Department of Systems and Computational Biology

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    Conformational studies on β‐bend containing a cis peptide unit
    ( 1992-01-01) NAGARAJARAM, H. A. ; PAUL, P. K.C. ; RAMANARAYANAN, K. ; SOMAN, K. V. ; RAMAKRISHNAN, C.
    Conformational studies have been carried out on the X‐cis‐Pro tripeptide system (a system of three linked peptide units, in the trans‐cis‐trans configuration) using energy minimization techniques. For X, residues Gly, L‐Ala, D‐Ala and L‐Pro have been used. The energy minima have been classified into different groups based upon the conformational similarity. There are 15, 20, 18 and 6 minima that are possible for the four cases respectively arid these fall into 11 different groups. A study of these minima shows that, (i) some minima contain hydrogen bonds ‐ either 4→1 or 1→2 type, (ii) the low energy minima qualify themselves as bend conformations, (iii) cis′ and trans′ conformations are possible for the prolyl residue as also the Cγ‐endo and Cγ‐exo puckerings, and (iv) for Pro‐cis‐Pro, cis′ at the first prolyl residue is ruled out, due to the high energy. The available crystal structure data on proteins and peptides, containing cis‐Pro segment have been examined with a view to find the minima that occur in solid state. The data from protein show that they fall under two groups. The conformation at X in X‐cis‐Pro is near extended when it is a non‐glycyl residue. In both peptides and proteins there exists a preference for trans′ conformation at prolyl residue over cis′ when X is a non‐glycyl residue. The minima obtained can be useful in modelling studies. Copyright © 1992, Wiley Blackwell. All rights reserved
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    Termination of right handed helices in proteins by residues in left handed helical conformations
    ( 1993-04-19) Nagarajaram, H. A. ; Sowdhamini, R. ; Ramakrishnan, C. ; Balaram, P.
    An analysis of 636 helical segments, ranging in length from 4 to 32 residues, from 123 independent protein crystal structures reveals that helix termination by residues in left handed (αL) helical conformations is a common occurrence. Gly and Asn residues are the most frequent αL helix terminators, with the former having a very high propensity to adopt such conformations. The αR-αR-αR-αL segment at the C termini of protein helices often possesses a 6 → 1 (π-type) hydrogen bond between the CO of residue i and the NH of residue i + 5 with residue i + 4 occurring in the αL conformation. A stereochemical analysis of 216 examples shows that in 62 cases the 6 → 1 hydrogen bond is absent. The present analysis provides a quantitative measure of the propensity of the 20 amino acids to adopt αL helix terminating conformations. © 1993.
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    Stereochemical studies on cyclic peptides: Detailed energy minimization studies on hydrogen bonded all-trans cyclic pentapeptide backbones
    ( 1995-12-01) Nagarajaram, H. A. ; Ramakrishnan, C.
    Conformational studies have been carried out on hydrogenbonded all-trans cyclic pentapeptide backbone. Application of a combination of grid search and energy minimization on this system has resulted in obtaining 23 minimum energy conformations, which are characterized by unique patterns of hydrogen bonding comprising of β- and γ-turns. A study of the minimum energy conformations vis-a-vis non-planar deviation of the peptide units reveals that non-planarity is an inherent feature in many cases. A study on conformational clustering of minimum energy conformations shows that the minimum energy conformations fall into 6 distinct conformational families. Preliminary comparison with available X-ray structures of cyclic pentapeptide indicates that only some of the minimum energy conformations have formed crystal structures. The set of minimum energy conformations worked out in the present study can form a consolidated database of prototypes for hydrogen bonded backbone and be useful for modelling cyclic pentapeptides both synthetic and bioactive in nature. © 1995 Indian Academy of Sciences.
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    A procedure for the prediction of temperature-sensitive mutants of a globular protein based solely on the amino acid sequence
    ( 1996-11-26) Varadarajan, R. ; Nagarajaram, H. A. ; Ramakrishnan, C.
    Temperature-sensitive (Ts) mutants of a protein are an extremely powerful tool for studying protein function in vivo and in cell culture. We have devised a method to predict those residues in a protein sequence that, when appropriately mutated, are most likely to give rise to a Ts phenotype. Since substitutions of buried hydrophobic residues often result in significant destabilization of the protein, our method predicts those residues in the sequence that are likely to be buried in the protein structure. We also indicate a set of amino acid substitutions, which should be made to generate a Ts mutant of the protein. This method requires only the protein sequence. No structural information or homologous sequence information is required. This method was applied to a test data set of 30 nonhomologous protein structures from the Protein Data Bank. All of the residues predicted by the method to be ≤95% buried were, in fact, buried in the protein crystal structure. In contrast, only 50% of all hydrophobic residues in this data set were ≤95% buried. This method successfully predicts several known Ts and partially active mutants of T4 lysozyme, λ repressor, gene V protein, and staphylococcal nuclease. This method also correctly predicts residues that form part of the hydrophobic cores of λ repressor, myoglobin, and cytochrome b562.
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    Stereochemical punctuation marks in protein structures: Glycine and proline containing helix stop signals
    ( 1998-02-06) Gunasekaran, K. ; Nagarajaram, H. A. ; Ramakrishnan, C. ; Balaram, P.
    An analysis on the nature of α-helix stop signals has been carried out, using a dataset of 1057 helices identified from 250 high resolution (≤ 2.0 Å), non-homologous, protein crystal structures. The backbone dihedral angles (φ, ψ) of the terminating residue (T) were found to cluster either in the left-handed helical region (α(L): φ = 20°to 125°and ψ = -45°to 90°; 469 helices (44%)) or in the extended region (E: φ = -180°to -30°and ψ = 60°to 180°and -180°to -150°; 459 helices (43%)) of the Ramachandran map. These two broad categories of helix stop signals, α(L) and E-terminated helices, were further examined for sequence preferences. Gly residues were found to have an overwhelming preference to occur as the 'α(L)-terminator (T)' resulting in the classical Schellman motif, with a strong preference for hydrophobic residues at position T - 4 and T + 1. In the case of E-terminated helices His, Asn, Leu and Phe were found to occur with high propensity at position T. Quite remarkably Pro residues, with single exception, were absent at position T, but had the highest propensity at position T + 1. Examination of the frequencies of hydrophobic (h) and polar (p) residues at positions flanking Gly/Pro permitted delineation of exclusive patterns and predictive rules for Gly-terminated helices and Pro-terminated helices. The analysis reveals that Pro residues flanked by polar amino acids have a very strong tendency to terminate helices. Examination of a segment ranging from T - 4 to T + 3 appeared to be necessary to determine whether helix termination or continuation occur at Gly residues. The two types of helix termination (α(L), E) signals also differed dramatically in their solvent accessibility. Gly and Pro residues at helix termini appeared to be strongly conserved in homologous sequences.
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    CAMPASS: A database of structurally aligned protein superfamilies
    ( 1998-09-15) Sowdhamini, R. ; Burke, David F. ; Huang, Jing Fei ; Mizuguchi, Kenji ; Nagarajaram, Hampapathalu A. ; Srinivasan, N. ; Steward, Robert E. ; Blundell, Tom L.
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    Protein three-dimensional structural databases: Domains, structurally aligned homologues/superfamilies
    ( 1998-11-01) Sowdhamini, R. ; Burke, David F. ; Deane, Charlotte ; Huang, Jing Fei ; Mizuguchi, Kenji ; Nagarajaram, Hampapathulu A. ; Overington, John P. ; Srinivasan, N. ; Steward, Robert E. ; Blundell, Tom L.
    This paper reports the availability of a database of protein structural domains (DDBASE), an alignment database of homologous proteins (HOMSTRAD) and a database of structurally aligned superfamilies (CAMPASS) on the World Wide Web (WWW). DDBASE contains information on the organization of structural domains and their boundaries; it includes only one representative domain from each of the homologous families. This database has been derived by identifying the presence of structural domains in proteins on the basis of inter-secondary structural distances using the program DIAL [Sowdhamini and Blundell (1995), Protein Sci. 4, 506-520]. The alignment of proteins in superfamilies has been performed on the basis of the structural features and relationships of individual residues using the program COMPARER [Sali and Blundell (1990), J. Mol. Biol. 212, 403-428]. The alignment databases contain information on the conserved structural features in homologous proteins and those belonging to superfamilies. Available data include the sequence alignments in structure-annotated formats and the provision for viewing superposed structures of proteins using a graphical interface. Such information, which is freely accessible on the WWW, should be of value to crystallographers in the comparison of newly determined protein structures with previously identified protein domains or existing families.
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    Analysis of interactive packing of secondary structural elements in α/β units in proteins
    ( 1999-01-01) Reddy, Boojala V.B. ; Nagarajaram, Hampapathalu A. ; Blundell, Tom L.
    An α-helix and a β-strand are said to be interactively packed if at least one residue in each of the secondary structural elements loses 10% of its solvent accessible contact area on association with the other secondary structural element. An analysis of all such 5,975 nonidentical α/β units in protein structures, defined at ≤2.5 Å resolution, shows that the interaxial distance between the α-helix and the β-strand is linearly correlated with the residue-dependent function, log[(V/nda)/n-int], where V is the volume of amino acid residues in the packing interface, nda is the normalized difference in solvent accessible contact area of the residues in packed and unpacked secondary structural elements, and n-int is the number of residues in the packing interface. The β-sheet unit (βu), defined as a pair of adjacent parallel or antiparallel hydrogen-bonded β-strands, packing with an α-helix shows a better correlation between the interaxial distance and log (V/nda) for the residues in the packing interface. This packing relationship is shown to be useful in the prediction of interaxial distances in α/β units using the interacting residue information of equivalent α/β units of homologous proteins. It is, therefore, of value in comparative modeling of protein structures.
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    Analysis and prediction of inter-strand packing distances between β-sheets of globular proteins
    ( 1999-01-01) Nagarajaram, Hampapathalu A. ; Reddy, Boojala V.B. ; Blundell, Tom L.
    Any two β-strands belonging to two different β-sheets in a protein structure are considered to pack interactively if each β-strand has at least one residue that undergoes a loss of one tenth or more of its solvent contact surface area upon packing. A data set of protein 3-D structures (determined at 2.5 Å resolution or better), corresponding to 428 protein chains, contains 1986 non-identical pairs of β-strands involved in interactive packing. The inter-axial distance between these is significantly correlated to the weighted sum of the volumes of the interacting residues at the packing interface. This correlation can be used to predict the changes in the inter-sheet distances in equivalent β-sheets in homologous proteins and, therefore, is of-value in comparative modelling of proteins.
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    An iterative structure-assisted approach to sequence alignment and comparative modeling
    ( 1999-01-01) Burke, David F. ; Deane, Charlotte M. ; Nagarajaram, Hampapathalu A. ; Campillo, Nuria ; Martin-Martinez, Mercedes ; Mendes, Joaquim ; Molina, Franck ; Perry, Jeff ; Reddy, B. V.B. ; Soares, Claudio M. ; Steward, Robert E. ; Williams, Mark ; Carrondo, Maria Armenia ; Blundell, Tom L. ; Mizuguchi, Kenji
    Correct alignment of the sequence of a target protein with those of homologues of known three-dimensional structure is a key step in comparative modeling. Usually an iterative approach that takes account of the local and overall structural features is required. We describe such an approach that exploits databases of structural alignments of homologous proteins (HOMSTRAD, http://www-cryst.bioc.cam.ac.uk/homstrad) and protein superfamilies (CAMPASS, http://www-cryst.bioc.cam.ac.uk/campass), in which structure-based alignments are analyzed and formatted with the program JOY (http://www- cryst.bioc.cam.ac.uk/joy) to reveal conserved local structural features. The databases facilitate the recognition of a family or superfamily, they assist in the selection of useful parent structures, they are helpful in alignment of the target sequences with the parent set, and are useful for deriving relationships that can be used in validating models. In the iterative approach, a model is constructed on the basis of the proposed sequence alignment and this is then reexpressed in the JOY format and realigned with the parent set. This is repeated until the model and sequence alignment is optimized. We examine the case for comparison and use of multiple structures of family members, rather than a single parent structure. We use the targets attempted by our group in CASP3 to assess the value of such procedures.
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    Incorporating knowledge-based biases into an energy-based side-chain modeling method: Application to comparative modeling of protein structure
    ( 2001-07-16) Mendes, Joaquim ; Nagarajaram, Hampapathalu A. ; Soares, Cláudio M. ; Blundell, Tom L. ; Carrondo, Maria Arménia
    The performance of the self-consistent mean field theory (SCMFT) method for side-chain modeling, employing rotamer energies calculated with the flexible rotamer model (FRM), is evaluated in the context of comparative modeling of protein structure. Predictions were carried out on a test set of 56 model backbones of varying accuracy, to allow side-chain prediction accuracy to be analyzed as a function of backbone accuracy. A progressive decrease in the accuracy of prediction was observed as backbone accuracy decreased. However, even for very low backbone accuracy, prediction was substantially higher than random, indicating that the FRM can, in part, compensate for the errors in the modeled tertiary environment. It was also investigated whether the introduction in the FRM-SCMFT method of knowledge-based biases, derived from a backbone-dependent rotamer library, could enhance its performance. A bias derived from the backbone-dependent rotamer conformations alone did not improve prediction accuracy. However, a bias derived from the backbone-dependent rotamer probabilities improved prediction accuracy considerably. This bias was incorporated through two different strategies. In one (the indirect strategy), rotamer probabilities were used to reject unlikely rotamers a priori, thus restricting prediction by FRM-SCMFT to a subset containing only the most probable rotamers in the library. In the other (the direct strategy), rotamer energies were transformed into pseudo-energies that were added to the average potential energies of the respective rotamers, thereby creating hybrid energy-based/ knowledge-based average rotamer energies, which were used by the FRM-SCMFT method for prediction. For all degrees of backbone accuracy, an optimal strength of the knowledge-based bias existed for both strategies for which predictions were more accurate than pure energy-based predictions, and also than pure knowledge-based predictions. Hybrid knowledge-based/energy-based methods were obtained from both strategies and compared with the SCWRL method, a hybrid method based on the same backbone-dependent rotamer library. The accuracy of the indirect method was approximately the same as that of the SCWRL method, but that of the direct method was significantly higher. © 2001 John Wiley & Sons, Inc.
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    Phosphoribosyltransferase superfamily: A comparative structural analysis
    ( 2001-12-01) Campillo, Nuria ; Nagarajaram, Hampapathalu A. ; Ghosh, Indira
    Purine phosphoribosyltransferases are members of a group of enzymes that are responsible for the formation of purine, pyrimidine and pyridine nucleotides. One feature of this family is a flexible loop, which is involved in the catalytic mechanism. This loop is variable both in sequence and structure in the phosphoribosyltransferase family. This paper describes the modelling and validation of a model of Plasmodium falciparum hypoxanthine-guanidine- phosphoribosyltransferase in an open conformation. A comparison of this model with 3D-structures of other members of the phosphorybosyltransferase family has allowed an assessment of the role of the open and closed conformations of the loop in the catalytic mechanism.
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    Identification of novel mutations causing familial primary congenital glaucoma in Indian pedigrees
    ( 2002-05-13) Panicker, Shirly G. ; Reddy, Aramati B.M. ; Mandal, Anil K. ; Ahmed, Niyaz ; Nagarajaram, Hampapathalu A. ; Hasnain, Seyed E. ; Balasubramanian, Dorairajan
    PURPOSE. To determine the possible molecular genetic defect underlying primary congenital glaucoma (PCG) in India and to identify the pathogenic mutations causing this childhood blindness. METHODS. Twenty-two members of five clinically well-characterized consanguineous families were studied. The primary candidate gene CYP1B1 was amplified from genomic DNA, sequenced, and analyzed in control subjects and patients to identify the disease-causing mutations. RESULTS. Five distinct mutations were identified in the coding region of CYP1B1 in eight patients of five PCG-affected families, of which three mutations are novel. These include a novel homozygous frameshift, compound heterozygous missense, and other known mutations. One family showed pseudodominance, whereas others were autosomal recessive with full penetrance. In contrast to all known CYP1B1 mutations, the newly identified frameshift is of special significance, because all functional motifs are missing. This, therefore, represents a rare example of a natural functional CYP1B1 knockout, resulting in a null allele (both patients are blind). CONCLUSIONS. The molecular mechanism leading to the development of PCG is unknown. Because CYP1B1 knockout mice did not show a glaucoma phenotype, the functional knockout identified in this study has important implications in elucidating the pathogenesis of PCG. Further understanding of how this molecular defect leads to PCG could influence the development of specific therapies. This is the first study to describe the molecular basis of PCG from the Indian subcontinent and has profound and multiple clinical implications in diagnosis, genetic counseling, genotype-phenotype correlations and prognosis. Hence, it is a step forward in preventing this devastating childhood blindness.
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    Design, synthesis, and evaluation of new noncross-linking pyrrolobenzodiazepine dimers with efficient DNA binding ability and potent antitumor activity
    ( 2002-10-10) Kamal, Ahmed ; Ramesh, G. ; Laxman, N. ; Ramulu, P. ; Srinivas, O. ; Neelima, K. ; Kondapi, Anand K. ; Sreenu, V. B. ; Nagarajaram, H. A.
    New sequence selective mixed imine-amide pyrrolobenzodiazepine (PBD) dimers have been developed that are comprised of DC-81 and dilactam of DC-81 subunits tethered to their C8 positions through alkanedioxy linkers (comprised of three to five and eight carbons). Thermal denaturation studies show that after 18 h of incubation with calf thymus DNA at a 5:1 DNA/ligand ratio, one of them (5c) increases the ΔTm value by 17.0 °C. Therefore, these unsymmetrical molecules exhibit significant DNA minor groove binding affinity and 5c linked through the pentanedioxy chain exhibits efficient DNA binding ability that compares with the cross-linking DSB-120 PBD dimer (ΔTm = 15.4 °C). Interestingly, this imine-amide PBD dimer has been linked with a five carbon chain linker unlike DSB-120, which has two DC-81 subunits with a three carbon chain linker, illustrating the effect of the noncross-linking aspect by introducing the noncovalent subunit. The binding affinity of the compounds has been measured by restriction endonuclease digestion assay based on inhibition of the restriction endonuclease BamHI. This study reveals the significance of noncovalent interactions in combination with covalent bonding aspects when two moieties of structural similarities are joined together. This allows the mixed imine-amide PBD dimer with a five carbon chain linker to achieve an isohelical fit within the DNA minor groove taking in to account both the covalent bonding and the noncovalent binding components. This has been supported by molecular modeling studies, which indicate that the PBD dimer with a five carbon chain linker gives rise to maximum stabilization of the complex with DNA at the minor groove as compared to the other PBD dimers with three, four, and eight carbon chain linkers. The energy of interaction in all of the complexes studied is correlated to the ΔTm values. Furthermore, this dimer 5c has significant cytotoxicity in a number of human cancer cell lines.
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    Influence of solvent molecules on the stereochemical code of glycyl residues in proteins
    ( 2002-11-15) Eswar, Narayanan ; Nagarajaram, H. A. ; Ramakrishnan, C. ; Srinivasan, N.
    The Ramachandran steric map and energy diagrams of the glycyl residue are symmetric. A plot of (φ,ψ) angles of glycyl residues in 250 nonhomologous and high-resolution protein structures is also largely symmetric. However, there is a clear aberration in the symmetry. Although there is a cluster of points corresponding to the right-handed α-helical region, the "equivalent" cluster is clearly shifted to in and around the (φ,ψ) values of (90°, 0°) instead of being centered at the left-handed α-helical region of (60°, 40°). This lack of symmetry exists even in the (φ,ψ) distribution of residues from non-α-helical regions in proteins. Here we provide an explanation for this observation. An analysis of glycyl conformations in small peptide structures and in "coil" proteins, which are largely devoid of helical and sheet regions, shows that glycyl residues prefer to adopt conformations around (±90°, 0°) instead of right- and left-handed α-helical regions. By using theoretical calculations, such conformations are shown to have highest solvent accessibility in a system of two-linked peptide units with glycyl residue at the central Cα atom. This finding is consistent with the observations from 250 nonhomologous protein structures where glycyl residues with conformations close to (±90°, 0°) are seen to have high solvent accessibility. Analysis of a subset of nonhomologous structures with very high resolution (1.5 Å or better) shows that water molecules are indeed present at distances suitable for hydrogen bond interaction with glycyl residues possessing conformations close to (±90°, 0°). It is suggested that water molecules play a key role in determining and stabilizing these conformations of glycyl residues and explain the aberration in the symmetry of glycyl conformations in proteins. © 2002 Wiley-Liss, Inc.
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    MICAS: a fully automated web server for microsatellite extraction and analysis from prokaryote and viral genomic sequences.
    ( 2003-01-01) Sreenu, Vattipally B. ; Ranjitkumar, Gundu ; Swaminathan, Sugavanam ; Priya, Sasidharan ; Bose, Buddhaditta ; Pavan, Mogili N. ; Thanu, Geeta ; Nagaraju, Javaregowda ; Nagarajaram, Hampapathalu A.
    MICAS is a web server for extracting microsatellite information from completely sequenced prokaryote and viral genomes, or user-submitted sequences. This server provides an integrated platform for MICdb (database of prokaryote and viral microsatellites), W-SSRF (simple sequence repeat finding program) and Autoprimer (primer design software). MICAS, through dynamic HTML page generation, helps in the systematic extraction of microsatellite information from selected genomes hosted on MICdb or from user-submitted sequences. Further, it assists in the design of primers with the help of Autoprimer, for sequences containing selected microsatellite tracts.
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    MICdb: Database of prokaryotic microstatellites
    ( 2003-01-01) Sreenu, Vattipally B. ; Alevoor, Vishwanath ; Nagaraju, Javaregowda ; Nagarajaram, Hampapathalu A.
    The MICdb (Microsatellites Database) (http://www.cdfd.org.in/micas) is a comprehensive relational database of non-redundant microsatellites extracted from fully sequenced prokaryotic genomes. The current version (1.0) of the database has been compiled from 83 genomes belonging to different phylogenetic groups. This database has been linked to MICAS, the web-based Microstatellite Analysis Server. MICAS provides a user-friendly front-end to systematically extract data on microsatellite tracts from genomes. The database contains the following information pertaining to the microsatellites: the regions (coding/non-coding, if coding, their GenBank annotations) containing microsatellite tracts; the frequencies of their occurrences, the size and the number of repeating motifs; and the sequences of the tracts. MICAS also provides an interface to Autoprimer, a primer design program to automatically design primers for selected microsatellite loci.
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    Persistence in an antiferromagnetic Ising system with conserved magnetisation
    ( 2003-02-01) Saharay, Moumita ; Sen, Parongama
    We obtain the persistence exponents for an antiferromagnetic Ising system in which the magnetisation is kept constant. This system belongs to model C (system with non-conserved order parameter with a conserved density) and is expected to have persistence exponents different from that of model A (system with no conservation) but independent of the conserved density. Our numerical results for both local persistence at zero temperature and global persistence at the critical temperature however indicate that the exponents are dependent on the conserved magnetisation in both two and three dimensions. This non-universal feature is attributed to the presence of the conserved field and is special to the persistence phenomena. © 2002 Elsevier Science B.V. All rights reserved.
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    AmpliBASE MT™: A Mycobacterium tuberculosis diversity knowledgebase
    ( 2004-04-12) Majeed, Ahmed A. ; Ahmed, Niyaz ; Rao, K. Rajender ; Ghousunnissa, S. ; Kauser, Farhana ; Bose, Buddhaditta ; Nagarajaram, H. A. ; Katoch, V. M. ; Cousins, Debby V. ; Sechi, Leonardo A. ; Gilman, Robert H. ; Hasnain, Seyed E.
    Summary: AmpliBASE MT™ is an online databank of high-resolution DNA fingerprints representing fluorescent amplified fragment length polymorphism (FAFLP) profiles or amplitypes developed for the Mycobacterium tuberculosis complex strains from 48 different countries. AmpliBASE MT™ is based on a relational database management system that is hyperlinked to visualize genotyping results in the form of DNA fingerprint images for individual strains. A flexible search system based on systematic comparisons of fragment sizes in base pairs allows inter-laboratory comparison of FAFLP profiles. Besides this, the database also displays previously published data on IS6110 profiles, spoligotypes, MIRU-VNTRs and large sequence polymorphisms along with the FAFLP records that will give the overall comparisons. Being the first of its kind, AmpliBASE MT™ is expected to be a very helpful tool in strengthening the concept of'geographic genomics'and will be very helpful to molecular epidemiologists and those interested in diagnostic development for tuberculosis. © Oxford University Press 2004; all rights reserved.
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    Ab initio molecular-dynamics study of supercritical carbon dioxide
    ( 2004-05-22) Saharay, Moumita ; Balasubramanian, Sundaram
    The microscopic structure and dynamics of supercritical carbon dioxide was studied using Car-Parrinello molecular dynamics simulations. The reorientational dynamics of carbon dioxide molecules was investigated through first- and second-order time correlation functions. The intramolecular vibrations of carbon dioxide were examined through an analysis of the velocity autocorrelation function of the atoms. The results indicate that in the supercritical state the carbon dioxide molecule is marginally nonlinear, and thus possesses a dipole moment.