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Proper Citation:
Hwa A. Lim, "Nanotechnology in diagnostics and drug delivery", Medicinal Chemistry Research, 13(6-7), 2005, pp. 401-413.

Abstract:
The current state of nanotechnology is comparable with the level of technological development in polymers and plastics in the 1930s. At that time, the polymer and plastic industry was in its nascent stage but the industry quickly grew, providing the materials for a large portion of manufactured goods. Nanotechnology industry is currently in an equivalent infant stage, but several basic breakthroughs have been made.1 Based on the polymer and plastic analogy, the annual market for products that carry nano-components, including all computer chips, half of pharmaceuticals and half of chemical catalysts, will reach $1 trillion by 2015. Nanotechnology is thus expected to thoroughly affect the way science addresses medicine, food, electronics and the environment.2 In this article I will take a cursory look at the basic concepts of nanotechnology, outline unique properties of certain nano-materials, and illustrate how these properties can be utilized to overcome current technological bottlenecks in disease detection systems for diagnostic purposes and in drug delivery systems for therapeutic purposes.
Keywords:
nanotechnology, nanobiotechnology, nanomedicine, diagnostics, drug delivery, nanocrystals, hepatitis B virus.

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Proper Citation:
Hwa A. Lim, "Bioinformatics and Cheminformatics in the Drug Discovery Cycle", In: Lecture Notes in Computer Science, Bioinformatics, R. Hofestaedt, T. Lengauer, M. Loffler and D. Schomburg (eds.), (Springer, Heidelberg, 1997), pp. 30-43.

Abstract:
We describe the paradigms of bioinformation and cheminformation. The rise of bioinformatics, a new subject area that has been receiving a lot of attention in recent months, is also chronicled. The dynamics forcing pharmaceutical companies to undertake major infrastructure investments in new, complex and very data-intensive drug discovery technologies are discussed, and the roles of bioinformatics and cheminformatics in the context of drug discovery are also given.
Keywords:
bioinformatics, computers, database, disease, drug, genome research, sequencing.

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Proper Citation:
Hwa A. Lim, "Electrophoresis of Topologically Nontrivial Macromolecules: Mathematical and Computational Studies", International Journal Modern Physics C, 7(2), (1996), pp. 217-271.

Abstract:
Mathematical and numerical models for studying the electrophoresis of topologically non-trivial molecules in two and three dimensions are presented. The molecules are modeled as polygons residing on a square and a cubic lattice whereas the electrophoretic media of obstacle network are simulated by removing vertices from the lattices at random. The dynamics of the polymeric molecules are modeled by configurational readjustments of segments of the polygons. Configurational readjustments arise from thermal fluctuations and they correspond to piecewise reptation in the simulation. A Metropolis algorithm is introduced to simulate these dynamics, and the algorithms are proven to be reversible and ergodic. Monte Carlo simulation of steady field random obstacle electrophoresis are performed and the results are presented.
Keywords:
DNA, electrophoresis, knot, macromolecules, Metropolis algorithm, Monte Carlo simulation, self-avoiding walk.

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Proper Citation:
Victor B. Strelets and Hwa A. Lim, "Compression of Protein Sequence Databases", Bioinformatics, 11(5), 557-561, (1995).

Abstract:
We have created an algorithm for compressing a PIR database to assist individual researchers and software developers who utilize sequence database information but may not have huge storage space. The resulting compact databank contains compressed PIR information and an interface written in C which allows fast direct access to the stored information without extensive decompression of corresponding files. The databank files as well as the interface C-file can be used on both PC- compatibles and UNIX-based computers without any modifications. The interface supports all standard PIR Request Network queries (i.e. gets databank SEQ number by entry; for a defined databank SEQ number, gets specified information like: name, organism(s), keyword(s), sequence, sequence features with coordinates, etc.). In contrast with PIR Request Network, our package allows us to call PIR-contained information directly from the C programs, even on a personal computer not on a network. Our PIR-derived databank, SAGITTARIUS PIR, was implemented in the form of separate file sets. Each file set contains database information of independent types (i.e. sequences, entry indexes, organisms, etc.). On a particular computer, the available configuration of the PIR information (and storage space) can be easily changed as needed by the user without affecting retrievals of other types of stored information. Due to an original alignment-based algorithm, in the compression of protein sequences themselves, our package out- performs the well-known ZIP file compressor. For PC-compatibles, a dialogue shell is available which supports all standard PIR Request Network queries plus homology searches, alignments, etc.
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Proper Citation:
Victor B. Strelets and Hwa A. Lim, "Ancient Splice Junction Shadows with Relation to Blocks in Protein Structure", BioSystems, 36, 37-41, (1995).

Abstract:
Splice junction shadows (ancient exon-exon junctions) presumably reflect the existence of amino acid primary blocks which were used in the course of evolution for the construction of new proteins. The lengths of such blocks (i.e. regions between splice junctions), as the lengths of corresponding inserted or duplicated ancient exons, should be divisible by three in order to store the preexisting coding frame in the course of evolution. In this paper, we will test the hypothesis of intron-mediated recombination in a model of block molecular evolution (exon shuffling) by revealing corresponding blocks in existing database-contained coding sequences. For this purpose, we use a weight matrix prediction of ancient splice junction shadows in coding regions of the nucleotide sequences in current databases. The usage of splice junction shadows allows us to test the block evolution hypothesis in better detail in comparison with previous methods which were based only on currently existing recent exons. Our result of block length distribution at the nucleotide level shows a clear tendency to be divisible by three. At the protein level, several unexpected favorable block lengths, which are six, nine, 12 and 15 amino acids in length, were observed. Further refinements in our method for revealing splice junction shadows (structural block boundaries) might reveal peptides which probably maintain stable folds in different structures. The latter can in turn be used for protein structure prediction.
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Proper Citation:
V.B. Strelets, I.N. Shindyalov, Hwa A. Lim, "Analysis of Peptides from Known Proteins: Clusterization in Sequence Space", J. Mole. Evolution, 39(6), 625-630, (1994).

Abstract:
A combinatorial sequence space (CSS) model was introduced to represent sequences as a set of overlapping k-tuples of some fixed length which correspond to points in the CSS. The aim was to analyze clusterization of protein sequences in the CSS and to test various hypotheses about the possible evolutionary basis of this clusterization. The authors developed an easy-to-use technique which can reveal and analyze such a clusterization in a multidimensional CSS. Application of the technique led to an unexpectedly high clusterization of points in the CSS corresponding to k-tuples from known proteins. The clusterization could not be inferred from nonuniform amino acid frequencies or be explained by the influence of homologous data. None of the tested possible evolutionary and structural factors could explain the clusterization observed either. It looked as if certain protein sequence variations occurred and were fixed in the early course of evolution. Subsequent evolution (predominantly neutral) allowed only a limited number of changes and permitted new variants which led to preservation of certain k-tuples during the course of evolution. This was consistent with the theory of exon shuffling and protein block structure evolution. Possible applications of sequence space features found were also discussed.
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Proper Citation:
V.B. Strelets, A.A. Ptitsyn, L. Milanesi, Hwa A. Lim, "Data Bank Homology Search Algorithm with Linear Computation Complexity", Bioinformatics, 10(3), 319-322, (1994).

Abstract:
A new algorithm for data bank homology search is proposed. The principal advantages of the new algorithm are: (i) linear computation complexity; (ii) low memory requirements; and (iii) high sensitivity to the presence of local region homology. The algorithm first calculates indicative matrices of k-tuple 'realization' in the query sequence and then searches for an appropriate number of matching k-tuples within a narrow range in database sequences. It does not require k-tuple coordinates tabulation and in-memory placement for database sequences. The algorithm is implemented in a program for execution on PC- compatible computers and tested on PIR and GenBank databases with good results. A few modifications designed to improve the selectivity are also discussed. As an application example, the search for homology of the mouse homeotic protein HOX 3.1 is given.
Keyowrds:

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Proper Citation:
I.N. Shindyalov, V.B. Streletc, N.A. Kolchanov, Hwa A. Lim, "A Method for Multiple Alignment and Its Application in Homolog Compilation", Protein Seq. Data Anal., 5(5), 219-225, (1993).

Abstract:
A method for alignment of multiple sequences is presented. The method is an extension of an approach used for alignment of a pair of sequences, and is based on a diagonal fragment statistical analysis. Using competitive replacement of the diagonal fragments, the method is believed to require less central processing unit time (scales as the length of the sequence) and be less memory bound. Preliminary tree reconstruction allows one to establish the optimal order in which sequences should be incorporated into alignment. Matrix (profile) depiction is used for intermediate alignment representation. Possible implementation of the method in homolog compilation is also discussed.
Keyowrds:

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Proper Citation:
V.V. Solovyev, S.V. Korolev, Hwa A. Lim, "A New Approach for the Classification of Functional Regions of DNA Sequences Based on Fractal Representation", Intl J. Genomic Res., 1(1), 109-128, (1993).

Abstract:
A new approach for the classification of functional regions of DNA and RNA sequences, based on the Fractal Representation of Sets of sequences (FRS), is presented. A new measure of similarity for dividing sequences of different protein families, such as alpha- and beta-actins, globulins, alpha- and beta-interferons and others is also introduced. It is shown that the FRS of exon and intron sequences are distinguished and the measure can be used for searching these regions in new genomic sequences.
Keywords:

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Proper Citation:
V.V. Solovyev, S.K. Salikhova and Hwa A. Lim, "Spatial Structure Calculations of alpha-Helical Domains of Protein Molecules Using Quasispherical Primary Approximations", In: Biomedical Modelling and Simulation, Ed. J. Eisenfeld, D.S. Levine and M. Witten, pp. 201-211 (Elsevier Science Publishers B.V., North Holland, 1992).

Abstract:
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Proper Citation:
Hwa A. Lim, V.V. Solovyev, "A New General Approach for Searching Functional Regions Using Fractal Representation of Nucleotide and Amino Acid Sequences ", In: Harnessing Biotechnology for the 21st Century, Ed. M.R. Ladisch and A. Bose, pp. 387-391 (American Chemical Society, Washington, D.C., 1992).

Abstract:
A new approach combining the technique of fractal geometry and intrinsic characteristics of nucleic and amino acid sequences is described. The approach, fractal representation of sets of sequences (FRS), is used in particular to study the functional regions of genomes. Global properties of sequences are also plotted to obtain information about 5', exon, intron, 3'-regions in eukaryotic genes.
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Proper Citation:
D.K. Kuznetsov, Hwa A. Lim, "VisiCoor-A Simple Program for Protein Visualization", J. Molecular Graphics, 10, 21-28, (1991).

Abstract:
A well-drawn picture acts as an excellent metaphor for something real, and human vision provides instant, random access to any part of which the picture represents. It is in this sense that pictures can convey information more effectively than words alone. The power of the graphics work-stations available today makes visual presentation of scientific results a reality. A molecular graphics program for investigating protein structures, as well as several sample plots that show the power of the program, are presented.
Keyowrds:

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Proper Citation:
Hwa A. Lim, G.W. Slater, J. Noolandi, "A Model of the DNA Transient Orientation Overshoot during Gel Electrophoresis", J. Chem. Phys., 92, 709-721, (1990).

Abstract:
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Proper Citation:
J. Noolandi, G.W. Slater, Hwa A. Lim, J.L. Viovy, "Generalized Tube Model of Biased Reptation for Gel Electrophoresis of DNA", Science, 243, 1456-1458, (1989).

Abstract:
A theoretical analysis of the reptational motion of DNA in a gel that includes the effects of molecular fluctuations has been used to explain the main features found in experiments involving periodic inversion of the electric field. The resonance-like decrease of the electrophoretic mobility as a function of pulse duration is related to transient "undershoots" in the orientation of the molecule, in agreement with recent experimental data. These features arise from a delicate interplay of internal and center of mass motion of the molecules under pulsed field conditions, and are important for the separation of DNA molecules in the size range 0.2 to 10 million base pairs.
Keyowrds:

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