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Book of Abstracts: Albany 2003

category image Albany 2003
Conversation 13
Abstract Book
June 17-21 2003
Showing 1 to 100 of 201 items.  Page: 1 3

4x4 DNA Tile and Lattices: Characterization, Self-Assembly and Metallization of a Novel DNA Nanostructure Motif

Hao Yan, Sung Ha Park, Liping Feng, Gleb Finkelstein, John Reif, Thomas H. LaBean

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A 10 Nanosecond Particle Mesh Ewald (PME) Periodic Boundary Solvated Molecular Dynamic Simulation of the Phage 434 cl Repressor Protein DNA Binding Domain in Complex with its Cognate Operator (OR2) DNA Sequence

Lester F. Harris, Michael R. Sullivan

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A Comparative Study of Fe(II) and Fe(III) Bindings to DNA Duplex. Molecular Modeling and Spectroscopic Analysis

H. A. Tajmir-Riahi, R. Ahmad, A. Ahmed Ouameur, S. Diamantoglou, H. Arakawa

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A Comparison Between Elastic Network Interpolation and MD Simulation of 16S Ribosomal RNA

Moon K. Kim, Wen Li, Bruce A. Shapiro, Gregory S. Chirikjian

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A Multicomponent, Multifunctional Intron Endonuclease, I-TevI

M. Belfort, David Edgell, David Shub, Patrick Van Roey, Vicky Derbyshire

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A New Chain Breakage/Closure Algorithm Yields Fast Conformational Equilibration of Nucleic Acid Structures in Monte Carlo Simulations

Heinz Sklenar, Remo Rohs

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A New RNA Fold: RNA Hairpins Containing Unusually Stable 2',5'-Linked r(UUCG) Loops

Rami N. Hannoush, Aleksej Denisov, Kalle Gehring, Masad J. Damha

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A Role for Z-DNA Binding in Vaccinia Virus Pathogenesis

Yang-Gyun Kim, Maneesha Muralinath, Teresa Brandt, Matthew Pearcy, Kevin Hauns, Ky Lowenhaupt, Bertram L. Jacobs, Alexander Rich

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A Very Tight Turn in an Unusual DNA Triplex Structure Containing a Pyrimidine-pyrimidine Fold Motif

Lou-sing Kan

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A-tract in a 31mer Hairpin DNA

Xian Mao, William H. Gmeiner

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Accurate Exon-intron Sequence Classification by Neural Networks using 3-base Frame-dependent NucleotIde Frequencies to Represent Sequences

Dang D. Long, Patrick Hoffman, Ivo Grosse, Kenneth A. Marx, Georges Grinstein

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Active Site Directed Drug Design In Silico: A Case Study of COX-2 Inhibitors

N. Latha, A.Gandhimathi, P. Sharma, S. Bose, T. Jain, A. Das, B. Jayaram

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Adaptability and Dynamics in RNA Ligand Interactions: The Malachite Green Binding Aptamer

Jeremy Flinders,, David Brackett, and, Thorsten Dieckmann

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An Unfolded Protein that Folds in Living Cells

Matthew M. Dedmon, Chetan N. Patel, Gregory B. Young, Gary J. Pielak

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Analysis of Contributions of the Enzyme-substrate Interactions to Purine Specificity of Barnase

Nina Struminskaya

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Analysis of Structure & Function of the Ob Gene Product ? Leptin

M. Ravishankar Ram, G. Beena, K. Chandrasekhar, R. Malathi

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Analysis, Prediction and Evolution of Protein-DNA Interactions

J. M. Thornton, S. Jones, H. Shanahan, N. Luscombe

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Antisense Genes, Codon Bias and the Evolution of the Genetic Code

W.L. Duax, A. Addlagatta, V. Pletnev, R. Huether, P. Yu

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Assembly of p53 Protein with T-loop Junction in Telomeres and Apoptosis

En-Hua Cao, Xian-Fe Guo, Yan Zhang, Zhi-gang Wang, Chun-li Bai

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Biophysical Studies of Telomerase RNA Structure and Mutations Linked to Disease

Juli Feigon, Carla A. Theimer, L. David Finger, Lukas Trantirek

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Breaking Base Pairs in a DNA Double Helix

Péter Várnai, Emmanuel Giudice, Richard Lavery

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CDK4 and CDK6 Differ in Their Binding Affinity to p21WAF

J. Müller, D. Tvrdík, R. Djaborkhel, A. Nagy, R. Kodet

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Cisplatin and Self Splicing Activity of Group-I Intron Ribozyme

K. Chandrasekhar, R. Malathi

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Complex of an Anticancer Drug Topotecan with dsDNA

S. A. Streltsov, A. L. Mikheikin, S. L. Grokhovsky, V. A. Oleinikov, I. A. Kudelina, A. L. Zhuze

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Complexes of Cisplatin with d(CCTGGTCC)·d(GGACCAGG) and d(CCTCTGGTCTCC)·d(GGAGACCAGAGG) by VCD and IR

Dimiter Tsankov, Berndt Kalisch, Hans van de Sande, Valery Andrushchenko, Hal Wieser

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Computational Proteomics: Genome-scale Analysis of Protein Structure, Function, & Evolution

Mark Gerstein, P. Harrison, J. Qian, R. Jansen, V. Alexandrov, P. Bertone, R. Das, D. Greenbaum, W. Krebs, Y. Liu, H. Hegyi, N. Echols, J. Lin, C. Wilson, A. Drawid, Z. Zhang, Y. Kluger, N. Lan, N. Luscombe, S. Balasubramanian

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Configurational Entropy Change in Protein-DNA Complexes: Estimates From Molecular Dynamics Trajectories

Surjit B. Dixit, David L. Beveridge

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Conformational Changes in 8-oxoguanine DNA Glycosylase Catalysis

O. Fedorova, V. Koval, S. Ryzhikova, N. Timofeyeva, N. Kuznetsov, A. Ishchenko, D. Zharkov, G. Nevinsky, K. T. Douglas

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Conformational Dynamics of HIV-1 Adenosine Rich Loop

Joanna Sarzynska, Tadeusz Kulinski

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Conformational Study of Virus Nucleic Acids: A Seira and Correlation Analysis Data

G. Dovbeshko, O. Repnytska, T. Pererva, A. Miruta, D. Kosenkov

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Conservation of Genetic Information Between Regulatory Proteins and their Cognate DNA/RNA Binding Sites: A Basis for Site-specific Protein/Nucleotide Recognition and the Origin of the Genetic Code

Lester F. Harris, Michael R. Sullivan

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Controlling Nucleic Acid Structural Transitions by Intercalation

Swapan S. Jain, Matjaz Polak, Nicholas V. Hud

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Crystal Structure of Purine Nucleoside Phosphorylase from Thermus Thermophilus

Tahir H. Tahirov, Eiji Inagaki, Seiki Kuramitsu, Shigeyuki Yokoyama, Masashi Miyano

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Crystal Structures of Photosystems I and II from the Cyanobacterium Synechococcus Elongatus

A. Zouni, P. Jordan, P. Orth, N. KrauB, P. Fromme, H. T. Witt, W. Saenger

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Density Functional Theory Study of Some Conformations of dGpdC and dGpdC?Na+ Complex

A. Les, V.I. Danilov, N.V. Shulyupina, N.A. Polteva, V.I. Poltev

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Directed Nucleation Assembly of Barcode Patterned DNA Lattices

Hao Yan, Thomas H. LaBean, Liping Feng, John H. Reif

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Disperse of Bound Ligands Method in Study of Adsorption Isotherm

P. O. Vardevanyan, A. P. Antonyan, M. A. Parsadanyan, H. G. Davtyan, A. Sh. Markaryan, R. S. Kazaryan, Yu. S. Babayan

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Dissecting α-Synuclein: A Natively Unfolded Protein

Anthony L. Fink, Vladimir N. Uversky

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Distribution of p53 Sites in the Human Genome Reflects the Versatility of p53 Binding and Its Tumor Suppressor Functions

Zhurkin V. B., Sirotin M., Robles A., Rauf K., Jernigan R. L., Zhurkin M.

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DNA Binding by the BRCT Domain of NAD+-dependent DNA Ligases

Manuel Lavesa-Curto, Adam Wilkinson, Andrew Hemmings, Richard Bowater

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DNA Fine Structure and Dynamics: The Impact of BI/BII Backbone Conformations on the DNA/protein Specific Recognition

Dragana Djuranovic, Brigitte Hartmann

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Does Dinucleotide Composition of Herepes Viruses Reflect the Evolutionary Transitions?

Aditi Kanhere, Manju Bansal

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Double-duplex Invasion of Pseudocomplementary Peptide Nucleic Acids into Duplex DNA at Elevated Salt Concentration

Peter Yakovchuk, Ekaterina Protozanova, Vadim Demidov, Maxim Frank-Kamenetskii

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Dynamics and Stability of Individual Base Pairs in TATA-Box DNA

Congju Chen, Irina M. Russu

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Dynamics, Base Ionization and Metal Binding in the Structure of U6 RNA

Nicholas J. Reiter, Dipali G. Sashital, Samuel E. Butcher

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Electrostatic Properties of Promoter DNA. Approach to Classification Analysis.

A. A. Sorokin, T. R. Dzhelyadin, N. N. Ivanova, R. V. Polozov, S. G. Kamzolova

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Encapsidation Signal of the Hepatitis B Virus, A Possible Target for a Drug Design Strategy. Structural Studies by NMR Spectroscopy.

F. Girard, J. Schleucher, M. Tessari, S. Flodell, K. Kidd-Ljunggren, S. Wijmenga

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Energy Landscapes of Folding and Function

Peter G. Wolynes

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Enzymes are Ordered and Signaling Proteins are Intrinsically Disordered

A. Keith Dunker

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Equilibrium O2 Distribution in the Zn2+-Protoporphyrin IX Deoxymyoglobin Mimic: Application to Oxygen Migration Pathway Analysis

Lynn McNaughton, Griselda Hernández, David M. LeMaster

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Evolution of Intrinsically Unstructured Protein

Celeste J. Brown

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Expanding Protein Universe and its Origin From the Biological Big Bang

Nikolay V. Dokholyan

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Experimental Characterization of ACCGAAAACGGT Dynamics by 15N NMR Relaxation Measurements

Norma H. Pawley, Ryszard Michalczyk

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Exploring the DNA Structure Preferences of Human O6-Alkylguanine-DNA Alkyltransferase (AGT)

Sambit R. Kar, Anthony E. Pegg, Michael G. Fried

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Formation of the Parallel Recombination-type Triplex by Human Telomeric Sequences

Anna K. Shchyolkina, Dmitry N. Kaluzhny, Olga F. Borisova, Donna J. Arndt-Jovin, Thomas M. Jovin, Victor B. Zhurkin

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From Folding to Function: Lessons of Protein-DNA Interactions

Leonid Mirny

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Genome-wide A-tract Distribution and DNA Packaging in Pro- and Eukaryotes

M. Tolstorukov, K. Virnik, S. Adhya, V. Zhurkin

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Genomic Screens for Small RNA-encoding Genes in Escherichia coli

Hanah Margalit

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GIDEON, A Program for Design and Sequence Optimization in Structural Nucleic Acid Technology

Jeffrey J. Birac, Nadrian C. Seeman

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Grabbing the Cat by the Tail: Studies of DNA Packaging by Single φ29 Bacteriophage Particles Using Optical Tweezers

Carlos Bustamante

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Group I Intron as Therapeutic Target: A Preliminary Study on the Growth Inhibition of Candida Albicans by Bleomycin

J. Prathiba, R. Malathi

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How Camptothecin Inhibits Human Topoisomerase I and How it forms an Alkali-Labile Complex with DNA (The Models)

Sergei A. Streltsov

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How Does a Protein Find its Site on the DNA?

M. Slutsky and L. Mirny

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In vivo and In vitro Self-association Interaction Studies on the N-terminal of Yeast Tata Binding Protein (TBP)

Claire A. Adams, James E. Hopper, Michael G. Fried

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Immunoreactive Conformation of the Principal Neutralization Site of Minnesota HIV-1 Isolate

Alexander M. Andrianov, Yuri A. Sokolov

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In Silico Structure-based Design of a Potent, Mutation Resilient, Small Peptide Inhibitor of HIV-1 Reverse Transcriptase

Gita Subba Rao, Sonika Bhatnagar

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Inferring Large-scale Motions and Functions from Structures

R. L. Jernigan, I. Bahar, Ozlem Keskin, David Covell, M.K. Kim, G.S. Chirikjian, Y. Wang

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Influence of Global DNA Topology on Local Structured Transitions

E. A. Oussatcheva, V. N. Potaman, J. Pavlicek, Y. L. Lyubchenko, L. S. Shlyakhtenko, R. R. Sinden

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Insight to Structural Subsite Recognition in Plant Thiol Protease?inhibitor Complexes: Understanding the Basis of Differential Inhibition and the Role of Water

Suparna Bhattacharya, Sarada Banerjee, Asok Banerjee

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Interaction of a breast cancer growth inhibiting cyclopeptide with the G-protein-coupled receptor model GPR30

Adel Hamza, , M. H. Sarma, and , R. H. Sarma

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Interaction of DMAPP:tRNA Prenyltransferase with Escherichia coli tRNAPhe

Edward P. Nikonowicz, Margaret Michnicka, Javier Cabello-Villegas

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Interaction of Plasmid pSM19035-encoded Regulatory Protein Omega with Operator DNA

L. Dostál, R. Misselwitz, K. Welfle, W. Saenger, J. C. Alonso, H. Welfle

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Intercalation of T·T Pairs and Duplex Inter-conversion within the I-motif Structure

Jean Louis Leroy

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Intracellular Protien NMR

Volker Doetsch

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Intramolecular Py·Pu·Py Triplex in the (GAA)n·(TTC)n Repeats Flanked by the Human Genomic Sequences is Stable at Neutral pH

V. N. Potaman, E. A. Oussatcheva, Y. L. Lyubchenko, L. S. Shlyakhtenko, R. R. Sinden

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Investigations of cis-Pt and its Analog DACH-Pt Interaction with DNA and Synthetic Oligonucleotides by Means of VCD, IR and CD Spectroscopy

Valery Andrushchenko, Alexander Polyanichko, Berndt Kalisch, Hal Wieser

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Isothermal Titration Calorimetry and Differential Scanning Calorimetry: Tools to Investigate Biomolecular Interactions

Verna Frasca, Lung-Nan Lin, John Brandts

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Ligand-induced DNA Polymerase Pausing on Double-stranded DNA

Irina V. Smolina, Vadim V. Demidov, Maxim D. Frank-Kamenetskii

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Lipids Participation in Cell Nucleus Signaling (Lipidomics) Analyzed by Biophysical Investigations, Liquid Chromatography and Biosensor Techniques

G. Bischoff , W. Lorenz, A. Shmyrina, R. Zhdanov

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Low Complexity Sequences in Proteins: New Perspectives for Sequence and Structure from Comparative Genomics

Tannistha Nandi, Srinivasan Ramachandran

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Measuring Protein-induced DNA Bending by Cyclization of Short DNA Fragments

Alexander Vologodskii

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Melting of Complexes of DNA-cis-DDP in Acidic Media

T. S. Haroutiunian, Sh. S. Sarkisyan, A. P. Antonyan, S. G. Haroutiunian, Y. B. Dalyan, P. O. Vardevanyan

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Model Describing the Formation of ?Bridges? Between Nuclear Acids in Liquid-crystalline Dispersions

V. F. Riabokon, Yu. D. Nechipurenko, S. V. Semenov, Yu. M. Yevdokimov

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Model of Formation of Liquid-Crystalline Dispersions in the Process of the DNA-Chitosan Binding

Yu. D. Nechipurenko, A. M.Wolf , V. I. Salyanov, Yu. M. Yevdokimov

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Modeling of a Leishmania Antigen eIF-4A : A Potential Epitope Implicated in the Adjuvant Effect is Identified

A. Hamza,, C. Kébaïer,, D. Vasilescu,, I. Guizani,, K. Dellagi,, M. H. Sarma and, R. H. Sarma

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Molecular Construction with DNA and Metal Nanoparticles: Applications in Molecular Nanotechnology and DNA Chip Detection

W. Fritzsche, A. Csaki, G. Maubach, R. Möller, A. Sondermann

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Molecular Dynamics of Guanine Quadruplex Molecules

N. Spackova, R. Stefl, I. Berger, E. Fadrna, J. Koca, T. E. Cheatham, III, J. Sponer

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Molecular Dynamics Simulation of Anthrax Edema Factor:Calmodulin Complexes with Mutations in the Edema Factor "Switch A" Region

Jingyan Zhao, Donald J. Nelson

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Molecular Dynamics Simulations of Papilloma Virus E2 DNA Sequences: Dynamical Models for Oligonucleotide Structures in Solution

K. Suzie Byun, D. L. Beveridge

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Molecular Dynamics Studies of RNA Hexaloop Stabilization by Base Interaction and Hydration

T. Kulinski, K. Kulinska, J. Sarzynska, R. W. Adamiak

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Molecular Machines for Protein Degradation

R. Huber

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Multiscale Modeling of DNA Bending Dynamics

Thomas C. Bishop, Ricardo Cortez, Oleksander Zhmudsky

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NMR Solution Structure of an Oxaliplatin 1,2-d(GG) Intrastrand Cross-Link in a DNA Dodecamer Duplex

Yibing Wu, Padmanava Pradhan, Jody Havener, Sharon L. Campbell, Stephen G. Chaney

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NMR Solution Structure of Bistranded Furan Abasic Site Lesions: Orientation Matters

Raphael D. Hazel, Carlos de los Santos

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NMR Structure Determination of the Anticodon Stem-Loop of Escherichia coli tRNAPhe

I. Tworowska, E. P. Nikonowicz

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NMR Studies Reveal an A⇐⇒B Structural Intermediate with N Type Sugar Pucker for 2?,5? Linked d(GGGGCCCC): Was the Optimization of Helix Topology a Factor in the Etiology of Nucleic Acid Backbone?

B.J. Premraj, S. Raja, N.S. Bhavesh, Ke Shi, R.V. Hosur, M. Sundaralingam, N. Yathindra

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Non-covalent Interactions of Highly Charged Polynuclear Platinum Compounds with DNA. Chemical and Biological Effects.

Amanda Harris, Yun Qu, Alexander Hegmans, Andrea Petz, Nicholas Farrell

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Non-Watson-Crick Base Pairing and Hydration in RNA motifs: Molecular Dynamics of 5S rRNA Loop E.

Kamila Réblová, Nada Spacková, Jaroslav Kocá, Neocles B. Leontis, Jiri Sponer

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Nuclear Uptake of DNA

Michael Elbaum

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On the Cooperativity of Metal Ion Binding to DNA

Vladimir Teif

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Showing 1 to 100 of 201 items.  Page: 1 3