Correlated motions are a fundamental property of B-sheets,
, Nat Commun, 10/2014, Volume 5, (2014)
Plasticity in oligomerization, operator architecture, and DNA binding in the mode of action of a bacterial B12-based photoreceptor,
, Journal of Biological Chemistry, 11/2018, Volume 293, Issue 46, p.17888 - 17905, (2018)
Characterization of compensated mutations in terms of structural and physico-chemical properties.,
, J Mol Biol, 2007 Jan 5, Volume 365, p.249-56, (2007)
Use of bioinformatics tools for the annotation of disease-associated mutations in animal models.,
, Proteins, 2005 Dec 1, Volume 61, p.878-87, (2005)
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 disease-associated single amino acid polymorphisms in terms of sequence and structure properties.,
, J Mol Biol, 2002 Jan 25, Volume 315, p.771-86, (2002)
nucleR: a package for non-parametric nucleosome positioning.,
, Bioinformatics, 2011 Aug 1, Volume 27, p.2149-50, (2011)
Fuzziness and noise in nucleosomal architecture.,
, Nucleic Acids Res, 2014 Apr, Volume 42, p.4934-46, (2014)
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)
Extension of the MST continuum solvation model to the RM1 semiempirical Hamiltonian.,
, J Comput Chem, 2008 Mar, Volume 29, p.578-87, (2008)
Molecular dynamics study of 2rotaxanes: influence of solvation and cation on co-conformation.,
, J Org Chem, 2003 Jun 13, Volume 68, p.4663-73, (2003)
Ligand-induced changes in the binding sites of proteins.,
, Bioinformatics, 2002 Jul, Volume 18, p.939-48, (2002)
VeriNA3d: an R package for nucleic acids data mining,
, Bioinformatics, 07/2019, (2019)
Efficient siRNA-peptide conjugation for specific targeted delivery into tumor cells,
, Chemical Communications, 03/2017, Volume 53, Issue 19, p.2870 - 2873, (2017)
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)
Targeting RNA structure in SMN2 reverses spinal muscular atrophy molecular phenotypes,
, Nature Communication, 2018/05/23, Volume 9, Issue 1, p.2032, (2018)
Classical molecular interaction potentials: improved setup procedure in molecular dynamics simulations of proteins.,
, Proteins, 2001 Dec 1, Volume 45, p.428-37, (2001)
Nucleic acids in modern molecular therapies: A realm of opportunities for strategic drug design,
, Current Opinion in Structural Biology, 08/2024, Volume 87, p.102838, (2024)
Controlled sulfur-based engineering confers mouldability to phosphorothioate antisense oligonucleotides,
, Nucleic Acids Research, 06/2023, Volume 51, Issue 10, p.4713 - 4725, (2023)
Inntags: small self-structured epitopes for innocuous protein tagging.,
, Nat Methods, 2015 Oct, Volume 12, p.955-8, (2015)
The structural role of SARS-CoV-2 genetic background in the emergence and success of spike mutations: The case of the spike A222V mutation,
, PLOS Pathogens, 07/2022, Volume 18, Issue 7, p.e1010631 - , (2022)
Essential role of glutamate 317 in galactosyl transfer by α3GalT: a computational study.,
, Carbohydr Res, 2012 Jul 15, Volume 356, p.204-8, (2012)
QM/MM Studies Reveal How Substrate–Substrate and Enzyme–Substrate Interactions Modulate Retaining Glycosyltransferases Catalysis and Mechanism,
, Advances in Protein Chemistry and Structural Biology, Volume 100, p.-, (2015)
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)
QM/MM Studies Reveal How Substrate–Substrate and Enzyme–Substrate Interactions Modulate Retaining Glycosyltransferases Catalysis and Mechanism,
, Advances in Protein Chemistry and Structural Biology, p.-, (2015)
Chapter 7 Molecular Modelling of Nucleic Acids,
, Computational Tools for Chemical Biology, p.165 - 197, (2017)
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)
Effect of zinc and calcium ions on the rat kidney membrane-bound form of dipeptidyl peptidase IV.,
, J Biosci, 2013 Sep, Volume 38, p.461-9, (2013)
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)
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)
DNAlive: a tool for the physical analysis of DNA at the genomic scale.,
, Bioinformatics, 2008 Aug 1, Volume 24, p.1731-2, (2008)