Abstracts Index

3-D STRUCTURES

• Role of tryptophan 135 in the combing site of Erythrina corallodendron lectin
  R. Adar, J. Angstrom, E. Moreno, H. Streicher and N.Sharon
• The crystal structure of Bacillus subtilis ferrochelatase - the terminal enzyme in heme biosynthesis
  Salam Al-Karadaghi, Mats Hansson, Bodil Jonsson, Stanislav Nikonov and Lars Hederstdet
• Detection of changes in pairwise interactions during allosteric transitions: coupling between local and global conformational changes in GroEL
  Amir Aharoni and Amnon Horovitz
• Towards phenotypic engineering
  M. Armas, M. Strauch and J. Lagunez-Otero
• Dialog between sequence homology and 3D crystal structure defines interaction of functional domains in a multi-enzyme complex
  Edward A. Bayer, Linda J.W. Shimon, Felix Frolow, Ely Morag, Raphael Lamed, Jose Tormo, Sima Yaron and Yuval Shoham
• Protein domain structure by means the distribution of non-covalent interactions in globule
  I.N. Berezovsky and V.G. Tumanyan
• A physical clssification of protein folds
  Henrik Bohr and Per-Anker Lindgaard
• Determination by MAD phasing of the 2.2Å X-ray structure of b-cryptogein, a fungal elicitor secreted by Phytophthora cryptogea
  G. Boissy, E. de La Fortelle, R. Kahn, J.-C. Huet, G. Bricogne, J.-C. Pernollet and S. Brunie
• Structure of H. sapiens N-acetylgalactosamine-4-sulfate sulfatase
  Charles S. Bond, Peter R. Clements, Charles A. Collyer, John J. Hopwood and J. Mitchell Guss
• Classification and characterization of structure motifs composed of one alpha-helix and two consecutive hydrogen-bonded beta-strands
  Nathalie S. Boutonnet, Andrey V. Kajava and Marianne J. Rooman
• Comparing sequence comparison
  Steven E. Brenner, Tim J. P. Hubbard, Alexey G. Murzin, Cyrus Chothia
• The structure and function of the Replication Terminator Protein from Bacillus subtilis, a protein responsible for mediating termination of chromosomal DNA replication
  Dirksen E. Bussiere, Deepak Bastia, Stephen White
• Procedure to calculate molecular envelope from a partial model
  Rene Coulombe and Miroslaw Cygler
• Solution structure of the immunodominant region of protein G of bovine respiratory syncytial virus
  Jurgen F. Doreleijers , Johannes P.M. Langedijk , Karl Herd , Rolf Boelens , Johan A.C. Rullmann , Wim M. Schaaper , Jan T. van Oirschot and Robert Kaptein
• Solution structure of photoactive yellow protein
  P. Dux, G. Rubinstenn, R. Boelens, F.A. Mulder, K. Herd, W.D. Hoff, A. Kroon, K. J. Hellingwerf, R. Kaptein
• The 3-D structure of the hexagonal form of the Erythrina corallodendron lectin: the unusual quaternary structure is the genuine dimer
  Sharona Elgavish and Boaz Shaanan
• NMR characterization of the native and molten globule states of apomyoglobin
  David Eliezer and Peter E. Wright
• Three dimensional structure of HIPIP II isolated from Ectothiorhodospira halophila at 1.7 Å resolution from a twinned monoclinic crystal
  C. Frazão, I. Bento, L. Sieker, F. Capozzi, C. Luchinat, Z. Dauter, K. Wilson, G. M. Sheldrick and M. A. Carrondo
• The crystal structure of holo-glyceraldehyde-3-phosphate dehydrogenase from Sacchromyces cerevisia (baker's yeast) at 2.1 Å resolution
  Rotem Gilboa, Alan J. Bauer and Gil Shoham
• Database-derived potentials for evaluating protein stability changes upon single site mutations
  Dimitri Gilis and Marianne Rooman
• Crystal structure of T. thermophilus phenylalanyl-tRNA synthetase complexed with tRNAPhe
  Goldgur, Y., Mosyak L., Reshetnikova, L., Khodyreva, S., Ankilova, V., Lavrik, O. and Safro, M.
• Structural studies of the actin binding domain of fimbrin
  S. Goldsmith, N. Pokola, A. Fedorov, P. Matsudaira, S. Almo
• The three dimensional structure of the thermostable, calcium activated, aminopeptidase from Streptomyces griseus
  Harry M. Greenblatt, Orna Almog, Bruno Maras, Ania Spungin-Bialik, Galia Papir, Donatella Barra, Shmaryahu Blumberg and Gil Shoham
• Understanding sequence relationships in enzymes families through comparison of active-site structures
  Miriam S. Hasson
• NMR structural studies of displayed peptides
  R. Jelinek, A.P. Valente, J.J. Gessel, S.J. Opella, T. Terry, P. Malek, R. N. Perham
• Monoclonal Antibodies that Specifically Recognize Crystals of Dinitrobenzene and Cholesterol
  Naama Kessler, Daniele Perl-Treves and Lia Addadi
• Crystallographic and modeling studies of a covalent complex between papain and an oxirane-based inhibitor
  Maciej Kozak, Elzbieta Kozian, Zbigniew Grzonka and Mariusz Jaskolski
• Position specific sequence characteristics of alpha helices in globular proteins
  Sandeep Kumar and Manju Bansal
• Short and medium length loops in globular proteins. A common classification
  Jean-Marc Kwasigroch, Jean-Paul Mornon and Jacques Chomilier
• Symbiosys of crystallography and chemical synthesis in exploring the structural basis of HIV-1 protease catalysis and inhibition
  Maria Miller, J.K.M. Rao, M. Baca, and S.B.H. Kent
• Geometric analysis of side-chain - base interactions
  Lena Nekludova and Carl O. Pabo
• Protein structure refinement using NMR chemical shift restraining molecular dynamics simulation
  Kyunglae Park and Wifred F. van Gunsteren
• Pi-turns in proteins and peptides: classification based on protein crystal structure data bank analysis
  K.R. Rajashankar and S. Ramakumar
• Laue diffraction studies on acetylcholinesterase
  Mia Raves, Raimond Ravelli, Jan Kroon, Michel Roth, Dominique Bourgeois, Ling Peng, Maurice Goeldner, Zhong Ren, Israel Silman and Joel L. Sussman
• Intelligent computational aids for crystal growth
  John M. Rosenberg, Patricia A. Wilkosz, Devika Subramanian, Daniel Hennessy and Bruce Buchanan
• Crystal structure of enolpyruvyltransferase, the target of the antibiotic fosfomycin
  S. Sack, S. Eschenburg, A. Perrakis, F. Krekel, N. Amrhein, E. Mandelkow, and E. Schoenbrunn
• From the structure and organization of synthetic fragments to functional structures of membrane proteins: the pore forming domains of B. thuringiensis delta-endotoxins
  Yechiel Shai and Ehud Gazit
• Computational tools for analysis of structural data in the PDB
  Vladimir Sobolev and Meir Edelman
• The topology of nucleic acids with overhangs
  Muttaiya Sundaralingam and Baocheng Pan
• The protein fold recognition based on the statistical hypothesis testing
  Shamil Sunyaev, Eugene Kuznetsov and Vladimir Tumanyan
• Automated solvent identification and refinement with ASIR working in conjugation with CCP4, X-PLOR and TNT: a case study with the determination of two types of 2.0 Å crystal structures of recombinant mouse ubiquitin-conjugating enzyme 9
  Harry Tong
• Distance signatures in protein structures. Distance signatures in protein structures
  Priya Viswanathan and S.Krishnaswamy
• Crystallization and properties of a complex between chaperonin GroEL and a molten globule-like folding intermediate of the bacteriophage HK97 capsid protein
  Patricia A. Wilkosz, Yuan-hua Ding, Robert Duda, Roger Hendrix and John M. Rosenberg
• The equine infectious anemia virus transactivator protein is a DNA binding protein
  Dieter Willbold, Armin U. Metzger, Karl Christian Gallert, Norbert Dank, Peter Bayer, Rina Rosin-Arbesfeld, Abraham Yaniv, Arnona Gazit, Roger Goody, Gerhard Krauss and Paul Roesch
• Structural classification and interaction modes of DNA-binding proteins of the HTH type
  Rene Wintjens and Marianne Rooman
• The three-dimensional structure of human ceruloplasmin at 3.0 Å resolution
  V.Zaitsev, I.Zaitseva, G.Card, B.Bax, A.Ralph and P.Lindley
• Comparison of the X-ray structures of fumarase and delta-crystallin
  I.Zaitseva, V.Zaitsev, L.Duke, P.Lindley, S.McSweeny, K.Gladilin, J.Keruchenko and I.Keruchenko

BIOLOGICAL SEQUENCES

• Construction of protein sequences families
  Jean-Christophe Aude and Jean-Paul Comet
• Non-local, interchanges of pairs of neighboring amino-acids in spatially conserved motifs
  Einat Azarya-Sprinzak, Dalit Naor, Haim J. Wolfson and Ruth Nussinov
• The bank of patterns PROF_PAT 1.0: construction procedure and computer programs
  Bachinsky A.G., Yarigin A.A. and Kulichkov V.A.
• The bank of patterns PROF_PAT 1.0: computer programs for rapid search for patterns in amino acid sequences
  Bachinsky A.G., Yarigin A.A., Gusev V.D., Nemitikova L.A. and Kulichkov V.A.
• Protein carboxyl termini are biased
  I.N. Berezovsky, G.T. Kilosanidze, V.G. Tumanyan and L.L. Kisselev
• Proline dependent oligomerization with arm exchange
  M. Bergdoll, C. Cagnon, M.H. Remy, J.M. Masson and P. Dumas
• Cleavage site analysis in picornaviral polyproteins: Discovering cellular targets by neural networks
  Nikolaj Blom, Jan Hansen, Dieter Blaas and Soren Brunak
• Structure based sequence alignment of endonucleases
  Taru Deva and S.Krishnaswamy
• Predicting the redox state of cysteins in proteins from multiple sequence alignments
  Andras Fiser, Istvan Simon and Geoffrey J. Barton
• Specie-invariant correlation in nucleotide content for different reading frame positions
  G.K. Frank and V.Ju. Makeev
• Interactive Multiple Protein Sequences Alignment with ProMSED, an application for Windows 3.11/95
  Anatoly Frolov and Alexey Eroshkin
• Distribution of bending propensity in genomic DNA
  Andrei Gabrielian and Sandor Pongor
• Understanding sequence relationships in enzymes families through comparison of active-site structures
  Miriam S. Hasson
• A Monte Carlo method to simulate the protein folding process
  D. Hoffmann, F. Sartori and E.W. Knapp
• Extraction of periodic nucleosome DNA pattern by resonance analysis
  I. Ioshikhes, A. Bolshoy & E.N. Trifonov
• Studying structure-activity and phenotype-genotype relationships in protein families. Methods, algorithms and applications
  Vladimir A. Ivanisenko, Irina S. Pika, Sergey I. Pinin, Tatiana I. Fomina, Alexey M. Eroshkin
• Searching protein sites with functionally important amino acid changes in the sets of natural and mutant proteins
  Vladimir A. Ivanisenko and Alexey M. Eroshkin
• Classification, fourier- and wavelet-transform of E.coli promoter and terminator sequences
  G.I. Kutuzova, R.V. Polozov, V.Ju. Makeev, G.K. Frank, N.G. Esipova and V.G. Tumanyan
• What evolution tells us about the location and composition of functional surfaces in proteins
  Olivier Lichtarge
• The third nucleotide of Gly-coding triplets remembers the gene tetraplication event
  Makeev V.Ju., Tumanyan V.G. and Esipova N.G.
• JavaCINEMA - A novel colour interactive editor for multiple alignments
  Parry-Smith, D.J., Payne, A.W.R., Michie, A.D. and Attwood, T.K.
• Regulatory proteins: a new approach in the transcription machinery
  Ernesto Pérez-Rueda, Jay D. Gralla, and Julio Collado-Vides
• Application of evolutionary algorithms to protein folding prediction
  A. Piccolboni and G. Mauri
• Function from Sequence - Identifying Similarities between Conserved Protein Regions
  Shmuel Pietrokovski
• Multiple Sequence Analysis of Olfactory Receptor Genes: Sequence, Structure and Function Relationships
  Yitzhak Pilpel, Daniel Segré, Doron Lancet, Yehudit Weissinger and Gustavo Glusman
• Computer analysis of nucleotide sequences from the family of interspersed repetitive elements MER1. Another oligonucleotide primer for the PCR assay of human DNA
  A.A.Ptitsyn, E.I.Jantsen, M.L.Filipenko, O.A. Baturina, A.I.Muravlev, N.P.Mertvetsov
• Object-oriented data handler for sequence analysis software development
  A.A. Ptitsyn and D.A. Grigorovich
• AutoGene: A computer system for nucleotide sequence analysis
  A.A. Ptitsyn, D. A. Grigorovich, I. B. Rogozin and N. A. Kolchanov
• Synonymous codon usage in relation to amino acid secondary structure preferences
  Sunita S and S.Krishnaswamy
• Introns and reading frames: correlation between splicing sites and their codon positions
  Masaru Tomita, Nobuyoshi Shimizu and Doug Brutlag
• Use of bioinformatics for analysis of an outer membrane protein (HMP-1) isolated from Bacterodes fragilis, the anaerobe most commonly involved in clinical infections
  Hannah M. Wexler
• Artificial neural networks (ANN) for sequence and structure analysis of proteins P.Wrede, G.Schneider, U.Hahn and J. Schuchhardt
• Working towards a comprehensive biological sequence comparison and analysis environment
  David P. Yee, Frank Zucker, Tim Hunkapiller, Emir Pasalic, Justin Laird, Eric Hackborn, Johnny Helmich, Tom Stidham, Elizabeth Kutter and Judith Bayard Cushing

MODELING & PREDICTION

• Use of cupredoxin core structure to define related structures
  Elinor T. Adman and Michael E.P. Murphy
• Homology model of salmonella typhi OmpC and analysis of its antigenic loops
  A. Arockiasamy and S. Krishnaswamy
• Conformation Space Mapping - A Novel Method for Structure Based Drug Design
  Oren Becker
• Prediction of transmembrane alpha-helices using a hydropathy scale derived from first principles
  Nir Ben-Tal & Barry Honig
• Analysis and prediction of hydrogen bonding in protein-DNA complexes using parallel processors
  Graham Campbell, Yuefan Deng, James Glimm, Yuan Wang, and Qiqing Yu, Moises Eisenberg and Arthur Grollman
• Prediction of long-range interactions in proteins using neural network algorithm
  Zsuzsanna Dosztanyi, Andras Fiser and Istvan Simon
• Dynamic contributions to the DNA binding entropy of the Eco RI and EcoRV restriction endonucleases
  Yong Duan, Patricia Wilkosz and John M. Rosenberg
• Assessment of protein fold predictions from sequence information: predicted alpha/beta-doubly wound fold of the von Willebrand factor type domain is similar to its crystal structure
  Yvonne J. K. Edwards and Stephen J. Perkins
• A gap penalty scheme for increased selectivity in profile searching
  Terry Farrah
• Electrostatic properties of cholinesterase models and their functional implications
  Clifford E. Felder, Israel Silman and Joel L. Sussman
• Advances in fold recognition: directional profiles and sequence-derived predictions
  Daniel Fischer, Robert Weiss, Danny W. Rice and David Eisenberg
• The UCLA-DOE fold recognition and genome analysis server
  Daniel Fischer, Danny Rice and David Eisenberg
• Computer simulation of titration behaviour in proteins
  Cynthia Gibas and Shankar Subramaniam
• Building of a potential of mean force limited to the side-chain interactions statistically significant
  S. Hazout and M.H. Mucchielli-Giorgi
• RIFLE - Rapid Identification by Fragment Length Evaluation
  Henning Hermjakob
• Simultaneous and coupled energy optimization of homologous proteins: A new tool for structure prediction
  Chen Keasar, Ron Elber and Jeffrey Skolnick
• Homology modelling of envelop glycoprotein of Japanese encephalitis virus
  Urmila Kulkarni-Kale and A.S. Kolaskar
• Exploring the limits of secondary structure prediction
  Jonathan M. Levin
• De novo design of proteins containing alpha-beta-beta motif
  Dawei Lin and Luhua Lai
• Conformational analysis of nucleic acid structures: the asymmetric E-loop of 5S RNA
  Alexandra Maier, Wolfgang Schulz and Heinz Sklenar
• Playing with interfaces: a model
  A.E. Miele, B. Vallone, P. Vecchini, E. Chiancone and M.Brunori
• Protein fold recognition and dynamics in the space of contact maps
  Leonid Mirny and Eytan Domany
• Prediction method of the protein side-chain contacts using a potential of mean force function of residue burial and residue location in secondary structure
  M.H. Mucchielli-Giorgi, P. Tuffery and S. Hazout
• The arrangement of helices in a membrane - a Monte Carlo simulation
  Annekathrin Mueller and Heinz Sklenar
• Use of mean-force potentials for tertiary structure prediction: successful prediction of coiled coil structures
  Sean I. O'Donoghue and Michael Nilges
• A model for hybrids interferons
  Pereira, H,M; Kroon, E.G.; Carvalho, A, F; Jacchieri. S.G; Santoro,M.M.; Ferreira, P.C.P
• A new method to analyze molecular dynamic simulations: an application to the evolution of barnase's hydrophobic cores during unfolding
  Luisa Pugliese, Martine Prevost and Shoshana Wodak
• Molecular modelling and site diected mutagenesis of the active site of endothelin converting enzyme
  C.E. Sansom, V.M. Hoang and A.J. Turner
• Structure, dynamics and electrostatics of L-asparaginase dimers: implications for reaction mechanism
  C.E. Sansom and Mariusz Jaskolski
• An ab initio approach to predict an active site : a case study of asparagine synthetase
  Sangeeta Sawant, Sheldon M. Schuster, A.S. Kolaskar
• Electrostatic forces in the association of proteins
  Gideon Schreiber Christian Frish Alan R. Fersht
• A new approach to modeling G-protein coupled receptors: a 3D model of GnRH receptor
  Shacham S, Naor Z. and Becker O.M.
• Structure and interactions of the membranal protein C5aR
  Naomi Siew and Amiram Goldblum
• A common binding pattern in the receptor complexes of some helical cytokines
  D.K. Smith and H.R. Treutlein
• Using structural data for molecular docking and ligand design
  Vladimir Sobolev, Tedd Moallem and Marvin Edelman
• Low frequency motion in proteins: comparison of normal mode and molecular dynamics of the protein Streptomyces griseus protease A
  Peter Stern, Pnina Dauber-Osguthorpe, David J. Osguthorpe and John Moult
• Virtual reality modeling for structural biology
  Jürgen Sühnel
• Beyond intra-base-pair hydrogen bonds in DNA structures: A comprehensive analysis
  Jürgen Sühnel and Klaus Lindauer
• How local minima become the global minima: a simple lattice model study
  Ron Unger
• A novel approach to the three dimensional modelling of polypeptide chains using a doublet (amino acid pair) data base
  M. A. Viswamitra and Ujjwal Kumar Das
• Directional profiles
  Robert Weiss, Daniel Fischer, Danny W. Rice and David Eisenberg
• A common architecture of the ligand binding domain of nuclear receptor
  Jean-Marie Wurtz

DATABASES

• An introduction to mmCIF: conversion between PDB format and mmCIF
  Frances C. Bernstein, Herbert J. Bernstein and Philip. E. Bourne
• Visualization, management and integration of GPCR related informations : the Viseur program
  F. Campagne, M. Cserzo, J.M. Bernassau and B. Maigret
• Sacch3D: Structural information for the S. cerevisiae genome
  Stephen A. Chervitz, J. Michael Cherry, and David Botstein
• Real-time, Online Conferencing for Biologists
  Gustavo Glusman and Jaime Prilusky
• Fast and easy-to-use PDB viewer for Mac and PC
  N. Guex and MC Peitsch
• DRES db: a tool for systematic identification of human cDNAs homologous to Drosophila genes through automated EST database screening
  A.Guffanti, S.Banfi, G.Borsani and G.Simon
• PDBCONS: PDB Database converter and browsing program
  Ramneek Gupta and S. Krishnaswamy
• TRRD and COMPEL: Databases on transcription regulation as a tool for analysis of gene structure
  A.E. Kel, O.V. Kel, A.G.Romaschenko, E.Wingender, N.A.Kolchanov
• IMGT, The Immungenetics database
  Marie-Paule Lefranc, Julia Bodmer, Werner Mueller, Veronique Giudicelli, Chantal Busin, Steven Marsh, Denis Chaume and Ansar Malik
• Protein Data Bank - reaching out to our users
  N.O.Manning, E.E.Abola, F.C.Bernstein, A.Bluestone, F.M.Cummings, B.R.Deroski, P.A.Esposito, A.Forman, J.Jiang, P.A.Langdon, M.D.Libeson, D.Lin, J.E.McCarthy, C.Metz, J.Prilusky, R.K.Shea, J.L.Sikora, B.R.Sylvain, D.Xue, and J.L.Sussman
• Databases for improved pattern recognition in protein sequences
  S.Pietrokovski, S.Henikoff, J.Henikoff and T.K.Attwood

Please report any problems or corrections with these pages to kurt@sgjs4.weizmann.ac.il