• Proceedings of the Korean Society for Bioinformatics Conference
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• 2004.11a
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• pp.221-233
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• 2004

Molecular docking falls into the general category of global optimization problems since its main purpose is to find the most stable complex consisting of a receptor and its ligand. Conformational space annealing (CSA), a powerful global optimization method, is incorporated with the Tinker molecular modeling package to perform molecular docking simulations of six receptor-ligand complexes (3PTB, 1ULB, 2CPP, 1STP, 3CPA and 1PPH) from the Protein Data Bank. In parallel, Monte Carlo with minimization (MCM) method is also incorporated into the Tinker package for comparison. The energy function, consisting of electrostatic interactions, van der Waals interactions and torsional energy terms, is calculated using the AMBER94 all-atom empirical force field. Rigid docking simulations for all six complexes and flexible docking simulations for three complexes (1STP, 3CPA and 1PPH) are carried out using the CSA and the MCM methods. The simulation results show that the docking procedures using the CSA method generally find the most stable complexes as well as the native -like complexes more efficiently and accurately than those using the MCM, demonstrating that CSA is a promising search method for molecular docking problems.

• Journal of the Korean Institute of Telematics and Electronics C
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• v.36C no.9
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• pp.28-43
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• 1999

In this paper, we present a gridless router for MultiChip Modules (MCM). Because our router uses corner stitching data structures, not a routing grid, to represent the routings status, it allows arbitrary location of pins, and routes variable-width wires, without a considerable waste of area from bulky vias. A routing speed is a very important factor because a gridless routing approach is known its computation is hard and complex, and MCM routing problem has so large routing area and layers. Our router completes the routing faster than the most of previously reported grid-based routers, with comparable routing result, by using SEGRAs routing algorithm whose very fast speed is proved, and the characteristics of the effective data structure.

• Korean Journal of Microbiology
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• v.36 no.2
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• pp.97-102
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• 2000

In order to use Metarhizizmn~ anisopliae as a biological pesticide, effect of envrionmental factors on nlycelial growth, spore formation, and extracellular enzyme activity in culture broth of M. anisopliae DGUM 35001 was determined. Optimal temperature was 26^{\circ}C.$ and optimal pH ranged from 5 to 9. Among the complex media tested, MCM and SDPY media were the most favorable for mycelial growth. When Czapek-Dox agar was used as a mnimal medium, glucose and sucrose among the saccharides were very excellent source of carbohydrate. Among the biopolyners tested. chitin was the most favorable source for mycelial growth and produced high aerial inycelia. Urea and ammonium phosphate as an inorganic nitrogen source and bacto-peptone and soytone as an organic nitrogen source enhanced the mycelial growth When serine as a source of amino acid was supplemented, excellent mycelial growth was shown. Large amount of spores could be obtained from the aerial mycelia of starch medium. When the culture broth was filtrated and then the concentrate with ammonium sulfate was used as a crnde enzyme solution, high enzyme activities of amylase and protease were shown. However, lipase and chitinase activities were comparatively low.

• The Korean Journal of Mycology
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• v.26 no.4 s.87
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• pp.466-477
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• 1998

Twenty-two Phellinus strains were characterized using colony morphologies and polymerase chain reaction (PCR) to divide into Phellinus linteus. There were some differences in mycelial growth and colony shapes among the strains when they were grown on various media such as PDA, MCM, MEA and YM. Phellinus linteus was slowly growing, formed golden-yellow colony, and produced blue pigment on PDA media. When the regions of internal transcribed spacer (ITS) were amplified from ribosomal RNA (rRNA) coding genes of P. igniarius and P. linteus strains by means of PCR, two types of band (700 bp and 800 bp) were appeared, respectively. For the amplified intergenic region I (IGRI), P. igniarius strains showed a different band among 500, 600, 700 and 800 bp according to the strains, whereas P. linteus strains did one specific band of 700 bp. By polymorphism analysis after digesting the amplified products with 6 different restriction enzymes, a band specific to P. linteus was generated when the products for ITS region were digested with HaeIII, suggesting that the enzyme digestion could provide effective method to distinguish between P. igniarius and P. linteus. And also, the analysis of genetic relationship showed that the genetic similarities were 89% and 95% in P. igniarius and P. linteus strains, respectively. Random amplification polymorphic DNA (RAPD) analysis using multiple primer sets and arbitrarily primed PCR (AP-PCR) with ITS3 primer could also result in a reproducible way to identify P. linteus strains.