Abstract: A system for measuring pitting corrosion in metal using a digital camera having a lens and an output unit for identifying said color of a metal coupon on a gray scale and providing an output in said midrange of said scale when non corroded and different output after exposure to a corrosive environment. A computer is connected to said output of said camera to display said photographs to permit observation of said gray scale output based upon a minimum and maximum threshold inputs which are adjustable based on an observation of pitting. The points of interest on said coupon representing observed pitting are recorded and summed to calculate an estimated corrosion area corresponding to pitting on said coupon as a percentage of said total coupon area.

Abstract: The invention comprises a material sampling interface that includes one or more inlet manifolds and one or more outlet manifolds and piping running to and from the manifolds. There are rungs connecting the inlet manifold to the outlet manifold. In addition, a bypass rung is positioned between the inlet manifold and the outlet manifold, with a bypass valve positioned on the bypass. Each of the rungs has piping connected to the inlet and outlet manifolds and a removable reservoir connected to the piping. The reservoir includes an internal removable sampler adapted to sample the material. There is an inlet valve connected to the piping between the reservoir and the inlet manifold and an outlet valve connected to the piping between the reservoir and the outlet manifold. The invention is capable of sampling any flowable material including fluids, gases, particles, etc.

Abstract: A method, and apparatus and computer program products for executing the method. The method includes obtaining a set of multiple images of a target feature location on an array of multiple features, each image of the set representing the target feature location following deposition of a corresponding sub-set of multiple droplets for that feature. An overlay composite may be generated from the image set. The overlay composite may be used as a quality control tool, or in interrogating the array or processing results of the interrogation.

Abstract: Method for generating intra-particle crystallographic parameter maps and histograms of a chemically pure crystalline particulate substance. Spectral imaging, in general, and focus-fusion multi-layer spectral imaging, in particular, combined with pattern recognition classification analysis are performed on individual particles for forming sets of single-particle spectral fingerprint data, characterized by single-particle spectral fingerprint spectra. Spectral shifts are identified in the single-particle spectral fingerprint data, for forming intra-particle crystallographic region groups each featuring sub-sets of intra-particle spectral fingerprint pattern data, where selected data elements in each sub-set are shifted relative to corresponding data elements in remaining sub-sets in the same intra-particle crystallographic region group.

Abstract: Methods which may be implemented in computer systems for characterizing sites on a target molecule, for identifying prospective binding sites on a target molecule, and for identifying a position for a candidate molecule in a computation involving the target molecule and candidate molecule.

Abstract: The present invention provides a method for producing a mass-coded combinatorial library comprising a set of compounds having the general formula X(Y)n, where X is a scaffold, each Y is, independently, a peripheral moiety, and n is an integer greater than 1. The method comprises selecting a peripheral moiety precursor subset from a peripheral moiety precursor set. The subset includes a sufficient number of peripheral moiety precursors that at least about 50 distinct combinations of n peripheral moieties derived from the peripheral moiety precursors in the subset exist. The subset of peripheral moiety precursors is selected so that at least about 90% of all possible combinations of n peripheral moieties derived from the subset have a molecular mass sum which is distinct from the molecular mass sums of all of the other combinations of n peripheral moieties. The method further comprises contacting the peripheral moiety precursor subset with a scaffold precursor which has n reactive groups.

Abstract: An method for generating intra-particle morphological concentration/density maps and histograms of a chemically pure particulate substance. Spectral imaging, in general, and focus-fusion multi-layer spectral imaging, in particular, combined with pattern recognition classification analysis are performed on individual particles for forming sets of single-particle spectral fingerprint data, characterized by single-particle spectral fingerprint spectra. Spectral shifts are identified in the single-particle spectral fingerprint data, for forming intra-particle region groups featuring sub-sets of intra-particle spectral fingerprint pattern data, each characterized by an intra-particle spectral fingerprint pattern spectrum.

Abstract: Method for developing a quantitative structure activity relationship that includes obtaining a training set of chemical compounds with molecular descriptors consisting of a number of multidimensional vectors with an activity class for each of the vectors; partitioning the multidimensional vectors into groups having interdependence; transforming the descriptors such that the interdependence of the groups is lessened; estimating a probability distribution of the descriptors by assuming that a probability distribution of a product of each of the groups is approximately equal to the probability distribution of the molecular descriptors; performing the partitioning, transforming and estimating steps for each of the activity classes; and, developing a probability distribution for the activity classes.

Abstract: A method and apparatus are provided for identifying unknown chemical structures that are related to one or more known structures. Measured masses of the unknown structures (US members) are compared with the expected masses of the known structures (DS members). The mass differences between US members and DS members are compared with changes in mass (&Dgr;M) between molecules analyzed as a function dependent upon structure (&Dgr;S). The mass difference is considered as a differential function, &Dgr;M/&Dgr;S, the result of which is calculated for each ion in the US when compared with each ion in the DS. These values are then correlated with values that would be expected based on assumed possible structural modifications. In addition, higher order differential functions, such as &Dgr;2M/&Dgr;S2, can be used as needed to allow for correlation of structures in which more than one structural motif has changed.

Abstract: An unliganded form of Staphylococcus aureus thymidylate kinase (S. aureus TMK) has been crystallized, and the three dimensional x-ray crystal structure has been solved to 2.3 Å resolution. The x-ray crystal structure is useful for solving the structure of other molecules or molecular complexes, and designing inhibitors of S. aureus TMK activity.

Abstract: A method of multivariate spectral analysis, termed augmented classical least squares (ACLS), provides an improved CLS calibration model when unmodeled sources of spectral variation are contained in a calibration sample set. The ACLS methods use information derived from component or spectral residuals during the CLS calibration to provide an improved calibration-augmented CLS model. The ACLS methods are based on CLS so that they retain the qualitative benefits of CLS, yet they have the flexibility of PLS and other hybrid techniques in that they can define a prediction model even with unmodeled sources of spectral variation that are not explicitly included in the calibration model. The unmodeled sources of spectral variation may be unknown constituents, constituents with unknown concentrations, nonlinear responses, non-uniform and correlated errors, or other sources of spectral variation that are present in the calibration sample spectra.

Abstract: The present invention relates to a computational method for predicting a desired property and/or performance of polymers, and/or identifying and designing polymers that provide said desired property and/or performance, wherein the desired property can be provided by the neat, undiluted polymers, or diluted polymers in a composition. The method is a QSAR approach wherein the descriptors used are structural descriptors which are experimentally generated and/or derived from one or more analytical methods.

Abstract: A method of predicting the composition of hydrocarbon products of a complex carbonaceous material when exposed to specific time and temperature conditions is disclosed. In one embodiment, the material is characterized to obtain elemental, chemical and structural parameters. A representative chemical structure of the material is constructed based on the characterization information. The representative chemical structure is then stochastically expanded to a molecular ensemble chemical structural model that includes heteroatoms. The chemical structural model is coupled to a compositional yield model and the composition of the material products is determined using kinetic modeling.

Abstract: This invention is directed to the crystal structure of Acyl Carrier Protein Synthase (ACPS) complexed with Acyl Carrier Protein (ACP), the solution structure of B. subtilis ACP, and to the use of these structures in rational drug design methods to identify agents that may interact with active sites of ACPS and ACP, and to the testing of these agents to identify agents that may represent novel antibiotics.

Abstract: The present disclosure includes a method for locating functionally relevant atoms in protein structures, and a representation of spatial arrangements of these atoms allowing for flexible description of active sites in proteins. The search method can be based on comparison of local structure features of proteins that share a common biochemical function. Generally, the method does not depend on overall similarity of structures and sequences of compared proteins, or on previous knowledge about functionally relevant residues. The compared protein structures can be condensed to a graph representation, with atoms as nodes and distances as edge labels. Protein graphs can then be compared to extract all possible Common Structural Cliques. These cliques can be merged to create structural templates: graphs that describe structural analogies between compared proteins. Structures of serine endopeptidases were compared in pairs using the presented algorithm with different geometrical parameters.

Abstract: A new method to analyze and predict the binding energy for enzyme-transition state inhibitor interactions is presented. Computational neural networks are employed to discovery quantum mechanical features of transition states and putative inhibitors necessary for binding. The method is able to generate its own relationship between the quantum mechanical structure of the inhibitor and the strength of binding. Feed-forward neural networks with back propagation of error can be trained to recognize the quantum mechanical electrostatic potential at the entire van der Waals surface, rather than a collapsed representation, of a group of training inhibitors and to predict the strength of interactions between the enzyme and a group of novel inhibitors. The experimental results show that the neural networks can predict with quantitative accuracy the binding strength of new inhibitors.

Abstract: Microcapsules prepared by encapsulating an aqueous solution of a protein, drug or other bioactive substance inside a semi-permeable membrane by are disclosed. The microcapsules are formed by interfacial coacervation under conditions where the shear forces are limited to 0-100 dynes/cm2 at the interface. By placing the microcapsules in a high osmotic dewatering solution, the protein solution is gradually made saturated and then supersaturated, and the controlled nucleation and crystallization of the protein is achieved. The crystal-filled microcapsules prepared by this method can be conveniently harvested and stored while keeping the encapsulated crystals in essentially pristine condition due to the rugged, protective membrane. Because the membrane components themselves are x-ray transparent, large crystal-containing microcapsules can be individually selected, mounted in x-ray capillary tubes and subjected to high energy x-ray diffraction studies to determine the 3-D structure of the protein molecules.

Abstract: The distribution of chemical compounds in high-dimensional molecular descriptor space can be viewed in two dimensions by applying the projection method of this invention. This method has particular usefulness for viewing the relationships of a large number of compounds such as found in a large scale HTS or virtual combinatorial library. After selecting a representative subset of the larger data set of comounds, initially components from the high-dimensional descriptor space are determined by PCA. In order to relax an NLM projection using the PCA components as a start, the stress function is modified to reflect a local horizon beyound which the separation of the compounds is not meaningfully measureable. The resulting two dimensional projections provide a clear insight into the distribution of the chemical compounds in the higher dimensional space.

Abstract: A computer based technique for the global investigation of property spaces is described. More particularly, a technique is described for the global investigation of chemical space, with reference to drugs, using a system comprised of molecules and descriptors that allows systematic mapping of the chemical space. The technique is used to generate a map of N-dimensional chemical space that allows one to examine, in a consistent manner with existing tools, the inner relationship between various molecules. The technique therefore allows one to investigate unexplored regions of the chemical space, avoiding redundancy, generating compounds with similar chemical information content, or to focus on subsets of the chemical space that are relevant to drug-like structures, without additional errors due to extrapolation.

Abstract: A segmentation method of a frame of image information including a plurality of spaced DNA spot images corresponding to a plurality of DNA spots. The image information includes image intensity level information corresponding to said DNA spots. A grid including a plurality of spaced grid points corresponding to selected DNA spot images is generated, such that each grid point includes position information indicating the position of the grid point within said frame. For each DNA spot image: (1) background and signal intensity levels are extracted from image characteristic values for the spot image, and (2) difference values between the background intensity levels and signal intensity levels are determined. For each DNA spot: (1) the corresponding difference values are related a range of graphic values, (2) a graphic value for each difference value is selected; and (3) the selected graphic values are displayed.

Abstract: Disclosed are crystals, crystal structure Fc&ggr;RIIa protein, three dimensional coordinates of Fc&ggr;RIIa protein, and structures and models derived from the Fc&ggr;RIIa structure. Also disclosed are crystals of Fc&egr;RI protein and three dimensional coordinates of Fc&egr;RI protein monomers and dimers derived from the Fc&ggr;RIIa structure. Also disclosed are three dimensional coordinates of Fc&ggr;RIIIb proteins and models of Fc&ggr;RIIIb derived from the Fc&ggr;RIIa structure. The present invention also includes methods to produce such crystals, crystal structures and models. Uses of such crystals, crystal structures and models are also disclosed, including structure based drug design and therapeutic compositions.

Abstract: Positional Hashing, a novel method for detecting similarities between texts such as DNA sequences, amino acid sequences, and texts in natural language is disclosed. The method is particularly well suited for large-scale comparisons such as that of mutual comparisons of millions of sequence fragments that result from mammalian-scale sequencing projects and for whole-genome comparisons of multiple mammalian genomes. Positional Hashing is carried out by breaking the sequence comparison problem along its natural structure, solving the subproblems independently, and then collating the solutions into an overall result. The decomposition of the problem into subproblems enables parallelization, whereby a large number of nodes in a computer cluster or a computer farm are concurrently employed on solving the problem without incurring the quadratic time performance penalty characteristic of prior art.

Abstract: Generally, the present invention provides and uses a set of descriptors of three-dimensional molecular property fields. A portion of the descriptors are calculated in such a way as to separate property fields from the underlying structure of the molecule. These descriptors are calculated through reference to a property field center. Thus, only if the property field changes, such as by moving an atom having a non-zero property value, will the descriptors need to be recalculated. Additionally, a portion of the descriptors do relate to the underlying molecular structure, only these descriptors contain information from more than one reference point. In particular, a displacement is determined between a property field center and the centroid of a molecule. This descriptor contains information from two reference points. Furthermore, components of a property field are mapped onto a principal geometric frame, which essentially references the property field to the molecular shape.

Abstract: A greedy method for designing combinatorial arrays. An array of reagents are initially selected from a list of candidate reagents in a combinatorial library. The reagents in the array that maximize a design objective are determined in an iterative manner, by examining each variation site in the combinatorial library in a strictly alternating sequence. During each step, each candidate reagent at a given variation site is evaluated by constructing and evaluating the sub-array resulting from the systematic combination of that reagent with the selected reagents at all the other variation sites in the library. The candidate reagents at that variation site are ranked according to the fitness of their respective sub-arrays, and the reagents with the highest fitness are selected. The process is repeated for each variation site in the combinatorial library, until the fitness of the full combinatorial array can no longer be improved.

Abstract: Methods which may be implemented in computer systems for screening a database of candidate molecules to determine whether any particular subset of candidate molecules may be docked to a target molecule. These methods determine the force field of a target molecule only once and may be used for screening a large number of candidate molecules.

Abstract: A technique is disclosed that is useful for determining the presence of specific hybridization expression within an output pattern generated from a digitized image of a biological sample applied to an arrayed platform. The output pattern includes signals associated with noise, and signals associated with the biological sample, some of which are degraded or obscured by noise. Signal processing, such as interferometry, or more specifically, resonance interferometry, and even more specifically quantum resonance interferometry or stochastic resonance interferometry, is used to amplify signals associated with the biological sample having an intensity lower than the intensity of signals associated with noise so that they may be clearly distinguished from background noise. The improved detection technique allows rapid, reliable, and inexpensive measurements of arrayed platform output patterns.

Abstract: A method and a device for measuring the characteristics of a sample by spectral analysis. According to the method, the characteristics are calculated from the spectral data obtained by the spectral analysis, using a calibration model that has been established on the basis of reference samples. In order to improve the stability of the measuring process, an additional calculation of the characteristics (16) of the samples (1) takes place, using at least one additional calibration model (14) that has been established on the basis of additional reference samples (1″). Deviations between the characteristics (12, 16) calculated by the respective calibration models (11, 14) are determined and output.

Abstract: A main object is to cope with an unknown structure substance thereby to identify the structure of a parent ion highly precisely and to derive a supposed structure. A method for analyzing mass spectrometric data is disclosed, which: acquires mass spectrometric data on an ionized sample and dissociated ions dissociated from the sample as a parent ion; derives dissociated ion candidates by analyzing the molecular orbits on the candidates of the structures of the parent ion; and displays the analytical results of the parent ion candidates and the dissociated ion candidates and compares the data of the dissociated ion candidates and the data of dissociated ions actually measured, to evaluate the structures of the parent ion candidates.

Abstract: The static and electrostatic interaction energy fields between probe atoms and the atoms of a topomerically aligned fragment placed in a three-dimensional grid may be used to derive a CoMFA model. The topomeric CoMFA model coefficients may be used to predict partial activity values for fragments not derived from molecules of the activity series. The partial activities can be summed to provide a predicted activity for all fragment positions of the activity series molecules. A Virtual Library in which topomerically aligned fragments are associated with their respective steric and electrostatic interaction energies can be searched for fragments similar in shape to the fragments derived from the molecules of the activity series. The identified fragments can be used with the topomeric CoMFA coefficients to predict their activity if used in the molecular activity series.

Abstract: Structure-activity methods based on molecular descriptors that are a combination of structural information about the through-space and through-bond relationships between components of a molecule's structure and spectral data attributable to those components are disclosed. In some embodiments, a molecule is described by multiple sets of such descriptors to account for flexibility in the structure of the molecule. In a particularly disclosed embodiment, predicted 13C—13C COSY data and 13C—13C distance data are used as descriptors. Models of molecular properties may be established using the disclosed spectral data-activity methods and used to predict the properties of molecules.

Abstract: A method for comparing DNA base sequences by comparing similarities between two amino acid sequences translated from two DNA base sequences, respectively, includes (1) a step of dividing each of the first DNA base sequence and the second DNA base sequence into groups of successive three nucleotides each, translating each of these groups of nucleotides into an amino acid, and thereby obtaining a first amino acid sequence and a second amino acid sequence, and (2) a step of determining similarities between each amino acid of the first translated amino acid sequence and each amino acid of the second translated amino acid sequence in view of nucleotide insertions or deletions in the first and second DNA base sequence and amino acid insertions or deletions in the first and second translated amino acid sequence. The method is repeated by shifting the base sequences one base at a time.

Abstract: A method for determining a property of an unknown material including the steps of determining the IR spectrum of the unknown material, fitting the IR spectrum to a linear combination of known spectra in a database, wherein a database includes spectra of reference materials whose assay properties are known, and determining the property of the unknown material from the assay properties of the reference materials.

Abstract: Method and apparatus for designing a synthesis route for a target molecule is provided. The method for designing a synthesis route for a target molecule comprises: generating a plurality of individuals, wherein each individual encodes a synthesis route; decoding each individual to produce a synthesis route comprising at least one reactant molecules and at least one reaction; and determining how well the synthesis route satisfies a design goal. A computer readable medium containing instructions for a computer program executable by the computer to perform a method for designing a synthesis route for a target molecule is also provided. The apparatus comprises a parallel computer system for executing instructions of a computer program to perform a method for designing a synthesis route for a target molecule.

Abstract: An exemplary embodiment of the invention relates to a method, system, apparatus, and storage medium for designing and locating chemical structures. The apparatus comprises a user accessible chemical design and query tool comprising a user interface including an interactive host and a database storing a graphical representation of at least one chemical design structure. Upon accessing the chemical design and query tool by a user, the user interface guides the user in selecting a chemical design structure, and submitting the chemical design structure to a provider system. The invention also includes a method, system, and storage medium.

Abstract: Methods, including computer implemented methods for calculating a characteristic property of a molecule from the 3D-structure of the molecule by correlation analysis, in which the characteristic property is equal to a contribution from the substituent parts of the molecule and a contribution from some measured property of the molecule such as the hydrophobicity and the contribution to the characteristic property from substituent parts of the molecule is equal to a function of the distance of the substituent part to a reaction center multiplied by a weight factor and substantially the same functional form of the distance function is used for calculating the contribution for each substituent part.

Abstract: A method and system for normalizing two or more molecular array data sets. Input molecular array data sets are separately globally normalized by, for example, dividing the feature-signal magnitudes of each data set by the geometric mean of the feature-signal magnitudes of the data set. The globally normalized feature signal magnitudes within each data set are ranked in ascending order. A numeric function is created that relates feature-signal magnitudes of the data sets. Only a subset of the features, obtained by selecting features that are similarly ranked in the separate feature-signal-magnitude rankings for the data sets, is used to construct the numeric function. The numeric function is smoothed by one of many possible different smoothing procedures.

Abstract: There is disclosed a method for visualizing secondary structures of RNA molecules, by which nearly overlap-free polygonal displays of RNA secondary structures are produced with minimal distortion to structural elements, with minimal search for positioning them, and with minimal user intervention. While vector and vector space are used to determine the direction and space of a structural element, two heuristics are adopted for the task of searching for the space and direction of structural elements. With the aid of the two heuristics, loops are positioned in decreasing order of their sizes and a helix is positioned, depending on the position of its adjacent loop which has been positioned. In consideration of both a potentially open and wide vector space and an allowed vector space, a structural element is positioned.

Abstract: Reactive sites on a substrate molecule, typically a drug, may be identified and the relative rates of their metabolism by the CYP enzymes may be determined. Determining these relative rates is an important factor in determining the absolute rate of metabolism of the individual sites and the substrate molecule as a whole. This information is also a critical factor in determining whether and how the substrate can be redesigned to improve its ADME/PK properties. In this regard, it is particularly important to know how the relative rates compare to the rate of a non-metabolic side reaction (branch pathway) such as water generation and regeneration of the substrate.

Abstract: The present invention is directed to the use of computational and other experimental data in the design of new pharmaceuticals, and in predicting the metabolism and toxicological profiles thereof. Computational and other information is used to further understand drug metabolism and toxicology, particulary in relation to monooxygenase enzymes, such as those of the CYP system, that are involved in drug metabolism. Information derived according to the practice of the invention is useful in determining the clearance or half-life of drugs, and the nature and toxicity of byproducts resulting from their metabolism. The invention provides novel and powerful new approaches to drug design.

Abstract: Disclosed is a method and system for measurement of periodic gratings which have deviations which result in more than two materials occurring along at least one line in the periodic direction. A periodic grating is divided into a plurality of hypothetical layers, each hypothetical layer having a normal vector orthogonal to the direction of periodicity, each hypothetical layer having a single material within any line parallel to the normal vector, and at least one of the hypothetical layers having at least three materials along a line in the direction of periodicity. A harmonic expansion of the permittivity &egr; or inverse permittivity 1/&egr; is performed along the direction of periodicity for each of the layers including the layer which includes the first, second and third materials.

Abstract: A magnetic interaction is calculated by expressing a localized magnetic orbital as a linear combination of molecular orbitals and determining a localized magnetic orbital to be calculated from a maximum overlap condition evaluated between a reference orbital localized in anatomic orbital and the localized magnetic orbital. Another magnetic interaction is calculated by expressing a localized magnetic crystal orbital as a linear combination of crystal orbitals and determining a localized magnetic crystal orbital to be calculated from the maximum overlap condition.

Abstract: A method of measuring the concentration of water in an ion exchange membrane cmprising: (i) measuring the absorbance of electromagnetic radiation transmitted through the membrane, said electromagnetic radiation comprising at least one frequency of an intensity such that it is at least partially, but not entirely, absorbed by water molecules within the membrane; (ii) measuring the thickness of the membrane; and (iii) using the values obtained in (i) and (ii) above to calculate the concentration of water molecules in the membrane.

Abstract: The present invention provides methods for producing high resolution crystals of ribosomes and ribosomal subunits as well as the crystals produced by such methods. The x-ray diffraction patterns of the crystals provided by the present invention are of sufficiently high resolution for determining the three-dimensional structure of ribosomes and ribosomal subunits, for identifying ligand binding sites on ribosomes and ribosomal subunits, and for molecular modeling of ligands which interact with ribosomes and ribosomal subunits. The present invention provides methods for identifying ribosome-related ligands and methods for designing ligands with specific ribosome-binding properties. Thus, the methods of the present invention may be used to produce ligands which are designed to kill or inhibit any specific target organism(s).

Abstract: Methods for generating multiple rounds of combinatorial libraries, which use Monte Carlo methods to search the multi-dimensional composition and non-composition space of variables in combinatorial chemistry; the combinatorial libraries generated and screened by such Monte Carlo methods; and an apparatus for generating and screening such libraries robotically. The process involves preparing a first set of samples, then changing the composition and non-composition variables of the samples using Monte Carlo sampling methods, and accepting proposed new samples according to a detailed balance acceptance criterion.

Abstract: The present invention relates to methods for identifying novel genes comprising: (i) generating one or more specialized databases containing information on gene/protein structure, function and/or regulatory interactions; and (ii) searching the specialized databases for homology or for a particular motif and thereby identifying a putative novel gene of interest. The invention may further comprise performing simulation and hypothesis testing to identify or confirm that the putative gene is a novel gene of interest.

Abstract: The present invention provides the atomic coordinates derived from high resolution x-ray diffraction of the cocrystal complex comprising mupirocin with its target enzyme, isoleucyl-tRNA synthetase from Staphylococcus aureus, and the cognate tRNAile from Escherichia coli. The present invention further provides methods of using the atomic coordinates to identify and design new agents which modulate protein synthesis as well as the agents themselves.

Abstract: The present invention concerns methods and systems for predicting the biological function(s) of proteins. The invention is based on the development of functional site descriptors for discrete protein biological functions. Functional site descriptors are geometric representations of protein functional sites in three-dimensional space, and can also include additional parameters, for example, conformational information. Following their development, one or more functional site descriptors (for one or more different biological functions) are used to probe protein structures to determine if such structures contain the functional sites described by the corresponding functional site descriptors. If so, the protein(s) containing the functional site(s) are predicted to have the corresponding biological function(s).

Abstract: Methods of obtaining directional information of a solvent-accessible surface of an atom or molecule are described. Also disclosed are methods for simulating the kinetic behavior of a solute molecule in a solvent are also described. The methods utilize a representation of the solvent-accessible surface of the solute molecule which includes information on the geometric orientation of the surface relative to the molecule, and using the representation in a corrected kinetic model to simulate the kinetic behavior of the solute molecule in the solvent.

Abstract: An apparatus and method for the repeatable detection and recording of low-threshold molecular electromagnetic signals. The sample material and detection apparatus are contained with a magnetically shielded faraday cage to shield them from extraneous electromagnetic signals. The detection apparatus includes a detection coil and Super Conducting Quantum Interference Device (“SQUID”). White noise is injected external to the SQUID and the signals emitted by the sample material enhanced by stochastic resonance.

Abstract: The invention features a sort computer which interfaces with a sorting device in order to control the sorting of beads on a bead by bead basis. The invention further features novel methods for the directed synthesis of encoded libraries of oligomers, e.g., oligonucleotides, on beads. These methods allow the synthesis of libraries that are sufficiently large to permit complex genomic analyses to be carried out. New methods of using the encoded libraries also are described.