Accurate calculation of hydration free energies using macroscopic solvent models

D Sitkoff, KA Sharp, B Honig - The Journal of Physical Chemistry, 1994 - ACS Publications
A reliable theoreticaltreatment of chemical processes which occur in aqueous solution
requires accurate methods for calcu-lating solvation free energies. A number of theoretical …

Accurate first principles calculation of molecular charge distributions and solvation energies from ab initio quantum mechanics and continuum dielectric theory

…, R Murphy, RA Friesner, D Sitkoff… - Journal of the …, 1994 - ACS Publications
In this paper, we combine high-level ab initio quantum chemical calculations with a continuum
description of the solvent to obtain accurate solvation free energies of organic solutes in …

New model for calculation of solvation free energies: correction of self-consistent reaction field continuum dielectric theory for short-range hydrogen-bonding effects

…, RB Murphy, MN Ringnalda, D Sitkoff… - The Journal of …, 1996 - ACS Publications
We present self-consistent reaction field (SCRF) calculations, utilizing correlated ab initio
quantum mechanics, of aqueous solvation free energies for a large data base of molecular …

Calculation of alkane to water solvation free energies using continuum solvent models

D Sitkoff, N Ben-Tal, B Honig - The Journal of Physical Chemistry, 1996 - ACS Publications
The FDPB/γ method and the PARSE parameter set have been recently shown to provide a
computationally efficient and accurate means of calculating hydration free energies. In this …

Theories of chemical shift anisotropies in proteins and nucleic acids

D Sitkoff, DA Case - Progress in nuclear magnetic resonance spectroscopy, 1998 - Elsevier
This review examines our theoretical understanding of the origins of chemical shift anisotropy
(CSA) in proteins and nucleic acids, based on theories for environmental and solvation …

Density functional calculations of proton chemical shifts in model peptides

D Sitkoff, DA Case - Journal of the American Chemical Society, 1997 - ACS Publications
Density-functional chemical shielding calculations are reported for the alanine dipeptide with
a variety of backbone torsion angles and for methane and N-methylacetamide complexes …

A comparative study of available software for high‐accuracy homology modeling: From sequence alignments to structural models

A Nayeem, D Sitkoff, S Krystek Jr - Protein Science, 2006 - Wiley Online Library
An open question in protein homology modeling is, how well do current modeling packages
satisfy the dual criteria of quality of results and practical ease of use? To address this …

Pharmacologic profile of the Adnectin BMS-962476, a small protein biologic alternative to PCSK9 antibodies for low-density lipoprotein lowering

T Mitchell, G Chao, D Sitkoff, F Lo… - … of Pharmacology and …, 2014 - ASPET
Proprotein convertase subtilisin kexin-9 (PCSK9) is an important pharmacological target for
decreasing low-density lipoprotein (LDL) in cardiovascular disease, although seemingly …

Free energy of amide hydrogen bond formation in vacuum, in water, and in liquid alkane solution

N Ben-Tal, D Sitkoff, IA Topol, AS Yang… - The Journal of …, 1997 - ACS Publications
The energy of dimerization of two N-methylacetamide (NMA) molecules in vacuum is calculated
using density functional theory. Natural orbital analysis suggests that the dimerization …

Synthesis of novel potent dipeptidyl peptidase IV inhibitors with enhanced chemical stability: interplay between the N-terminal amino acid alkyl side chain and the …

…, A Wang, M Cap, L Xin, L Tao, DF Sitkoff… - Journal of medicinal …, 2004 - ACS Publications
A series of methanoprolinenitrile-containing dipeptide mimetics were synthesized and assayed
as inhibitors of the N-terminal sequence-specific serine protease dipeptidyl peptidase IV (…