User profiles for T. Steinbrecher

Thomas Steinbrecher

Schrödinger GmbH
Verified email at schrodinger.com
Cited by 14168

The biomechanics of seed germination

T Steinbrecher… - Journal of Experimental …, 2017 - academic.oup.com
From a biomechanical perspective, the completion of seed (and fruit) germination depends
on the balance of two opposing forces: the growth potential of the embryonic axis (radicle–…

[PDF][PDF] Amber 10

…, J Vanicek, X Wu, SR Brozell, T Steinbrecher… - 2008 - infoscience.epfl.ch
… For reasons we don’t understand, some MPI implementations require a null file for stdin,
even though sander doesn’t take any input from there. This is true for some SGI and HP …

Towards accurate free energy calculations in ligand protein-binding studies

T Steinbrecher, A Labahn - Current medicinal chemistry, 2010 - ingentaconnect.com
… The state of the system at any time t can be derived from a given starting conformation via
a … T. Koslowski for a critical read of the manuscript and many helpful suggestions. Financial …

Accurate and reliable prediction of relative ligand binding potency in prospective drug discovery by way of a modern free-energy calculation protocol and force field

…, JL Knight, T Steinbrecher, T Beuming… - Journal of the …, 2015 - ACS Publications
Designing tight-binding ligands is a primary objective of small-molecule drug discovery. Over
the past few decades, free-energy calculations have benefited from improved force fields …

[HTML][HTML] Tissue and cellular mechanics of seeds

T Steinbrecher, G Leubner-Metzger - Current Opinion in Genetics & …, 2018 - Elsevier
Distinct plant seed/fruit structures evolved to support reproduction and dispersal in distinct
environments. Appropriate biomechanical properties and interactions of the various seed …

Nonlinear scaling schemes for Lennard-Jones interactions in free energy calculations

T Steinbrecher, DL Mobley, DA Case - The Journal of chemical physics, 2007 - pubs.aip.org
Alchemical free energy calculations provide a means for the accurate determination of free
energies from atomistic simulations and are increasingly used as a tool for computational …

Revised AMBER parameters for bioorganic phosphates

T Steinbrecher, J Latzer, DA Case - Journal of chemical theory …, 2012 - ACS Publications
We report AMBER force field parameters for biological simulations involving phosphorylation
of serine, threonine, or tyrosine. The initial parameters used RESP fitting for the atomic …

Soft‐core potentials in thermodynamic integration: Comparing one‐and two‐step transformations

T Steinbrecher, IS Joung… - Journal of computational …, 2011 - Wiley Online Library
… 1, and 6 for t, s, and n of eq. (2), respectively.[17] We will keep the t and s values unchanged
… where σ ∂V/∂λ is the standard deviation, τ is the autocorrelation time of ∂V/∂λ, and t sim …

Large-scale assessment of binding free energy calculations in active drug discovery projects

…, K Schiemann, R Schulz, T Steinbrecher… - Journal of Chemical …, 2020 - ACS Publications
… Experimental affinities were converted to ΔG values using the equation ΔG exp ≈ k B T
log IC 50 . FEP+ accuracy varies between different targets and chemical series. Predictions …

DELAY OF GERMINATION 1 mediates a conserved coat-dormancy mechanism for the temperature- and gibberellin-dependent control of seed germination

K Graeber, A Linkies, T Steinbrecher… - Proceedings of the …, 2014 - National Acad Sciences
Seed germination is an important life-cycle transition because it determines subsequent
plant survival and reproductive success. To detect optimal spatiotemporal conditions for …