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At least 217 records · Page 12Linked to original sources
PubMed2006

Prediction of h5-HT2A receptor antagonistic activity of arylindoles: computational approach using topochemical descriptors.

Relationship between the topochemical indices and h5-HT2A receptor antagonistic activity of arylindoles has been investigated. Three topochemical indices, Wiener's topochemical index--a distance-based topochemical descriptor, molecular connectivity topochemical index--an adjacency-based topochemical descriptor and eccentric connectivity topochemical index--an adjacency-cum-distance based topochemical descriptor, were used for the present investigation. A data set comprising 31 differently substituted arylindoles was selected for the present study. The values of the Wiener's topochemical index, molecular connectivity topochemical index and eccentric connectivity topochemical index were computed for all the analogues involved in the data set using an in-house computer program. Resultant data was analyzed and suitable models were developed after identification of the active ranges. Subsequently, a biological activity was assigned to each analogue using these models, which was then compared with the reported h5-HT2A receptor antagonistic activity. Accuracy of prediction was found to vary from a minimum of approximately 81% to a maximum of approximately 84%.

Computer Simulation↗
PubMed2006

Embryonic cleavage modeling as a computational approach to sphere packing problem.

Embryonic cleavage depends on the distribution in the cytosol of molecular signals that influence mitotic spindle positioning. By implementing the New Kind of Science (NKS) theory in which a simple rule can evolve with a complex overall behavior, here we propose a new theoretical approach that is capable of modeling the mechanisms of early embryonic cleavage dynamics in the ascidian Styela Partita. The model shows that the same spindle pole orientation rule governs the first five embryonic cleavages, which progressively allow the transition from one to thirty-two daughter cells. Finally, we present evidence of a strong similarity between Kepler's Sphere Packing Problem and embryonic cleavage, which thus represents a prominent example of natural computing.

Algorithms↗
PubMed1994

Genetically evolved receptor models: a computational approach to construction of receptor models.

Given the three-dimensional structure of a receptor site, there are several methods available for designing ligands to occupy the site; frequently, the three-dimensional structure of interesting receptors is not known, however. The GERM program uses a genetic algorithm to produce atomic-level models of receptor sites, based on a small set of known structure-activity relationships. The evolved models show a high correlation between calculated intermolecular energies and bioactivities; they also give reasonable predictions of bioactivity for compounds which were not included in model generation. Such models may serve as starting points for computational or human ligand design efforts.

Aspartame↗
PubMed2003

Predicting acyl-coenzyme A: cholesterol O-acyltransferase inhibitory activity: computational approach using topological descriptors.

Relationship between the topological indices and acyl-coenzyme A:cholesterol O-acyltransferase (ACAT) inhibitory activity of (aminosulfonyl)ureas has been investigated. Three topological indices, Wiener's index--a distance-based topological descriptor, molecular connectivity index--an adjacency-based topological index, and eccentric connectivity index--an adjacency-cum-distance-based topological descriptor, were used for the present investigations. A data set comprising 41 analogues of substituted (aminosulfonyl)ureas was selected for the present studies. The values of wiener's index, eccentric connectivity index, and molecular connectivity index for each of the 41 compounds comprising the data set were computed using an in-house computer program. Resultant data were analyzed and suitable models were developed after identification of active ranges. Subsequently, a biological activity was assigned to each compound using these models, which was then compared with the reported in vitro ACAT inhibitory activity. Accuracy of prediction using these models was found to vary from a minimum of approximately 83% to a maximum of approximately 91%.

Algorithms↗
PubMed2002

SCORE: a computational approach to the identification of cis-regulatory modules and target genes in whole-genome sequence data. Site clustering over random expectation.

A large fraction of the information content of metazoan genomes resides in the transcriptional and posttranscriptional cis-regulatory elements that collectively provide the blueprint for using the protein-coding capacity of the DNA, thus guiding the development and physiology of the entire organism. As successive whole-genome sequencing projects--including those of mice and humans--are completed, we have full access to the regulatory genome of yet another species. But our ability to decipher the cis-regulatory code, and hence to link genes into regulatory networks on a global scale, is currently very limited. Here we describe SCORE (Site Clustering Over Random Expectation), a computational method for identifying transcriptional cis-regulatory modules based on the fact that they often contain, in statistically improbable concentrations, multiple binding sites for the same transcription factor. We have carried out a Drosophila genomewide inventory of predicted binding sites for the Notch-regulated transcription factor Suppressor of Hairless [Su(H)] and found that the fly genome contains highly nonrandom clusterings of Su(H) sites over a broad range of sequence intervals. We found that the most statistically significant clusters are very heavily enriched in both known and logical targets of Su(H) binding and regulation. The utility of the SCORE approach was validated by in vivo experiments showing that proper expression of the novel gene Him in adult muscle precursor cells depends both on Su(H) gene activity and sequences that include a previously unstudied cluster of four Su(H) sites, indicating that Him is a likely direct target of Su(H).

Animals↗
PubMed2002

Predicting anti-HIV activity of TIBO derivatives: a computational approach using a novel topological descriptor.

A novel highly discriminating adjacency-cum-distance-based topological descriptor, termed the adjacent eccentric distance sum index, has been conceptualized and its discriminating power investigated with regard to the anti-HIV activity of 4,5,6,7-tetrahydro-imidazo-[4,5,1- jk] [1,4] benzodiazepin-2 (1 H)-one (TIBO) derivatives. The discriminating power of the adjacent eccentric distance sum index was compared with that of the eccentric connectivity index - another adjacency-cum-distance-based topological descriptor. The values of the eccentric connectivity index and the adjacent eccentric distance sum index of each of 121 analogues comprising the data set were computed and active ranges were identified. Subsequently, a biological activity was assigned to each analogue involved in the data set and this was then compared with the reported anti-HIV activity. Excellent correlations were observed between anti-HIV activity and both the topological descriptors. Although the overall accuracy of prediction was found to be approximately 84% in case of the eccentric connectivity index and approximately 86% in case of adjacent eccentric distance sum index, the predictability using the adjacent eccentric distance sum index in the active range itself was >92%. The proposed index offers a vast potential for structure-activity/property studies.

Anti-HIV Agents↗
PubMed2006

Computational approaches to the identification of heparin-binding sites on the surfaces of proteins.

The identification of heparin-binding sites is important for understanding the physiological function of many secreted proteins. Most of the experimental techniques for mapping these sites do not define them to atomic resolution. The use of automated docking methods can aid this process by facilitating both the design of experiments and visualization of their results. A method designed for a systematic search over the whole protein surface for heparin-binding sites, using heparin oligosaccharide structures as ligands, is described, with its validation and details of several published applications. The scope and limitations of this crude but effective computational chemistry method are discussed.

Animals↗
PubMed1991

Radiographic evaluation of apical periodontitis and endodontic treatment results: a computer approach.

Chronic apical periodontitis is diagnosed primarily by radiography. Whereas subjective, chairside evaluations of radiographs have serious limitations as regards accuracy of endodontic diagnosis, digitalization of radiological data allows quantification of the information obtained. In clinical practice, digitalization may improve the diagnostic sensitivity and reduce the radiation dose; in clinical endodontic research, digitalization of radiographs provides a means of unbiased and quantitative assessment of apical periodontitis. Automated measurements of the radiographic density of the periapical area have been applied in a study of the effect of different endodontic sealers on the healing of apical periodontitis. Changes in radiographic density could be detected as early as 3 weeks after completion of endodontic treatment, and the computer-based analyses provided numeric values for the progression of the healing process in the periapical region.

Adult↗
PubMed2005

Predicting dopamine receptors binding affinity of N-[4-(4-Arylpiperazin-1-yl) butyl]aryl carboxamides: computational approach using topological descriptors.

Relationship between the topological indices and Dopamine D3 and D4 receptor binding affinities of N-[4-(4-Arylpiperazin-1-yl)butyl]aryl carboxamides has been investigated. Three topological indices, the Wiener's Index- a distance-based topological descriptor, molecular connectivity index- an adjacency based topological descriptor and eccentric connectivity index- an adjacency-cum-distance based topological descriptor were used for the present investigations. A data set comprising of 37 substituted N-[4-(4-Arylpiperazin-1-yl)butyl]aryl carboxamides was selected for the present studies. The values of the Wiener's index, eccentric connectivity index and molecular connectivity index for each of the 37 analogues comprising the data set were computed using in-house computer program. Resultant data was subsequently analyzed and suitable models were developed after identification of active ranges. Subsequently, a biological activity was assigned to each analogue using these models, which was then compared with the reported D3 and D4 receptor binding affinity. These models exhibited exceptionally high predictability.

Amides↗
PubMed2005

Q-S (lag or anticipated) synchronization backstepping scheme in a class of continuous-time hyperchaotic systems--a symbolic-numeric computation approach.

First, a Q-S (lag or anticipated) synchronization of continuous-time dynamical systems is defined. Second, based on a backstepping design with one controller, a systematic, concrete, and automatic scheme is developed to investigate the Q-S (lag or anticipated) synchronization between the drive system and response system with a strict-feedback form. Two identical hyperchaotic Tamasevicius-Namajunas-Cenys(TNC) systems as well as the hyperchaotic TNC system and hyperchaotic Rossler system are chosen to illustrate the proposed scheme. Numerical simulations are used to verify the effectiveness of the proposed scheme. The scheme can also be extended to study Q-S (lag or anticipated) synchronization between other dynamical systems with strict-feedback forms. With the aid of symbolic-numeric computation, the scheme can be performed to yield automatically the scalar controller in computer.

Algorithms↗
PubMed2006

Selective terminal heck arylation of vinyl ethers with aryl chlorides: a combined experimental-computational approach including synthesis of betaxolol.

Reaction conditions have been developed for palladium-catalyzed terminal (beta-) arylation of acyclic vinyl ethers with high regioselectivity using inexpensive aryl chlorides as starting materials and the P(t-Bu)3 releasing preligand [(t-Bu3)PH]BF4 as the key additive. This swift and straightforward protocol exploits non-inert conditions and controlled microwave heating to minimize handling and processing times and uses aqueous DMF or environmentally friendly PEG-200 as the reaction medium. The selectivity for linear beta-product in PEG-200 is slightly higher than in aqueous DMF. DFT calculations support a ligand-driven selectivity rationale, where the electronic and steric influence of bulky P(t-Bu)3 ligand provides improved beta-selectivity in the essential insertion step also with electron-rich aryl chlorides. A tentative computational rationalization of the improved selectivity in non-methylated PEG is discussed. Finally the synthetic methodology was used to provide efficient access to linear p-[2-(cyclopropylmethoxy)ethyl] phenol from p-nitrophenyl chloride, a key intermediate in the synthesis of the beta-adrenergic blocking agent Betaxolol.

Betaxolol↗
PubMed2001

Computational approach for determining the spectrum of DNA damage induced by ionizing radiation.

To study the characteristics of molecular damage induced by ionizing radiation at the DNA level, Monte Carlo track simulation of energetic electrons and ions in liquid water, a canonical model of B-DNA, and a comprehensive classification of DNA damage in terms of the origin and complexity of damage were used to calculate the frequencies of simple and complex strand breaks. A threshold energy of 17.5 eV was used to model the damage by direct energy deposition, and a probability of 0.13 was applied to model the induction of a single-strand break produced in DNA by OH radical reactions. For preliminary estimates, base damage was assumed to be induced by the same direct energy threshold deposition or by the reaction of an OH radical with the base, with a probability of 0.8. Computational data are given on the complexity of damage, including base damage by electrons with energies of 100-4500 eV and ions with energies of 0.3-4.0 MeV/nucleon (59-9 keV microm(-1) protons and 170-55 keV microm(-1) alpha particles). Computational data are presented on the frequencies of single- and double-strand breaks induced as a function of the LET of the particles, and on the relative frequencies of complex single- and double-strand breaks for electrons. The modeling and calculations of strand breaks show that: (1) The yield of strand breaks per unit absorbed dose is nearly constant over a wide range of LET. (2) The majority of DNA damage is of a simple type, but the majority of the simple single-strand breaks are accompanied by at least one base damage. (3) For low-energy electrons, nearly 20-30% of the double-strand breaks are of a complex type by virtue of additional breaks. The proportion of this locally clustered damage increases with LET, reaching about 70% for the highest-LET alpha particles modeled, with the complexity of damage increasing further, to about 90%, when base damage is considered. (4) The extent of damage in the local hit region of the DNA duplex is mostly limited to a length of a few base pairs. (5) The frequency of base damage when no strand breaks are present in the hit segment of DNA varies between 20-40% as a function of LET for protons and alpha particles.

Alpha Particles↗
PubMed2006

Fast-Find: a novel computational approach to analyzing combinatorial motifs.

BACKGROUND: Many vital biological processes, including transcription and splicing, require a combination of short, degenerate sequence patterns, or motifs, adjacent to defined sequence features. Although these motifs occur frequently by chance, they only have biological meaning within a specific context. Identifying transcripts that contain meaningful combinations of patterns is thus an important problem, which existing tools address poorly. RESULTS: Here we present a new approach, Fast-FIND (Fast-Fully Indexed Nucleotide Database), that uses a relational database to support rapid indexed searches for arbitrary combinations of patterns defined either by sequence or composition. Fast-FIND is easy to implement, takes less than a second to search the entire Drosophila genome sequence for arbitrary patterns adjacent to sites of alternative polyadenylation, and is sufficiently fast to allow sensitivity analysis on the patterns. We have applied this approach to identify transcripts that contain combinations of sequence motifs for RNA-binding proteins that may regulate alternative polyadenylation. CONCLUSION: Fast-FIND provides an efficient way to identify transcripts that are potentially regulated via alternative polyadenylation. We have used it to generate hypotheses about interactions between specific polyadenylation factors, which we will test experimentally.

Algorithms↗
PubMed2004

Predicting anti-HIV activity of 2,3-diaryl-1,3-thiazolidin-4-ones: computational approach using reformed eccentric connectivity index.

The eccentric connectivity index, which has recently been employed successfully for the development of numerous mathematical models for the prediction of biological activities of diverse nature, has been reformed to overcome its limitations caused by degeneracy and insensitivity towards heteroatoms. The reformed eccentric connectivity index, termed the eccentric connectivity topochemical index, overcomes the limitations of the eccentric connectivity index by exhibiting very low degeneracy and displaying sensitivity to both the presence and relative position of heteroatoms without compromizing the discriminating power of the eccentric connectivity index. The relationship of the eccentric connectivity topochemical index, eccentric connectivity index and Wiener's index with regard to the anti-HIV activity of 2, 3-diaryl-1, 3-thiazolidin-4-one derivatives was subsequently investigated. The values of the eccentric connectivity topochemical index, the eccentric connectivity index and Wiener's index of each of 31 analogues comprizing the data set were computed using in-house computer program. Resultant data was analyzed and suitable models developed after identification of active ranges. Subsequently, each derivative was assigned a biological activity using these models, which was then compared with the reported anti-HIV activity. The accuracy of prediction using these models was found to vary from 81 to 90%. The proposed index offers a vast potential for virtual screening of combinatorial libraries, structure property/activity studies and drug design. [figure]. Basic structure of 2,3-diaryl-1, 3-thiazoidin-4-ones.

Anti-HIV Agents↗
PubMed2005

Computational approaches for identification of conserved/unique binding pockets in the A chain of ricin.

MOTIVATION: Specific and sensitive ligand-based protein detection assays that employ antibodies or small molecules such as peptides, aptamers or other small molecules require that the corresponding surface region of the protein be accessible and that there be minimal cross-reactivity with non-target proteins. To reduce the time and cost of laboratory screening efforts for diagnostic reagents, we developed new methods for evaluating and selecting protein surface regions for ligand targeting. RESULTS: We devised combined structure- and sequence-based methods for identifying 3D epitopes and binding pockets on the surface of the A chain of ricin that are conserved with respect to a set of ricin A chains and unique with respect to other proteins. We (1) used structure alignment software to detect structural deviations and extracted from this analysis the residue-residue correspondence, (2) devised a method to compare corresponding residues across sets of ricin structures and structures of closely related proteins, (3) devised a sequence-based approach to determine residue infrequency in local sequence context and (4) modified a pocket-finding algorithm to identify surface crevices in close proximity to residues determined to be conserved/unique based on our structure- and sequence-based methods. In applying this combined informatics approach to ricin A, we identified a conserved/unique pocket in close proximity (but not overlapping) the active site that is suitable for bi-dentate ligand development. These methods are generally applicable to identification of surface epitopes and binding pockets for development of diagnostic reagents, therapeutics and vaccines.

Algorithms↗
PubMed2006

Q-S (complete or anticipated) synchronization backstepping scheme in a class of discrete-time chaotic (hyperchaotic) systems: a symbolic-numeric computation approach.

First, a type of Q-S (complete or anticipated) synchronization is defined in discrete-time dynamical systems. Second, based on backstepping design with a scalar controller, a systematic, concrete and automatic scheme is presented to investigate Q-S (complete or anticipated) synchronization between the discrete-time drive system and response system with strict-feedback form. Finally, the proposed scheme is used to illustrate Q-S (complete or anticipated) synchronization between the two-dimensional discrete-time Lorenz system and Fold system, as well as the three-dimensional hyperchaotic discrete-time Rossler system and generalized discrete-time Rossler system. Moreover numerical simulations are used to verify the effectiveness of the proposed scheme. Our scheme can be also extended to investigate Q-S (complete or anticipated) synchronization between other discrete-time dynamical systems with strict-feedback forms. With the aid of symbolic-numeric computation, the scheme can be performed to yield automatically the scalar controller and to verify its effectiveness in computer.

Journal Article↗
PubMed2002

A novel computational approach to integrate NMR spectroscopy and capillary electrophoresis for structure assignment of heparin and heparan sulfate oligosaccharides.

Heparin and heparan sulfate (HS) glycosaminoglycans (GAGs) are cell surface polysaccharides that bind to a multitude of signaling molecules, enzymes, and pathogens and modulate critical biological processes ranging from cell growth and development to anticoagulation and viral invasion. Heparin has been widely used as an anticoagulant in a variety of clinical applications for several decades. The heterogeneity and complexity of HS GAGs pose significant challenges to their purification and characterization of structure-function relationships. Nuclear magnetic resonance (NMR) spectroscopy is a promising tool that provides abundant sequence and structure information for characterization of HS GAGs. However, complex NMR spectra and low sensitivity often make analysis of HS GAGs a daunting task. We report the development of a novel methodology that incorporates distinct linkage information between adjacent monosaccharides obtained from NMR and capillary electrophoresis (CE) data using a property encoded nomenclature (PEN) computational framework to facilitate a rapid and unbiased procedure for sequencing HS GAG oligosaccharides. We demonstrate that the integration of NMR and CE data sets with the help of the PEN framework dramatically reduces the number of experimental constraints required to arrive at an HS GAG oligosaccharide sequence.

Carbohydrate Conformation↗
PubMed2001

Towards improved acetylcholinesterase inhibitors: a structural and computational approach.

During the last years, solving the X-ray crystallographic structure of both the unliganded acetylcholinesterase (AChE) and AChE complexes with various inhibitors has provided valuable knowledge of the interactions that mediate inhibitor binding. This structural information allows us to rationalize differences in binding affinities for related analogues, and more importantly opens new strategies to design compounds with improved pharmacological properties. This is illustrated in the case of the recently reported huprines, which are a new class of very potent and selective acetylcholinesterase inhibitors.

Acetylcholinesterase↗