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Results for “virtual screening”

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At least 793 records · Page 44Linked to original sources
PubMed2006

Tissue expression map of a large number of expressed sequence tags and its application to in silico screening of stress response genes in common wheat.

In order to assess global changes in gene expression patterns in stress-induced tissues, we conducted large-scale analysis of expressed sequence tags (ESTs) in common wheat. Twenty-one cDNA libraries derived from stress-induced tissues, such as callus, as well as liquid cultures and abiotic stress conditions (temperature treatment, desiccation, photoperiod, moisture and ABA) were constructed. Several thousand colonies were randomly selected from each of these 21 cDNA libraries and sequenced from both the 5' and 3' ends. By computing abundantly expressed ESTs, correlated expression patterns of genes across the tissues were monitored. Furthermore, the relationships between gene expression profiles among the stress-induced tissues were inferred from the gene expression patterns. Multi-dimensional analysis of EST data is analogous to microarray experiments. As an example, genes specifically induced and/or suppressed by cold acclimation and heat-shock treatments were selected in silico. Four hundred and ninety genes showing fivefold induction or 218 genes for suppression in comparison to the control expression level were selected. These selected genes were annotated with the BLAST search. Furthermore, gene ontology was conducted for these genes with the InterPro search. Because genes regulated in response to temperature treatment were successfully selected, this method can be applied to other stress-treated tissues. Then, the method was applied to screen genes in response to abiotic stresses such as drought and ABA treatments. In silico selection of screened genes from virtual display should provide a powerful tool for functional plant genomics.

Abscisic Acid↗
PubMed1983

Anion influence on the binding of divalent cations to phosphatidylcholine.

We have used the osmotic pressure technique of Rand, Parsegian and co-workers (Nature 259 (1976) 601-603) to investigate the effect of anion species on the binding of M2+ to dipalmitoylphosphatidylcholine bilayers. Calcium and magnesium salts show a complex behavior which is consistent with both anion binding and screening. We observe virtually no change, within the accuracy of our experiment, in the decay of repulsive pressure with inter-bilayer separation for the acetate and nitrate salts of magnesium and calcium; however, the chloride salt does show a different pressure decay. At any given bilayer separation, 35 A less than dw less than 75 A, with calcium and magnesium salts present, the anions produce a decrease in the repulsive pressure in the order acetate- greater than Cl- greater than NO-3.

Anions↗
PubMed2004

Sulfonyl-phenyl-ureido benzamidines; a novel structural class of potent antimalarial agents.

The high throughput in silico screening of a virtual library into the structure of the P. falciparum lactate dehydrogenase (LDH) with the 4SCan technology yielded a series of biphenyl urea compounds. These were chemically optimized to a new structural class of potent antimalarial agents. The compounds did not inhibit plasmodium LDH enough to fully explain their potency. Therefore we conclude that an unknown mode of action may be the cause of the antimalarial activity.

Animals↗
PubMed2006

Crystal structure of Bacillus cereus HlyIIR, a transcriptional regulator of the gene for pore-forming toxin hemolysin II.

Production of Bacillus cereus and Bacillus anthracis toxins is controlled by a number of transcriptional regulators. Here we report the crystal structure of B. cereus HlyIIR, a regulator of the gene encoding the pore-forming toxin hemolysin II. We show that HlyIIR forms a tight dimer with a fold and overall architecture similar to the TetR family of repressors. A remarkable feature of the structure is a large internal cavity with a volume of 550 A(3) suggesting that the activity of HlyIIR is modulated by binding of a ligand, which triggers the toxin production. Virtual ligand library screening shows that this pocket can accommodate compounds with molecular masses of up to 400-500 Da. Based on structural data and previous biochemical evidence, we propose a model for HlyIIR interaction with the DNA.

Amino Acid Sequence↗
PubMed2002

A real-time EMG-driven virtual arm.

An EMG-driven virtual arm is being developed in our laboratories for the purposes of studying neuromuscular control of arm movements. The virtual arm incorporates the major muscles spanning the elbow joint and is used to estimate tension developed by individual muscles based on recorded electromyograms (EMGs). It is able to estimate joint moments and the corresponding virtual movements, which are displayed in real-time on a computer screen. In addition, the virtual arm offers artificial control over a variety of physiological and environmental conditions. The virtual arm can be used to examine how the neuromuscular system compensates for the partial or total loss of a muscle's ability to generate force as might result from trauma or pathology. The purpose of this paper is to describe the design objectives, fundamental components and implementation of our real-time, EMG-driven virtual arm.

Arm↗
PubMed2003

Prospective evaluation of criteria for obtaining thoracolumbar radiographs in trauma patients.

This study examined if use of clinical screening criteria for selective radiography of blunt trauma patients can identify all patients with thoracolumbar (TL) spine injuries. The study was a prospective cohort of patients undergoing TL spine radiographs following blunt trauma. Patients were considered at risk for TL spine injury if they had any of the following clinical criteria: 1) complaints of TL spine pain, 2) TL spine tenderness, 3) a decreased level of consciousness, 4) intoxication with ethanol or drugs, 5) a neurologic deficit, or 6) a painful distracting injury. Patients without any of these findings were considered at low risk for TL spine injury. Severity of mechanism of injury was also recorded. Data sheets were completed prior to TL radiography. Injury status was determined by the final faculty radiologist interpretation of all radiographic studies. A total of 2404 patients were enrolled. TL spine injuries were identified in 152 patients. Of these 152 patients with spine injuries, all 152 (100%, 95% confidence interval 98-100%) were considered high risk by having at least one of the high-risk criteria. These criteria have a specificity of 3.9%, a positive predictive value of 6.6%, and a negative predictive value of 100%. All of the high-risk criteria but intoxication with ethanol or drugs were important as sole predictors of TL spine injury. The use of high-risk clinical screening criteria identified virtually all blunt trauma patients with acute TL spine injuries. These criteria, however, have poor specificity and positive predictive value.

Adolescent↗
PubMed2002

Radiology of colorectal cancer.

In the past 20 years, the radiology of colorectal cancer has evolved from the barium enema to advanced imaging modalities like phased array magnetic resonance imaging (MRI), virtual colonoscopy and positron emission tomography (PET). Nowadays, primary rectal cancers are preferably imaged with transrectal ultrasound or MRI, while barium enema is still the most often used technique for imaging of colonic cancers. Virtual colonoscopy is rapidly evolving and might considerably change the imaging of colorectal cancer in the near future. The use of virtual colonoscopy for screening purposes and imaging of the colon in occlusive cancer or incomplete colonoscopies is currently under evaluation. The main role of PET is in detecting tumour recurrences, both locally and distantly. Techniques to fuse cross-sectional anatomical (computer tomography (CT) and MRI) and functional (PET) images are being developed. Apart from diagnostic imaging, the radiologists has added image-guided minimally invasive treatments of colorectal liver metastases to their arsenal. The radio-frequency ablation technique is now widely available, and can be used during laparotomy or percutaneously in selected cases.

Barium Sulfate↗
PubMedDate not supplied

A new rapid and effective chemistry space filter in recognizing a druglike database.

To develop a new chemistry space filter with high efficiency and accuracy, an analysis on distributions of as many as 50 structural and physicochemical properties was carried out on both druglike and nondruglike databases, viz. MACCS-II Drug Data Report (MDDR), Comprehensive Medicinal Chemistry (CMC), and Available Chemicals Directory (ACD). Based on the analysis results, a chemistry space filter was developed that can effectively discriminate a druglike database from a nondruglike database. The filter is composed of two descriptors: one is a molecular saturation related descriptor, and the other is associated with the proportion of heteroatoms in a molecule. Both are molecular size independent. Therefore, the profiles of a druglike database could be characterized as proper molecular saturation and proper percentage of heteroatoms, revealing direct indices for designing and optimizing combinatorial libraries. The application of the new filter on the Chinese Natural Product Database (CNPD) suggested that CNPD is, as expected, a potential druglike database, testifying that the new filter is reliable. Therefore, this newly developed chemistry space filter should be a potent tool for identifying druglike molecules, thus, it would have potential applications in the research of combinatorial library design and virtual high throughput screening using computational approaches for drug discovery.

Combinatorial Chemistry Techniques↗
PubMed2004

Structural interaction fingerprint (SIFt): a novel method for analyzing three-dimensional protein-ligand binding interactions.

Representing and understanding the three-dimensional (3D) structural information of protein-ligand complexes is a critical step in the rational drug discovery process. Traditional analysis methods are proving inadequate and inefficient in dealing with the massive amount of structural information being generated from X-ray crystallography, NMR, and in silico approaches such as structure-based docking experiments. Here, we present SIFt (structural interaction fingerprint), a novel method for representing and analyzing 3D protein-ligand binding interactions. Key to this approach is the generation of an interaction fingerprint that translates 3D structural binding information from a protein-ligand complex into a one-dimensional binary string. Each fingerprint represents the "structural interaction profile" of the complex that can be used to organize, analyze, and visualize the rich amount of information encoded in ligand-receptor complexes and also to assist database mining. We have applied SIFt to tackle three common tasks in structure-based drug design. The first involved the analysis and organization of a typical set of results generated from a docking study. Using SIFt, docking poses with similar binding modes were identified, clustered, and subsequently compared with conventional scoring function information. A second application of SIFt was to analyze approximately 90 known X-ray crystal structures of protein kinase-inhibitor complexes obtained from the Protein Databank. Using SIFt, we were able to organize the structures and reveal striking similarities and diversity between their small molecule binding interactions. Finally, we have shown how SIFt can be used as an effective molecular filter during the virtual chemical library screening process to select molecules with desirable binding mode(s) and/or desirable interaction patterns with the protein target. In summary, SIFt shows promise to fully leverage the wealth of information being generated in rational drug design.

Binding Sites↗
PubMed2002

Three-dimensional craniofacial reconstruction imaging.

This review article aims to describe and discuss the imaging techniques most commonly used in medicine and dentistry to obtain three-dimensional images of the craniofacial complex. Three-dimensional imaging techniques provide extensive possibilities for the detailed and precise analysis of the whole craniofacial complex, for virtual (on-screen) simulation and real simulation of orthognathic surgery cases on biomodels before treatment, as well as for the detailed evaluation of the effects of treatment. Laser scanning in combination with the stereolithographic biomodeling seems to be a very promising combination for three-dimensional imaging, although there is still considerable room for improvement. Constant efforts should be made in the direction of developing and enhancing the existing techniques as well as exploring the potential for developing new methods based on emerging sectors of technology.

Cephalometry↗
PubMed2006

Genome wide gene expression studies in mood disorders.

Microarrays offer the possibility of screening in parallel virtually all genes expressed in a given tissue or to study the molecular signature associated with available treatments. As such, this technology has been increasingly used to investigate multifactorial and polygenic complex traits such as psychiatric disorders, in particular, schizophrenia and mood disorders. This review focuses on microarray studies investigating mood disorders. Study designs, methodologic approaches and limitations, subsequent follow-up strategies, and confirmation of results are discussed. Despite the apparent disparate and not always concordant results, it appears evident that this technology is a powerful and inevitable approach for the study of mood disorders, especially when phenotype-specific confounders are properly accounted for. Thus, alterations of mitochondrial, oligodendrocyte, and myelin related genes in bipolar disorder, of signaling and olidendroglial related genes in depression, and of GABA-glutamate related genes in depression and suicide have been observed and have confirmed new avenues for the study and the treatment of these complex disorders.

Gene Expression Profiling↗
PubMed1998

Assessment of Turner's syndrome by molecular analysis of the X chromosome in growth-retarded girls.

Turner's syndrome (TS) is a common disorder (1/2500 to 1/5000 female births) which is diagnosed at birth in approximately 20% of patients and during childhood or at puberty for the rest. Growth retardation is the most frequent clinical feature of TS, so we systematically searched for TS in female patients referred to our center because of short stature. Three hundred seventy-five female patients, 1 month to 18 yr old (mean +/- SD = 9(7/12) +/- 3(9/12), with growth retardation (less than -2 SD) and/or decreased height velocity were included in the study. Mean growth retardation was -2.57 SD +/- 0.79 (range: -1 to -7). Thirty-two percent of the patients had reached puberty. GH provocative tests were performed in 329 patients (87.7%), and 36 of these patients (11%) had impaired GH secretion (5 complete and 31 partial GH deficiency). TS was evaluated by Southern blot analysis of leukocyte DNA using a multiallelic polymorphic X chromosome marker (88% heterozygosity rate). Y chromosome PCR analysis was carried out if a pattern indicative of TS was obtained. Leukocyte DNA analysis produced an abnormal restriction pattern for 20 of the 375 cases (5.3%). There was a single hybridizing band in 13 cases, an allelic disproportion indicative of mosaicism in 6 cases, and 3 hybridizing bands in 1 case. One patient tested positive in the Y chromosome PCR analysis. Cytogenetic analysis showed 47 XXX trisomy in the patient with a 3-hybridizing-band pattern and confirmed the diagnosis of TS for 17 of the 19 suspected cases: 45 X: n = 7; 45 X/46 Xi(Xq): n = 4; 45 X/46 XX: n = 2; 46 Xi(Xq): n = 1; 45 X/46 Xr(X): n = 1; 45 X/46 XX/47 XXX: n = 1; 45 X/46 XY: n = 1. Cytogenetic analysis was normal (46 XX) for the 2 other patients. The TS phenotype is variable: dysmorphism is often missing or mild (particularly in cases of mosaicism), but growth is reduced in virtually all patients. Screening of 375 growth-retarded girls identified 18 cases of TS, of which 17 were diagnosed by molecular analysis. This incidence (4.8%) was significantly higher than the expected incidence in this population (0.8-1.6%: P < 0.001).

Adolescent↗
PubMed2006

Computational methods in developing quantitative structure-activity relationships (QSAR): a review.

Virtual filtering and screening of combinatorial libraries have recently gained attention as methods complementing the high-throughput screening and combinatorial chemistry. These chemoinformatic techniques rely heavily on quantitative structure-activity relationship (QSAR) analysis, a field with established methodology and successful history. In this review, we discuss the computational methods for building QSAR models. We start with outlining their usefulness in high-throughput screening and identifying the general scheme of a QSAR model. Following, we focus on the methodologies in constructing three main components of QSAR model, namely the methods for describing the molecular structure of compounds, for selection of informative descriptors and for activity prediction. We present both the well-established methods as well as techniques recently introduced into the QSAR domain.

Models, Molecular↗
PubMed2004

Comparison of predictive ability of water solubility QSPR models generated by MLR, PLS and ANN methods.

ADME/Tox computational screening is one of the most hot topics of modern drug research. About one half of the potential drug candidates fail because of poor ADME/Tox properties. Since the experimental determination of water solubility is time-consuming also, reliable computational predictions are needed for the pre-selection of acceptable "drug-like" compounds from diverse combinatorial libraries. Recently many successful attempts were made for predicting water solubility of compounds. A comprehensive review of previously developed water solubility calculation methods is presented here, followed by the description of the solubility prediction method designed and used in our laboratory. We have selected carefully 1381 compounds from scientific publications in a unified database and used this dataset in the calculations. The externally validated models were based on calculated descriptors only. The aim of model optimization was to improve repeated evaluations statistics of the predictions and effective descriptor scoring functions were used to facilitate quick generation of multiple linear regression analysis (MLR), partial least squares method (PLS) and artificial neural network (ANN) models with optimal predicting ability. Standard error of prediction of the best model generated with ANN (with 39-7-1 network structure) was 0.72 in logS units while the cross validated squared correlation coefficient (Q(2)) was better than 0.85. These values give a good chance for successful pre-selection of screening compounds from virtual libraries, based on the predicted water solubility.

Chemical Phenomena↗
PubMed2005

Reverse pharmacognosy: application of selnergy, a new tool for lead discovery. The example of epsilon-viniferin.

The aim of reverse pharmacognosy is to find new biological targets for natural compounds by virtual or real screening and identify natural resources that contain the active molecules. To demonstrate the applicability of this concept, we report here a study on epsilon-viniferin, an active ingredient for cosmetic development. Nevertheless, this natural substance is weakly defined in terms of biological properties. SELNERGY, an inverse docking computer software, was used to identify putative binding biological targets for epsilon-viniferin. Among the 400 screened proteins two targets were retained. For cosmetic application, cyclic nucleotide phosphodiesterase 4 (PDE4) was the most interesting candidate. Moreover, other PDE subtypes (1, 2, 3, 5 and 6) were not retained, indicating a selectivity for PDE4. The experimental binding tests on the 6 subtypes of PDE revealed a significant selectivity of epsilon-viniferin for the PDE4 subtype. This selectivity was confirmed by evaluation of epsilon-viniferin on the secretion of TNF-alpha and Interleukin-8. Our data demonstrated that epsilon-viniferin possesses anti-inflammatory properties by inhibiting PDE4 subtype. In conclusion, reverse pharmacognosy and its inverse docking component cannot only be integrated into a program for new lead discovery but is also a useful approach to find new applications for identified compounds.

Benzofurans↗
PubMed2026

Multimodal artificial intelligence and machine learning in oncology: from data integration to precision cancer care.

Cancer remains a major global health burden, with approximately 20 million new cases and 9.7 million cancer-related deaths reported globally in 2022. While advances in radiological imaging, molecular profiling, and clinical data have enhanced the interpretation of disease progression, the availability of multiple such modalities still does not meet the needs of a large patient population. This narrative review focuses on the role of multimodal artificial intelligence and machine learning in bridging the gap in interpreting heterogeneous modalities to improve risk prediction, prognostic assessment, and treatment decision-making in precision oncology. Multimodal frameworks such as Pathomic Fusion illustrate how complementary histopathological and genomic information can be integrated for cancer diagnosis and prognostic modeling. Multimodal models have demonstrated potential in virtual biopsy, cancer screening, prognostic prediction, radiotherapy planning, intraoperative guidance, and clinical-trial design using digital twins and synthetic control arms. The major limitations of incorporating multimodal artificial intelligence and machine learning in oncology include data heterogeneity, demographic or institutional biases, and reproducibility challenges that hinder translation. Accordingly, appropriate data-governance strategies, fairness audits, and privacy-preserving approaches such as federated learning should be considered where appropriate. Future progress will depend on the development of standardized benchmarking datasets, robust external validation, seamless integration with electronic health records and picture archiving and communication systems, and the implementation of explainable, secure, and clinically validated multimodal artificial intelligence frameworks that support precision oncology in routine clinical practice.

deep learning↗
PubMed1999

Structure-based drug design: combinatorial chemistry and molecular modeling.

Drug discovery efforts are shifting to include the rapid synthetic procedures of combinatorial chemistry and the elegance of rational library design. The wealth of computational methods which explore both the receptor structure and the ultimate pharmacophore complementarity, provide novel avenues for chemists to discover new lead compounds or design virtual libraries for screening prior to the synthetic stage. This mini-review provides an overview of a few current methodologies of library generation, highlighting docking procedures which have utility in both the discovery and optimization stages of drug development. Three specific examples of different approaches to the use of docking are provided. These describe the development of inhibitors to the human A3 adenosine receptor and HIV-1 protease, and the evaluation of the activity of novel inhibitors of the redox regulator protein, human thioredoxin.

Chemistry, Organic↗
PubMed2004

Geographical slant facilitates navigation and orientation in virtual environments.

Theoretical considerations and earlier experimental findings indicate that traveling over slanted terrain can lead to an enrichment of the perceived spatial cues relevant for navigation. We investigated the proposed facilitation of a uniformly slanted environment on navigation and orientation performance with a virtual environment presented on a large 180 degrees screen, using as material a virtual town with eight places and twenty-four landmarks. In the control condition, this town was placed on a flat surface; in the two experimental conditions, the town was placed on a slope with a uniform angle of 4 degrees. Pedaling on a bicycle simulator, participants first explored the environment, then solved navigation tasks, pointed from various positions to distant landmarks, judged the relative elevation of pairs of distant landmarks from memory, and finally drew a sketch map of the environment. In comparison to the control condition, the number of navigation errors was significantly lower in the slanted conditions, and the deviations in the pointings to distant landmarks were massively reduced. Participants from the slant conditions also showed good knowledge of the relative elevations of pairs of distant locations. However, no differences in map-drawing quality were found. The results lend additional support to the proposition that our spatial knowledge, which is used in navigation and orientation, contains vertical information.

Adolescent↗