Biblio
3dRS, a Web-Based Tool to Share Interactive Representations of 3D Biomolecular Structures and Molecular Dynamics Trajectories,
, Frontiers in Molecular Biosciences, 08/2021, Volume 8, p.795, (2021)
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)
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)
BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows,
, Nature Scientific Data, 09/2019, Volume 6, Issue 1, p.169, (2019)
BioExcel Building Blocks REST API (BioBB REST API), programmatic access to interoperable biomolecular simulation tools,
, Bioinformatics, 05/2022, Volume 38, Issue 12, p.3303, (2022)
BioExcel Building Blocks Workflows (BioBB-Wfs), an integrated web-based platform for biomolecular simulations,
, Nucleic Acids Res, 05/2022, Volume 50, Issue W1, p.W107, (2022)
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)
Coarse-grained representation of protein flexibility. Foundations, successes, and shortcomings.,
, Adv Protein Chem Struct Biol, 2011, Volume 85, p.183-215, (2011)
A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community),
, F1000Research, 04/2020, Volume 9, (2020)
A consensus view of protein dynamics.,
, Proc Natl Acad Sci U S A, 2007 Jan 16, Volume 104, p.796-801, (2007)
Developments and applications of the OPTIMADE API for materials discovery, design, and data exchange,
, Digital Discovery, 04/2024, p. - , (2024)
DFFR: A New Method for High-Throughput Recalibration of Automatic Force-Fields for Drugs,
, Journal of Chemical Theory and Computation, 08/2020, (2020)
DNA structure directs positioning of the mitochondrial genome packaging protein Abf2p,
, Nucleic Acids Research, 11/2016, (2016)
Exploration of conformational transition pathways from coarse-grained simulations.,
, Bioinformatics, 2013 Aug 15, Volume 29, p.1980-6, (2013)
Exploring The Conformational Landscape Of Bioactive Small Molecules,
, Journal of Chemical Theory and Computation, 08/2020, (2020)
A fast method for the determination of fractional contributions to solvation in proteins.,
, Protein Sci, 2006 Nov, Volume 15, p.2525-33, (2006)
Finding Conformational Transition Pathways from Discrete Molecular Dynamics Simulations,
, Journal of Chemical Theory and Computation, 2012/11/13, Volume 8, p.4707 - 4718, (2012)
FlexServ: an integrated tool for the analysis of protein flexibility.,
, Bioinformatics, 2009 Jul 1, Volume 25, p.1709-10, (2009)
High-throughput molecular dynamics simulations: toward a dynamic view of macromolecular structure,
, Wiley Interdisciplinary Reviews: Computational Molecular Science, Volume 3, p.364–377, (2013)
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)
How accurate are accurate force-fields for B-DNA?,
, Nucleic Acids Research, 01/2017, Volume 45, Issue 7, p.4217-4230, (2017)
How B-DNA Dynamics Decipher Sequence-Selective Protein Recognition,
, Journal of Molecular Biology, 07/2019, (2019)
Long-timescale dynamics of the Drew-Dickerson dodecamer.,
, Nucleic Acids Res, 2016 May 19, Volume 44, p.4052-66, (2016)
Making Canonical Workflow Building Blocks Interoperable across Workflow Languages,
, Data Intelligence, 2022, p.1 - 16, (2022)
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)
Mechanism of Structural Tuning of the Hepatitis C Virus Human Cellular Receptor CD81 Large Extracellular Loop,
, Structure, 01/2017, Volume 25, p.53-65, (2017)
MoDEL (Molecular Dynamics Extended Library): a database of atomistic molecular dynamics trajectories.,
, Structure, 2010 Nov 10, Volume 18, p.1399-409, (2010)
Modulation of the helical properties of DNA: next-to-nearest neighbour effects and beyond,
, 01/2019, (2019)
Molecular dynamics simulations: advances and applications.,
, Adv Appl Bioinform Chem, 2015, Volume 8, p.37-47, (2015)
Molecular Dynamics Study of Naturally Existing Cavity Couplings in Proteins,
, PLoS ONE, 2015/03/27, Volume 10, p.e0119978 -, (2015)
Molywood: streamlining the design and rendering of molecular movies,
, Bioinformatics, 06/2020, (2020)
A multi-modal coarse grained model of DNA flexibility mappable to the atomistic level,
, Nucleic Acids Research, 01/2020, (2020)
The Multiple Roles of Waters in Protein Solvation,
, The Journal of Physical Chemistry B, 01/2017, Issue Klaus Schulten Memorial Issue, (2017)
NAFlex: a web server for the study of nucleic acid flexibility.,
, Nucleic Acids Res, 2013 Jul, Volume 41, p.W47-55, (2013)
A new paradigm for molecular dynamics databases: the COVID-19 database, the legacy of a titanic community effort,
, Nucleic Acids Res, 04/2024, Volume 52, Issue D1, p.D393 - D403, (2024)
Nucleosome Dynamics: a new tool for the dynamic analysis of nucleosome positioning,
, Nucleic Acids Research, 08/2019, (2019)
Oncogenic mutations at the EGFR ectodomain structurally converge to remove a steric hindrance on a kinase-coupled cryptic epitope,
, Proceedings of the National Academy of Sciences, 04/2019, (2019)
Parmbsc1: a refined force field for DNA simulations.,
, Nat Methods, 2016 Jan, Volume 13, p.55-8, (2016)
Predicting the limit of intramolecular H-Bonding with classical molecular dynamics,
, Angewandte Chemie International Edition, 01/2019, (2019)
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)
A procedure for identifying homologous alternative splicing events.,
, BMC Bioinformatics, 2007, Volume 8, p.260, (2007)
The Role of Unconventional Hydrogen Bonds in Determining BII Propensities in B-DNA,
, The Journal of Physical Chemistry Letters, 01/01/2017, Volume 8, p.21 - 28, (2017)
Sequence-Dependent Properties of the RNA Duplex,
, Journal of Chemical Information and Modeling, 08/2023, Volume 63, Issue 16, p.5259 - 5271, (2023)
Sequence-dependent structural properties of B-DNA: what have we learned in 40 years?,
, Biophysical Reviews, 11/2021, (2021)
Small Details Matter: The 2′-Hydroxyl as a Conformational Switch in RNA,
, Journal of the American Chemical Society, 12/2016, Volume 138, Issue 50, p.16355 - 16363, (2016)
The static and dynamic structural heterogeneities of B-DNA: extending Calladine–Dickerson rules,
, Nucleic Acids Research, 10/2019, (2019)
Surviving the deluge of biosimulation data,
, Wiley Interdisciplinary Reviews: WIREs Comput Mol Sci, 11/2019, Volume n/a, Issue n/a, p.e1449, (2019)