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The ff94 force field that is commonly associated with the Amber simulation package is one of the most widely used parameter sets for biomolecular simulation. After a decade of extensive use and testing, limitations in this force field, such as over-stabilization of alpha-helices, were reported by us and other researchers. This led to a number of attempts to(More)
Type 3 neuronopathic Gaucher's disease (GD3) is phenotypically heterogeneous. In many GD3 patients, progressive myoclonus and dementia dominate the illness, with death secondary to progressive CNS disease. We have designated this group as GD3a. We studied 14 children with Gaucher's disease, isolated horizontal supranuclear gaze palsy, and aggressive(More)
Alchemical free energy calculations hold increasing promise as an aid to drug discovery efforts. However, applications of these techniques in discovery projects have been relatively few, partly because of the difficulty of planning and setting up calculations. Here, we introduce lead optimization mapper, LOMAP, an automated algorithm to plan efficient(More)
Although many popular docking programs include a facility to account for covalent ligands, large-scale systematic docking validation studies of covalent inhibitors have been sparse. In this paper, we present the development and validation of a novel approach for docking and scoring covalent inhibitors, which consists of conventional noncovalent docking,(More)
Niemann-Pick disease type C (NP-C) is a neurovisceral lipidosis characterized by defective intracellular trafficking of cholesterol and lysosomal accumulation of unesterified cholesterol, believed to be an offending metabolite. We studied the effect of cholesterol-lowering agents on hepatic and plasma cholesterol levels in NP-C by randomly assigning 25(More)
Due to its fundamental importance to molecular biology, great interest has continued to persist in developing novel techniques to efficiently characterize the thermodynamic and structural features of liquid water. A particularly fruitful approach, first applied to liquid water by Lazaridis and Karplus, is to use molecular dynamics or Monte Carlo simulations(More)
LDL cholesterol (LDL-C) is cleared from plasma via cellular uptake and internalization processes that are largely mediated by the low-density lipoprotein cholesterol receptor (LDL-R). LDL-R is targeted for lysosomal degradation by association with proprotein convertase subtilisin-kexin type 9 (PCSK9). Gain of function mutations in PCSK9 can result in(More)
assisted with the data collection and quality assurance. Programming for the Web survey and data analysis was supervised and Linda Gentzik assisted with the programming and data analysis. Roy Grisham edited the report and Gloria Gustus and Rosita Turkel prepared the final report.
Predicting protein-ligand binding free energies is a central aim of computational structure-based drug design (SBDD)--improved accuracy in binding free energy predictions could significantly reduce costs and accelerate project timelines in lead discovery and optimization. The recent development and validation of advanced free energy calculation methods(More)
AIMS The Questionnaire for Urinary Incontinence Diagnosis (QUID), a 6-item urinary incontinence (UI) symptom questionnaire, was developed and validated to distinguish stress and urge UI. This study's objective was to evaluate QUID validity and responsiveness when used as a clinical trial outcome measure. METHODS Participants enrolled in a multi-center(More)