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Dyall K.G.,Schrodinger
Theoretical Chemistry Accounts | Year: 2011

Relativistic basis sets of double-zeta, triple-zeta, and quadruple-zeta quality have been optimized for the 6d elements Rf-Cn. The basis sets include SCF exponents for the occupied spinors and for the 7p shell; exponents of correlating functions for the valence shell, the 6s and 6p shells, and the 5f shell; and exponents of functions for dipole polarization of the 6d shell. A finite nuclear size was used in all optimizations. Prescriptions are given for constructing contracted basis sets. The use of the basis sets is demonstrated for some atomic and molecular systems. The basis sets are available as an Internet archive and from the Dirac program Web site, http://dirac.chem.sdu.dk. © 2011 Springer-Verlag.

Chaudhary D.,Nimbus Discovery | Robinson S.,Schrodinger | Romero D.L.,Nimbus Discovery
Journal of Medicinal Chemistry | Year: 2015

IRAK4, a serine/threonine kinase, plays a key role in both inflammation and oncology diseases. Herein, we summarize the compelling biology surrounding the IRAK4 signaling node in disease, review key structural features of IRAK4 including selectivity challenges, and describe efforts to discover clinically viable IRAK4 inhibitors. Finally, a view of knowledge gained and remaining challenges is provided. © 2014 American Chemical Society.

Van Wullen C.,Schrodinger
Zeitschrift fur Physikalische Chemie | Year: 2010

This work describes the implementation of an efficient two-component quasirelativistic density functional and Hartree-Fock program. The fact that the basis functions are real can be exploited if a special internal representation of operators and density matrices is used. This also leads to a considerable reduction of the effort in the closed shell case. While in most applications to open shell molecules, the noncoLlinear approach to define a relativistic spin density is preferable, the collinear approach finds its application in the calculation of magnetic anisotropy energies. Linear algebra steps in the SCF procedure have a higher relative weight compared to the nonrelativistic case, therefore some care was necessary to make them fast when parallelizing the code. The quasirelativistic Hamiltonians that have been implemented are the 'zeroth-order regular approximation' (ZORA) Hamiltonian, the Douglas-Kroll-Hess Hamiltonian up to the sixth order, together with an accurate approximation to treat the picture change effect of the electron interaction, and effective core potential (ECP) matrix elements. Geometry gradients are available for the ZORA and ECP methods. © by Oldenbourg Wissenschaftsverlag.

Methods for assessing the consistency and reliability of the calculations using cycle closures in relative binding free energy calculation paths. The methods are used for determining relative strength of binding between a receptor and individual members of a set ligands to form complexes between individual ligand set members and the receptor, in which the binding free energy difference with the lowest error is determined by probabilistic determination of the free energy differences and error distributions about those differences along each of the legs of the closed thermodynamic cycle that probabilistically lead to the hysteresis(es) value(s) observed for each closed of the closed thermodynamic cycle.

A method and system for calculating the free energy difference between a target state and a reference state. The method includes determining one or more intermediate states using a coupling parameter, performing molecular simulations to obtain ensembles of micro-states for each of the system states, and calculating the free energy difference by an analysis of the ensembles of micro-states of the system states. The method can be particularly suited for calculating physical or non-physical transformation of molecular systems such as ring-opening, ring-closing, and other transformations involving bond breaking and/or formation. A soft bond potential dependent on a bond stretching component of the coupling parameter and different from the conventional harmonic potential is used in the molecular simulations of the system states for the bond being broken or formed during the transformation.

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