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M Stahl

Publications and source records attributed to M Stahl.

At least 37 records · Page 2Linked to original sources
PubMed2001

Detailed analysis of scoring functions for virtual screening.

We present a comprehensive study of the performance of fast scoring functions for library docking using the program FlexX as the docking engine. Four scoring functions, among them two recently developed knowledge-based potentials, are evaluated on seven target proteins whose binding sites represent a wide range of size, form, and polarity. The results of these calculations give valuable insight into strengths and weaknesses of current scoring functions. Furthermore, it is shown that a well-chosen combination of two of the tested scoring functions leads to a new, robust scoring scheme with superior performance in virtual screening.

Databases, Factual↗
PubMed2001

Growth and recombination of phage lambda in the presence of exonuclease V from Bacillus subtilis.

When expressed in Escherichia coli, the AddAB exonuclease/recombinase from Bacillus subtilis blocks the growth of phage lambda. Mutants of lambda that are deleted for ea47, a gene of unknown function which is expressed early in the lytic cycle, are not blocked for growth. The blocked-growth phenotype of lambda ea47+ in the presence of AddAB is expressed only when phage DNA replication is permitted.

Bacillus subtilis↗
PubMed2001

Similarity searching in large combinatorial chemistry spaces.

We present a novel algorithm, called Ftrees-FS, for similarity searching in large chemistry spaces based on dynamic programming. Given a query compound, the algorithm generates sets of compounds from a given chemistry space that are similar to the query. The similarity search is based on the feature tree similarity measure representing molecules by tree structures. This descriptor allows handling combinatorial chemistry spaces as a whole instead of looking at subsets of enumerated compounds. Within few minutes of computing time, the algorithm is able to find the most similar compound in very large spaces as well as sets of compounds at an arbitrary similarity level. In addition, the diversity among the generated compounds can be controlled. A set of 17,000 fragments of known drugs, generated by the RECAP procedure from the World Drug Index, was used as the search chemistry space. These fragments can be combined to more than 10(18) compounds of reasonable size. For validation, known antagonists/inhibitors of several targets including dopamine D4, histamine H1, and COX2 are used as queries. Comparison of the compounds created by Ftrees-FS to other known actives demonstrates the ability of the method to jump between structurally unrelated molecule classes.

Algorithms↗
PubMed2001

Optimization of preanalytical conditions and analysis of plasma glucose. 1. Impact of the new WHO and ADA recommendations on diagnosis of diabetes mellitus.

The new diagnostic criteria for type 2 diabetes from the American Diabetes Association (ADA) and World Health Organization (WHO) recommend measurements on plasma and a lowering of the glucose threshold for diabetes by 0.8 mmol/L. This narrows the distance between the upper end of the reference limit and the discriminatory level to a degree where analytical quality becomes critical. The quality demands for the preanalytical and analytical phase and their consequences on diagnostic performance have to be established in the new technical system, measuring in plasma rather than in capillary whole blood. Because of the instability of glucose in blood samples it is necessary to clarify the influence of different preanalytical and analytical factors on the number of false-positive and false-negative classifications. Thus the aim of the present study was to find optimal conditions for sampling, additives, storage, transport and analysis of plasma glucose combining feasibility with an analytical bias close to zero and a within-imprecision around 1%. We have documented the analytical performance of the method itself and its traceability to an international standard. The preanalytical conditions, such as influence of antiglycolytic agent NaF, conditions for plasma separation, storage temperature and storage time before and after plasma separation were investigated. In conclusion, we recommend that blood should be drawn in tubes containing heparin and NaF and kept on ice water for not more than 1 h until centrifugation at minimum 1000 x g for 10 min. The plasma is then stable for at least 48 h at room temperature.

Anticoagulants↗
PubMed2001

Plasma glucose reference interval in a low-risk population. 2. Impact of the new WHO and ADA recommendations on the diagnosis of diabetes mellitus.

The aim of the study was to establish a reference interval of fasting venous plasma glucose (FPG) from healthy individuals. A prospective modified cross-sectional population-based study was made with random selection of 2100 persons in age-stratified groups > or = 18 years identified from the local Personal Identification Register. The invitation was accepted by 755 persons, of which 726 aged 18-92 years were eligible. They did not have a diabetes diagnosis, were non-pregnant and capable of fasting for 8 h. All participants filled in a questionnaire on medical risk factors. Blood for the FPG and haemoglobin Alc (HbAlc) measurements was drawn in accordance with a standardized procedure. A total of 302 participants carried diabetes risk indicators and were ruled out. The FPG concentrations in the remaining low-risk population (n=424) was ln Gaussian distributed. The FPG 97.50 centile in this group was 6.4 mmol/L (95% CI: 6.3-6.5 mmol/L), in contrast to the WHO and ADA theoretical limit of 6.1 mmol/L. Their diagnostic decision limit of 7.0 mmol/L FPG corresponded to the 99.86 centile of the FPG reference distribution (95% CI: 6.8-7.1). Subclassification of the reference population showed increasing FPG with increasing BMI and age and was higher in men than in women. The study determined the FPG 95% interfractile reference interval in a healthy population. The interval in glucose concentration between the 97.5 centile of the reference interval and the ADA-WHO diagnostic limit is very narrow. The clinical application of the diagnostic discriminator and the interpretation of the WHO-ADA grey zone from 6.1 to 7.0 mmol/L FPG may consequently be biased because of poorly defined limits and influence from BMI, age and gender.

Adolescent↗
PubMed2001

Evaluation of systematic and random factors in measurements of fasting plasma glucose as the basis for analytical quality specifications in the diagnosis of diabetes. 3. Impact of the new WHO and ADA recommendations on diagnosis of diabetes mellitus.

On behalf of the Danish Society of Clinical Endocrinology and the Danish Society of Clinical Chemistry we were commissioned to evaluate the influence of analytical and pre-analytical systematic and random factors on the diagnosis of diabetes, in order to provide a tool for conclusions on the analytical quality specifications needed to diagnose diabetes. A systems analysis was performed in accordance with the principles for evaluation of analytical quality specifications. The clinical setting was defined--diagnosis of diabetes in accordance with the WHO and ADA criteria with determination of fasting plasma glucose concentration (FPG) > or =7.0 mmol/L in two independent samples--with well-documented data on In (loge)-Gaussian distribution of reference values from a low-risk population and values for within-subject biological variation taken from the literature. An investigation was made of the consequences for the clinical setting of assumed errors related to the measurement of FPG. Four approaches were investigated for a single sampling and measurement and also for two independent samples: one showing the percentage of healthy individuals who had values > or = 7.0 mmol/L, one illustrating the origin of biological set-points for results > or = 7.0 mmol/L, one showing the risk of being measured > or =7.0 mmol/L when the biological set-point is known, and one showing the combined bias and imprecision for assumed percentages of false-positive (FP), defined as measurements > or = 7.0 mmol/L for the low-risk population and false-negative (FN), defined as measurements <6.4 mmol/L (the upper reference limit) for diabetics. This leaves a "grey zone" which includes the upper part of low-risk individuals, and defined by ADA and WHO as "impaired fasting glucose" (IFG). In the analysis, increasing systematic and random errors (combined analytical and pre-analytical) were assumed, and for each error condition the fractions of FP and FN were calculated. This gave plots from which the combined allowable systematic and random errors could be read off for pre-determined clinically acceptable fractions of FP and FN. The analysis does not distinguish between pre-analytical and analytical errors, as specified information on one of these is needed for specification of the other. The investigation provides a reliable basis for estimation of the needed analytical quality, and thereby for decisions about analytical quality specifications for analysis of FPG in relation to diagnosis of diabetes under optimized pre-analytical and analytical conditions. Consequences of deviations from these ideal conditions are illustrated in the figures, and should be considered for the different approaches with different performance conditions.

Blood Glucose↗
PubMed2001

Failure of root coverage of shallow gingival recessions employing GTR and a bioresorbable membrane.

The aim of the present study was to compare the postsurgical outcome of two different modes of surgical root coverage of predominantly shallow, Class I or II, gingival recessions. Fourteen facial recessions in nine patients were subjected to a coronally repositioned flap in combination with a bioresorbable membrane, and 14 sites in 13 patients were treated with a connective tissue graft employing an envelope technique. Immediately before surgery and after 6 and 12 months, gingival dimensions as well as root coverage and attachment gain were assessed. At baseline, mean recession depths amounted to 2.77+/-1.67 mm and 2.49+/-1.07 mm for patients treated with a bioresorbable membrane and a free connective tissue graft, respectively. Acceptable and stable root coverage of 81% to 82% of baseline recession depth and 78% of its width was achieved by grafting. In contrast, guided tissue regeneration (GTR) resulted in only 50% coverage of recession depth and, after 12 months, only 11% of its width (P < 0.01). Logistic regression revealed that the odds of obtaining success, ie, at least 80% root coverage, were 3.3 times greater in cases treated with a connective tissue graft (P < 0.05). In addition, the odds ratio was 2.3 in cases of recessions below 2.5 mm compared to deeper recessions and 2 at canines compared to premolars. It was concluded that shallow recessions in the 1.5 to 3.5 mm range should not be treated with GTR. In these situations, predictable results are achieved with free connective tissue grafts employing an envelope technique.

Absorbable Implants↗
PubMed2000

Crystal structures of substrate binding to Bacillus subtilis holo-(acyl carrier protein) synthase reveal a novel trimeric arrangement of molecules resulting in three active sites.

BACKGROUND: Holo-(acyl carrier protein) synthase (AcpS), a member of the phosphopantetheinyl transferase superfamily, plays a crucial role in the functional activation of acyl carrier protein (ACP) in the fatty acid biosynthesis pathway. AcpS catalyzes the attachment of the 4'-phosphopantetheinyl moiety of coenzyme A (CoA) to the sidechain of a conserved serine residue on apo-ACP. RESULTS: We describe here the first crystal structure of a type II ACP from Bacillus subtilis in complex with its activator AcpS at 2.3 A. We also have determined the structures of AcpS alone (at 1.8 A) and AcpS in complex with CoA (at 1.5 A). These structures reveal that AcpS exists as a trimer. A catalytic center is located at each of the solvent-exposed interfaces between AcpS molecules. Site-directed mutagenesis studies confirm the importance of trimer formation in AcpS activity. CONCLUSIONS: The active site in AcpS is only formed when two AcpS molecules dimerize. The addition of a third molecule allows for the formation of two additional active sites and also permits a large hydrophobic surface from each molecule of AcpS to be buried in the trimer. The mutations Ile5-->Arg, Gln113-->Glu and Gln113-->Arg show that AcpS is inactive when unable to form a trimer. The co-crystal structures of AcpS-CoA and AcpS-ACP allow us to propose a catalytic mechanism for this class of 4'-phosphopantetheinyl transferases.

Acyl Carrier Protein↗
PubMed2000

[Chemotherapy in colorectal carcinoma. From "one-drug-show" to therapeutic multiplicity].

Over the past decade, the chemotherapeutic options in the treatment of colorectal carcinoma have improved considerably. Up into the nineties, chemotherapy for this condition was purely a "one-drug show", while, today, a range of effective substances and combinations are available, and these have considerably improved the prognosis of this tumour entity. Both the first and second line treatments are today firmly established. Determination of the most appropriate sequence and combination of these new drugs (primary combination therapy, sequential administration of the substances, etc.) is the subject of ongoing and planned future studies.

Antineoplastic Combined Chemotherapy Protocols↗
PubMed2000

Charged residues dominate a unique interlocking topography in the heterodimeric cytokine interleukin-12.

Human interleukin-12 (IL-12, p70) is an early pro-inflammatory cytokine, comprising two disulfide-linked subunits, p35 and p40. We solved the crystal structures of monomeric human p40 at 2.5 A and the human p70 complex at 2.8 A resolution, which reveals that IL-12 is similar to class 1 cytokine-receptor complexes. They also include the first description of an N-terminal immunoglobulin-like domain, found on the p40 subunit. Several charged residues from p35 and p40 intercalate to form a unique interlocking topography, shown by mutagenesis to be critical for p70 formation. A central arginine residue from p35 projects into a deep pocket on p40, which may be an ideal target for a small molecule antagonist of IL-12 formation.

Arginine↗
PubMed2000

The bacterial cell-division protein ZipA and its interaction with an FtsZ fragment revealed by X-ray crystallography.

In Escherichia coli, FtsZ, a homologue of eukaryotic tubulins, and ZipA, a membrane-anchored protein that binds to FtsZ, are two essential components of the septal ring structure that mediates cell division. Recent data indicate that ZipA is involved in the assembly of the ring by linking FtsZ to the cytoplasmic membrane and that the ZipA-FtsZ interaction is mediated by their C-terminal domains. We present the X-ray crystal structures of the C-terminal FtsZ-binding domain of ZipA and a complex between this domain and a C-terminal fragment of FtsZ. The ZipA domain is a six-stranded beta-sheet packed against three alpha-helices and contains the split beta-alpha-beta motif found in many RNA-binding proteins. The uncovered side of the sheet incorporates a shallow hydrophobic cavity exposed to solvent. In the complex, the 17-residue FtsZ fragment occupies this entire cavity of ZipA and binds as an extended beta-strand followed by alpha-helix. An alanine-scanning mutagenesis analysis of the FtsZ fragment was also performed, which shows that only a small cluster of the buried FtsZ side chains is critical in binding to ZipA.

Amino Acid Sequence↗
PubMed2000

De novo design of molecular architectures by evolutionary assembly of drug-derived building blocks.

An evolutionary algorithm was developed for fragment-based de novo design of molecules (TOPAS, TOPology-Assigning System). This stochastic method aims at generating a novel molecular structure mimicking a template structure. A set of approximately 25,000 fragment structures serves as the building block supply, which were obtained by a straightforward fragmentation procedure applied to 36,000 known drugs. Eleven reaction schemes were implemented for both fragmentation and building block assembly. This combination of drug-derived building blocks and a restricted set of reaction schemes proved to be a key for the automatic development of novel, synthetically tractable structures. In a cyclic optimization process, molecular architectures were generated from a parent structure by virtual synthesis, and the best structure of a generation was selected as the parent for the subsequent TOPAS cycle. Similarity measures were used to define 'fitness', based on 2D-structural similarity or topological pharmacophore distance between the template molecule and the variants. The concept of varying library 'diversity' during a design process was consequently implemented by using adaptive variant distributions. The efficiency of the design algorithm was demonstrated for the de novo construction of potential thrombin inhibitors mimicking peptide and non-peptide template structures.

Algorithms↗
PubMed2000

Dynamics of mucosal dimensions after root coverage with a bioresorbable membrane.

BACKGROUND: So far, the clinical effects of the placement of a resorbable membrane for guided tissue regeneration have not been studied in humans in great detail. The dynamics of the resorptive processes, in particular, appear to be rather speculative. In the present longitudinal study, specific alterations of the dimensions of the dentogingival mucosa were explored after surgical root coverage by using a bioresorbable membrane and a coronally-repositioned flap. METHODS: The study population consisted of 14 patients with a total of 31 predominantly shallow, Miller class I, II or III recessions. The thickness of the masticatory and lining mucosa before and after surgical intervention was measured with an ultrasonic device. RESULTS: Mean (+/-sd) recession depth and width were 2.85+/-1.29 and 4.46+/-1.14 mm, respectively. After 12 months, 51+/-29% of the recession depth (p<0.001) and 13+/-35% of its width (n.s.) were covered. Root coverage seems to be rather defect-type sensitive with best results obtained at canines with relatively shallow recessions. Mucosal thickness was considerably increased after surgery with a gradual decrease during the following 9 months. Thus, thickness of the marginal tissue rose from 0.82+/-0.27 mm to 1.49+/-0.54 mm 3 months after placement of the membrane (p<0.001). After 12 months, a mean thickness of 1.03+/-0.40 mm was observed (p<0.001). Even more pronounced alterations were noted for the alveolar lining mucosa with a threefold increase of thickness 3 months after surgery and a gradual decrease to about 1 mm after 12 months. CONCLUSIONS: The present results point to the considerable space making capacity of the bioresorbable membrane which probably allows for the ingrowth of a granulation tissue derived from the underlying structures. The gradual decline in mucosal thickness between months 6 and 9 after surgery may be paralleled by the maturation of the granulation tissue while complete resorption of the membrane had been accomplished.

Absorbable Implants↗
PubMed2000

Calcium channel blockers, ACE inhibitors, and the risk of cancer in hypertensive patients: a report from the Department of Health Hypertension Care Computing Project (DHCCP)

OBJECTIVE: Recent studies have shown inconsistent results on the risk of cancer in hypertensive patients using calcium channel blockers (CCBs) and angiotensin-converting enzyme (ACE) inhibitors. We investigated a large number of patients from the Department of Health Hypertension Care Computing Project (DHCCP) observational database treated with these drugs for hypertension to see whether the use of CCBs for hypertension is associated with an increased risk of cancer mortality and the use of ACE inhibitors with a reduction. DESIGN: Matched case-control study and a longitudinal study of survival from 1 year after presentation. PATIENTS: A total of 11663 patients treated for hypertension from 1971 through 1987. They were recruited on presentation to one of the hospital hypertension clinics or general practices involved. MAIN OUTCOME MEASURES: Death with any mention of cancer on the death certificate in patients treated with an Index drug group; CCBs, ACE inhibitors, beta adrenergic blocking drugs (BBs), or receiving a diuretic. The treatment groups were mutually exclusive. RESULTS: A total of 391 cases of cancer were matched with 1050 controls. In this case-control study the adjusted relative risk estimate in comparison to diuretic treatment for CCBs was 0.79 (95% CI 0.37 to 1.69), and for CCBs plus a diuretic, 1.05 (0.65 to 1.69). Non-significant results were also observed for ACE inhibitors (1.48 (0.43 to 5.1), and 1.40 (0.56 to 3.50) with a diuretic), and also for the BB and methyldopa groups. In the longitudinal survival study, the adjusted relative risk estimate for CCBs was 1.1 (0.60 to 1.94) and 1.0 (0.53 to 1.86) for CCBs plus a diuretic, and for ACE inhibitors 1.33 (0.37 to 4.76) and 1.47 (0.67 to 3.23), respectively. CONCLUSIONS: In this population there was no increased cancer mortality with the use of CCBs and a relative risk greater than 1.7 to 2.0 was excluded with 95% confidence. The suggestion that ACE inhibitors reduce cancer mortality was not supported with best estimates of relative risk of 1.3 to 1.5 and exclusion of values less than 0.4 to 0.7.

Adolescent↗
PubMed2000

Colorectal cancer and metastasectomy: treatment of advanced disease.

Systemic therapy of advanced colorectal cancer has become a well established and widely accepted approach for advanced colorectal cancer. The results of prospective randomised trials have demonstrated that first and second line chemotherapy improves the outcome compared with best supportive care. With modern chemotherapy concepts, objective response rates of 30-50% and median survival times of 14-17 months can be achieved which is a step ahead in the management of this disease. Moreover, first experiences with 'preoperative' chemotherapy in technically or prognostically not curatively resectable metastases indicate that active chemotherapy regimens may offer a chance for cure in some subsets of patients with liver metastases. It is still a matter of debate whether combination chemotherapy should be used upfront in all patients or whether the same outcome can be achieved with the sequential use of the available drugs. Ongoing and planned trials dedicated to these issues (preoperative therapy, sequential or combination chemotherapy, etc.) will hopefully contribute to a more differentiated and individualised use of the available treatment options.

Antineoplastic Agents↗
PubMed2000

Mapping of protein surface cavities and prediction of enzyme class by a self-organizing neural network.

An automated computer-based method for mapping of protein surface cavities was developed and applied to a set of 176 metalloproteinases containing zinc cations in their active sites. With very few exceptions, the cavity search routine detected the active site among the five largest cavities and produced reasonable active site surfaces. Cavities were described by means of solvent-accessible surface patches. For a given protein, these patches were calculated in three steps: (i) definition of cavity atoms forming surface cavities by a grid-based technique; (ii) generation of solvent accessible surfaces; (iii) assignment of an accessibility value and a generalized atom type to each surface point. Topological correlation vectors were generated from the set of surface points forming the cavities, and projected onto the plane by a self-organizing network. The resulting map of 865 enzyme cavities displays clusters of active sites that are clearly separated from the other cavities. It is demonstrated that both fully automated recognition of active sites, and prediction of enzyme class can be performed for novel protein structures at high accuracy.

Algorithms↗