Biblio
Exploring the reasons for the large density of triplex-forming oligonucleotide target sequences in the human regulatory regions.,
, BMC Genomics, 2006, Volume 7, p.63, (2006)
Determining promoter location based on DNA structure first-principles calculations.,
, Genome Biol, 2007, Volume 8, p.R263, (2007)
The Yottaflop Frontier of Atomistic Molecular Dynamics Simulations,
, Theoretical and Quantum Chemistry at the Dawn of the 21st Century, p.597-616, (2018)
Triplex-forming oligonucleotide target sequences in the human genome.,
, Nucleic Acids Res, 2004, Volume 32, p.354-60, (2004)
Characterization of p38α autophosphorylation inhibitors that target the non-canonical activation pathway,
, Nature Communications, 06/2023, Volume 14, Issue 1, p.3318, (2023)
Molecular stripping underpins derepression of a toxin–antitoxin system,
, Nat Struct Mol Biol, 2024/03/27, (2024)
The catalytic site structural gate of adenosine deaminase allosterically modulates ligand binding to adenosine receptors.,
, FASEB J, 2013 Mar, Volume 27, p.1048-61, (2013)
8-Amino guanine accelerates tetramolecular G-quadruplex formation.,
, Chem Commun (Camb), 2008 Jul 7, p.2926-8, (2008)
Seven-Membered Ring Nucleoside Analogues: Stereoselective Synthesis and Studies on Their Conformational Properties,
, Organic Letters, 11/2015, Volume 17, Issue 21, p.5416 - 5419, (2015)
Cooperativity in Drug-DNA Recognition: A Molecular Dynamics Study,
, Journal of the American Chemical Society, 2001/12/01, Volume 123, Issue 50, p.12658 - 12663, (2001)
Misincorporation of 2'-deoxyoxanosine into DNA: a molecular basis for NO-induced mutagenesis derived from theoretical calculations,
, Nucleic Acids Research, Volume 28, p.4873-4883, (2000)
Deficient Endoplasmic Reticulum-Mitochondrial Phosphatidylserine Transfer Causes Liver Disease,
, Cell, 05/2019, Volume 177, Issue 4, p.881 - 895.e17, (2019)
Epigenomic analysis detects aberrant super-enhancer DNA methylation in human cancer,
, Genome Biology, 01/2016, Volume 17, p.11, (2016)
Surviving the deluge of biosimulation data,
, Wiley Interdisciplinary Reviews: WIREs Comput Mol Sci, 11/2019, Volume n/a, Issue n/a, p.e1449, (2019)
High-throughput molecular dynamics simulations: toward a dynamic view of macromolecular structure,
, Wiley Interdisciplinary Reviews: Computational Molecular Science, Volume 3, p.364–377, (2013)
BIGNASim: a NoSQL database structure and analysis portal for nucleic acids simulation data.,
, Nucleic Acids Res, 2016 Jan 4, Volume 44, Issue D1, p.D272-8, (2016)
NAFlex: a web server for the study of nucleic acid flexibility.,
, Nucleic Acids Res, 2013 Jul, Volume 41, p.W47-55, (2013)
Molecular dynamics simulations: advances and applications.,
, Adv Appl Bioinform Chem, 2015, Volume 8, p.37-47, (2015)
MD-DATA: the legacy of the ABC Consortium,
, Biophysical Reviews, 04/2024, (2024)
MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations.,
, Bioinformatics, 2012 May 1, Volume 28, p.1278-9, (2012)
The Multiple Roles of Waters in Protein Solvation,
, The Journal of Physical Chemistry B, 01/2017, Issue Klaus Schulten Memorial Issue, (2017)
Benzoderivatives of nucleic acid bases as modified DNA building blocks.,
, J Phys Chem A, 2006 Jan 19, Volume 110, p.510-8, (2006)
Local aromaticity in natural nucleobases and their size-expanded benzo-fused derivatives.,
, J Phys Chem A, 2006 Nov 9, Volume 110, p.12249-58, (2006)
Conformational dynamics of the human propeller telomeric DNA quadruplex on a microsecond time scale.,
, Nucleic Acids Res, 2013 Feb 1, Volume 41, p.2723-35, (2013)
Parmbsc1: a refined force field for DNA simulations.,
, Nat Methods, 2016 Jan, Volume 13, p.55-8, (2016)
Ligand-induced formation of transient dimers of mammalian 12/15-lipoxygenase: a key to allosteric behavior of this class of enzymes?,
, Proteins, 2012 Mar, Volume 80, p.703-12, (2012)
Quantification of Pathway Cross-talk Reveals Novel Synergistic Drug Combinations for Breast Cancer,
, Cancer Research, 01/2017, Volume 77, Issue 2, p.459, (2017)
Consistent View of Protein Fluctuations from All-Atom Molecular Dynamics and Coarse-Grained Dynamics with Knowledge-Based Force-Field,
, Journal of Chemical Theory and Computation, 2013/01/08, Volume 9, Issue 1, p.119 - 125, (2012)
Epigenetic loss of RNA-methyltransferase NSUN5 in glioma targets ribosomes to drive a stress adaptive translational program,
, Acta neuropathologica, 12/2019, Volume 138, Issue 6, p.1053 - 1074, (2019)
A deletion at ADAMTS9-MAGI1 locus is associated with psoriatic arthritis risk.,
, Ann Rheum Dis, 2015 Oct, Volume 74, p.1875-81, (2015)
A genome-wide association study on a southern European population identifies a new Crohn’s disease susceptibility locus at RBX1-EP300.,
, Gut, 2013 Oct, Volume 62, p.1440-5, (2013)
Risk variants for psoriasis vulgaris in a large case-control collection and association with clinical subphenotypes.,
, Hum Mol Genet, 2012 Oct 15, Volume 21, p.4549-57, (2012)
A genome-wide association study identifies SLC8A3 as a susceptibility locus for ACPA-positive rheumatoid arthritis.,
, Rheumatology (Oxford), 2016 Jun, Volume 55, p.1106-11, (2016)
A genome-wide association study identifies a novel locus at 6q22.1 associated with ulcerative colitis.,
, Hum Mol Genet, 2014 Dec 20, Volume 23, p.6927-34, (2014)
Theoretical study of the mechanisms of substrate recognition by catalase.,
, J Am Chem Soc, 2001 Oct 3, Volume 123, p.9665-72, (2001)
DNA double-strand break-derived RNA drives TIRR/53BP1 complex dissociation,
, Cell Reports, 10/2022, Volume 41, Issue 4, (2022)
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)
Inhibition of Human Enhancer of Zeste Homolog 2 with Tambjamine Analogs,
, Journal of Chemical Information and Modeling, 08/2017, (2017)
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)
Epigenomic analysis detects widespread gene-body DNA hypomethylation in chronic lymphocytic leukemia.,
, Nat Genet, 2012 Nov, Volume 44, p.1236-42, (2012)
Changes in the free-energy landscape of p38α MAP kinase through its canonical activation and binding events as studied by enhanced molecular dynamics simulations,
, eLife, 04/2017, Volume 6, p.e22175, (2017)
An In-Depth Look at DNA Crystals through the Prism of Molecular Dynamics Simulations,
, Chem, 03/2019, Volume 5, Issue 3, p.649 - 663, (2019)
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)
Nucleic acid simulations themed issue.,
, Phys Chem Chem Phys, 2009 Dec 7, Volume 11, p.10541-2, (2009)
COCO: a simple tool to enrich the representation of conformational variability in NMR structures.,
, Proteins, 2009 Apr, Volume 75, p.206-16, (2009)
A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA.,
, Nucleic Acids Res, 2010 Jan, Volume 38, p.299-313, (2010)
Proton Dynamics in Protein Mass Spectrometry,
, The Journal of Physical Chemistry Letters, 03/2017, Volume 8, Issue 6, p.1105 - 1112, (2017)
PMut: a web-based tool for the annotation of pathological variants on proteins, 2017 update,
, Nucleic Acids Research, 04/2017, Volume 45, Issue W1, p.W222-W228, (2017)
Correlated motions in DNA: beyond base-pair step models of DNA flexibility,
, Nucleic Acids Research, 06/2023, Volume 51, Issue 6, p.2633 - 2640, (2023)
Polarization effects in molecular interactions,
, WIREs Comput Mol Sci, 2011, Volume 1, p.844 - 854, (2011)