Molecular dynamics (MD) simulation is a special discipline of molecular modelling. Based on molecular mechanics, it addresses numerical solutions of Newton's equations of motion on an atomistic or similar model of a molecular system to obtain information about its time-dependent properties.

Applications

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Beginning in theoretical physics, the method of MD gained popularity in material science and since the 1970s also in biochemistry and biophysics. In chemistry, MD serves as an important tool in protein structure determination and refinement (see also crystallography, NMR). In physics, MD is used to examine the dynamics of atomic-level phenomena that cannot be observed directly, such as thin film growth and ion-subplantation. It is also used to examine the physical properties of nanotechnology devices that have not or cannot yet be created.

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Clinical Chemistry current issue

[Editorials] Protein Quantitation through Targeted Mass Spectrometry: The Way Out of Biomarker Purgatory?
Carr, S. A., Anderson, L. Tue, 28 Oct 2008 00:00:00 -0000

[Editorials] Screening Algorithms for Monoclonal Gammopathies
Katzmann, J. A., Dispenzieri, A. Tue, 28 Oct 2008 00:00:00 -0000

[Perspective] Translating Hemoglobin A1c into Average Blood Glucose: Implications for Clinical Chemistry
Sacks, D. B. Tue, 28 Oct 2008 00:00:00 -0000

[Reviews] Current Status of Salivary Hormone Analysis
Groschl, M. Tue, 28 Oct 2008 00:00:00 -0000
Background: Saliva, which offers a noninvasive and stress-free alternative to plasma and serum, is a widely accepted sample source for analysis of steroids and also of certain amines and peptides. In recent years, numerous publications have described the use of salivary hormone analysis in many fields of clinical and basic research. Content: This review provides an overview of the current applications of salivary hormone analysis. A description of the different modes of hormone entry into saliva is followed by a detailed description of analytical methods and approaches for reliable collection of saliva, including several interesting applications in diverse fields including psychiatry, stress research, clinical endocrinology, sports medicine, and veterinary medicine. Summary: Although saliva has not yet become a mainstream sample source for hormone analysis, it has proven to be reliable and, in some cases, even superior to other body fluids. Nevertheless much effort will be required for this approach to receive acceptance over the long term, especially by clinicians. Such effort includes the development of specific and standardized analytical tools, the establishment of defined reference intervals, and implementation of round-robin trials. One major problem, the lack of compliance sometimes seen in outpatient saliva donors, requires strict standardization of both collection and analysis methods to achieve better comparability and assessment of published salivary hormone data.
[Reviews] A Personalized Approach to Cancer Treatment: How Biomarkers Can Help
Duffy, M. J., Crown, J. Tue, 28 Oct 2008 00:00:00 -0000
Background: The present approach to cancer treatment is often referred to as "trial and error" or "one size fits all." This practice is inefficient and frequently results in inappropriate therapy and treatment-related toxicity. In contrast, personalized treatment has the potential to increase efficacy and decrease toxicity. Content: We reviewed the literature relevant to prognostic, predictive, and toxicity-related markers in cancer, with particular attention to systematic reviews, prospective randomized trials, and guidelines issued by expert panels. To achieve personalized treatment for cancer, we need markers for determining prognosis, predicting response to therapy, and predicting severe toxicity related to treatment. Among the best-validated prognostic markers currently available are serum concentrations of -fetoprotein (AFP), human chorionic gonadotropin (hCG), and lactate dehydrogenase (LDH) for patients with nonseminoma germ cell tumors and tissue concentrations of both urokinase plasminogen activator and plasminogen activator inhibitor 1 (PAI-1) for breast cancer patients. Clinically useful therapy predictive markers are estrogen and progesterone receptors to select patients with breast cancer for treatment with endocrine therapy and human epidermal growth factor receptor 2 (HER-2) to select breast cancer patients for treatment with trastuzumab (Herceptin). Markers available for identifying drug-induced adverse reactions include thiopurine methyltransferase (TPMT) to predict toxicity from thiopurines in the treatment of acute lymphoblastic leukemia and uridine diphosphate glucuronyltransferase to predict toxicity from irinotecan in the treatment of colorectal cancer. Conclusions: Validated prognostic, predictive, and toxicity markers should help cancer treatment move from the current trial-and-error approach to more personalized treatment.
[Proteomics and Protein Markers] Impact of Epitope Specificity and Precursor Maturation in Pro-B-Type Natriuretic Peptide Measurement
Goetze, J. P., Dahlstrom, U., Rehfeld, J. F., Alehagen, U. Tue, 28 Oct 2008 00:00:00 -0000
Background: Cardiac-derived natriuretic peptides are sensitive plasma markers of cardiac dysfunction. Recent reports have disclosed a more complex molecular heterogeneity of B-type natriuretic peptide precursor (proBNP)-derived peptides than previously suggested. In this study, we examined the impact of epitope specificity and precursor maturation on plasma measurement of proBNP-derived peptides. Methods: We compared 2 assays, N-terminal proBNP and proBNP 1–76, in a randomly collected set of human plasma specimens (n = 370). Additionally, we evaluated the clinical performance of 4 assays with different epitope specificities in a cohort of elderly patients presenting with symptoms associated with heart failure (n = 415). Results: Comparison of N-terminal proBNP with proBNP 1–76 measurement in plasma revealed a high correlation on regression analysis (r2 = 0.91, P < 0.0001). Nevertheless, the proBNP 1–76 assay measured lower concentrations in the high range than the N-terminal proBNP assay. Correlations between assay measurements in a clinical setting were comparable for all the assays (r2 approximately 0.57–0.83), and ROC analyses revealed area-under-the-curve values ranging between 0.77 and 0.81 for identifying reduced left ventricular ejection fraction. In parallel, all assays displayed comparable abilities in predicting long-term mortality. Conclusions: Our results reveal marked assay differences in analytical assay comparison, contrasting the overall comparable clinical performance in cardiovascular diagnostics or prognosis in the elderly.

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