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Albany 2013: Book of Abstracts

category image Albany 2013
Conversation 18
June 11-15 2013
©Adenine Press (2012)
Showing 101 to 200 of 219 items.  Page: 2

The melting of DNA in the presence of meso-tetra-pyridyl Porphyrins with different peripheral substituents

L.R. Aloyan , Y.B. Dalyan

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The Role of the Linker and Aromatic Pendent in Zn(II) Complexes for Recognition to Non-Canonical Thymine in DNA

Stephanie A. Sander , Janet R. Morrow

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Bridging the Gap: From 1D to 3D Genomics

Lin Yang, Tianyin Zhou, Remo Rohs

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Exploring the 3D spatial organization of the genome

Frank Alber

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Genome engineering nucleases derived from GIY-YIG homing endonucleases

David Edgell, Benjamin Kleinstiver, Jason M. Wolfs, Li Wang, Tomasz Kolaczyk, Brendon McDowell, Adam Bogdanove

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Probing DNA shape and methylation state on a genomic scale with DNase I

Allan Lazarovici , Tianyin Zhou, Anthony Shafer, Ana Carolina Dantas Machado , Richard Sandstrom, Peter J. Sabo , Yan Lu, Remo Rohs, John A. Stamatoyannopoulos, Harmen J. Bussemaker

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Probing DNA Shape on Molecular and Genomic Scales

Tianyin Zhou , Remo Rohs

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Activity of DNA Ligase on Substrates Containing Non-canonical Structures

Katharina Bilotti, Kelly Schermerhorn, and Sarah Delaney

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Deriving Force Field Dihedral Angle Parameters That Account For Conformation-Dependent Solvation Effects

Petr Jurečka, Marie Zgarbová, F. Javier Luque, Jiří Šponer, and Michal Otyepka

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Genomes to Hit Molecules In Silico - A Country Path Today, a Highway Tomorrow: A Case Study of Chikungunya

Anjali Soni, Priyanka Dhingra, Avinash Mishra, Tanya Singh, Goutam Mukherjee, B. Jayaram

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Individual-Particle Electron Tomography: A method for studying macromolecule dynamics

Lei Zhang, Gang Ren

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Molecular Dynamics Done Quick: Efficient Trajectory Analysis Software

Alexander V. Popov, Yuri N. Vorobjev, Dmitry O. Zharkov

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Refinement of Force Field Torsion Parameters for Nucleic Acids Based on Inclusion of Conformation-Dependent Solvation Effects

Marie Zgarbová , Michal Otyepka, Pavel Banáš, F. Javier Luque, Thomas E. Cheatham, III, Jiří Šponer, Petr Jurečka

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The importance of being modified: Tautomeric forms of pyrimidines provide expanded use of the genetic code

William A. Cantara , Franck A.P. Vendeix, Franck V. Murphy IV, Graźyna Leszcyńska, Kimberly Harris, Estella M. Gustilo, Brian Sproat, Rob Kaiser, Andrzej Malkiewicz , Paul F. Agris

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Towards the Manifold Representations of Biological Object

Yu.N. Zhuravlev, M.A. Guzev, E.E. Skurichin

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Conformational dynamics of human 8-oxoguanine-DNA glycosylase

Nikita A. Kuznetsov, Olga S. Fedorova

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Kinetic and thermodynamic basis for damaged bases excision by 8-oxoguanine-DNA glycosylases

Anton Endutkin, Dmitry Zharkov

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The Rate of hOGG1-mediated 8-oxoG Removal from Nucleosomal DNA

Eric D. Olmon , Sarah Delaney

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Deamination of both methyl- and normal-cytosine by the foreign DNA restriction enzyme APOBEC3A

Michael A. Carpenter , Ming Li, Anurag Rathore, Lela Lackey, Emily K. Law, Allison M. Land, Brandon Leonard, Shivender M. D. Shandilya, Markus-Frederik Bohn, Celia A. Schiffer, William L Brown, Reuben S. Harris

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DNA Structure-induced Genetic Instability in Mammals

Guliang Wang, Laura A. Christensen, Karen M. Vasquez

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Evaluation of Different DNA Polymerases for their Effectiveness in Using a Cytosine Analogue During Real-time PCR Amplification

Cyntia R. Flores-Juárez, Eva González-Jasso, Anaid Antaramian, Reynaldo C. Pless

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Fork stalling at AT-rich sequences and failure of origin activation lead to chromosomal instability at fragile sites

Efrat Ozeri-Galai, Michal Irony-Tur Sinai , Batsheva Kerem

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Genome-wide mapping of DNA strand breaks in Saccharomyces cerevisiae

Hari K. K. Subramanian, Sarah E. BernardCheryl Chiang, Stephen C. J. Parker, Thomas D. Tullius

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Influence of changes in DNA conformation on thermodynamic contribution during interaction of human genomic DNA and its mutant with anticancer drugs

Debjani Ghosh, Subrata Kumar Dey, Chabita Saha

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Kinetics of Apurinic/Apyrimidinic Endonuclease 1 (APE1) on an Authentic AP Site or an AP Site Analog

Kelly M. Schermerhorn , Sarah Delaney

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Mini-chromosome Maintenance Complexes Form A Filament To Remodel DNA Structure and Topology

Ian M Slaymaker, Yang Fu, Daniel B. Toso, Nimna Ranatunga, Aaron Brewster, Susan L Forsburg, Z. Hong Zhou, Xiaojiang S. Chen

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Non-B DNA Structure-induced Genetic Instability in Mammalian Cells

Guliang Wang , Laura A. Christensen, Scott A. Spitser, Karen M. Vasquez

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Put a stop to it: termination of mitochondrial transcription

Yakubovskaya E, Mejia E, Byrnes J, Hambardjieva E, Garcia-Diaz M.

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Replication impairment as a source of transcription- and R-loop- associated recombination

Maikel Castellano-Pozo , Irene Felipe-Abrio, María L. García-Rubio, Juan F Lafuente-Barquero, Jose María Santos-Pereira, Tatiana García-Muse, Andrés Aguilera,

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Some Derivatives of 1,3-diazaadamantane Strongly Stimulate Strand Exchange Reaction between Short Oligonucleotides

Anna Gabrielian, Tatiana N. Bocharova, Elena A. Smirnova , Alexander A.Volodin, Amalya Harutjunyan, Knarik Gevorkyan, Gayane Harutjunyan

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Template-switching during DNA replication

Susan T. Lovett

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The Molecular Mechanism of Breakage at Fragile Site FRA16D

Simran Kaushal, Soo-Mi Alison Lee, Nealia House, Keerthana Gnanapradeepan, Adam Snider, Xiaofeng Allen Su, Catherine H. Freudenreich

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Transcription Blockage by Single-strand Breaks in Various Sequences and the General Model for Transcription Blockage by R-loop Formation

Boris P. Belotserkovskii , Alexander J. Neil , Syed Shayon Saleh , Jane Hae Soo Shin , Sergei M. Mirkin , Philip C. Hanawalt

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Using whole-genome sequencing to search for trans-modifiers of repeat expansions

Ryan McGinty, Anna Aksenova, Eric Wang, David Hausman, Sergei Mirkin

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Designed DNA Crystals with a Triple-Helix Veneer

Arun Richard Chandrasekaran, David A. Rusling,, Yoel P. Ohayon, Ruojie Sha, Nadrian C. Seeman

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Impact of Sticky End Length on the Diffraction of Self-Assembled DNA Crystals

Yoel P. Ohayon , Arun Richard Chandrasekaran, Esra Demirel, Sabrine I. Obbad, Rutu C. Shah, Victoria T. Adesoba, Matthew Lehmann, Jens J. Birktoft, Ruojie Sha, Paul M. Chaikin, Nadrian C. Seeman

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Encapsulation of Antitumor Drugs Tamoxifen, 4-Hydroxytamoxifen and Endoxifen by Chitosan Nanoparticles

H. A. Tajmir-Riahi , D. Agudelo , S. Sanyakamdhorn

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Arranging enzymes and receptors with nanometer-scale precision on molecular switchboards

Ngo Anh Tien, Eiji Nakata, Takashi Morii

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Dendritic Alkyl Chains on DNA Cages: A Geometry-Dependent Inter- or Intramolecular “Handshake”

Thomas G.W. Edwardson , Karina M.M. Carneiro , Christopher K. McLaughlin, , Christopher J. Serpell , Hanadi F. Sleiman

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Development and application of crop exudate specific aptamers

Emily Mastronardi, Maureen Mckeague, Carlos Monreal, Maria DeRosa

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Development of nanoscale aptamer films for controlled release of encapsulated payloads

Amanda G. Foster, Yasir Sultan, Carlos Monreal, Maria C. DeRosa

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DNA Nanostructure Serum Stability: Greater Than The Sum Of Their Parts

Justin W. Conway , Christopher K. McLaughlin, Katherine J. Castor, Hanadi Sleiman

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DNA origami as a platform for assembly of nanophotonic elements

Yan Liu

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Non-canonical base pairing motifs in DNA crystal design

Chun Geng, Stephanie E. Muser, and Paul J. Paukstelis

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Optimizing DNA Nanotube Design for Future Applications

Graham D. Hamblin , Hanadi F. Sleiman

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Orientational ordering of short DNA fragments in the polymer matrix

Zareh A. Grigoryan , Yevgeni Sh. Mamasakhlisov, Armen T. Karapetian

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Porous three-dimensional DNA crystals as biomolecular containers for catalysis

Chun Geng, Paul J. Paukstelis

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Sculpting Light with DNA Origami

Anton Kuzyk, Robert Schreiber, Zhiyuan Fan, Günther Pardatscher, Eva-Maria Roller, Alexander Högele, Friedrich C. Simmel, Alexander O. Govorov, Tim Liedl

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Single-molecule observation of enzymes and DNA structural changes in the DNA nanostructures

Hiroshi Sugiyama , Masayuki Endo

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Amyloid Fibril Polymorphism Probed by Advanced Vibrational Spectroscopy

Igor K. Lednev, and Dmitry Kurouski

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Characterizing the Conformational Space of Two Disordered Peptides in Different Solutions

Ana V. Rojas, David Easterhoff, John T. M. DiMaio, Stephen Dewhurst, Alan Grossfield, Hongyu Miao, and Bradley L. Nilsson

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Evolutionary Dynamics of Conformational Flexibility

Juan F. Ortiz , Patrick Masterson , Madolyn Macdonald, Vladimir N. Uversky, Jessica Siltberg-Liberles

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Generating context-specific functions with intrinsically disordered domains

Ying Liu, Kathleen S. Matthews, and Sarah E. Bondos

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Getting A Grip On Alpha-Synuclein Amyloid Oligomers

Vinod Subramaniam

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Network Inference and Analysis of Parkinson’s Disease

Antonio Del Sol Mesa

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Order from disorder: Defining structure in disordered proteins

Shana Elbaum-Garfinkle, Garrett Cobb, Abhinav Nath, Elizabeth Rhoades

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Protein folding and binding funnels: a common driving force and a common mechanism

Yue-Hui Xie , Peng Sang, Yan Tao , Shu-Qun Liu

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Wonderful roles of the entropy in protein dynamics, binding and folding

Yue-Hui Xie , Yan Tao , Shu-Qun Liu

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3-D QSAR and protein-protein interaction studies on neuraminidase against Clostridium perfringens: An Approach towards target identification using structure based drug designing

Pallavi Somvanshi , Suruchi Rai, Bhartendu Nath Mishra

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A cutting - edge to drug discovery in Cancer; Cyclins as novel targets - an in silico technique

P. Sarita Rajender , K. Bhargavi, D. Ramasree , V. Uma

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A Dynamic Model for the Linker Histone

Stefjord Todolli, Wilma K. Olson

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A Molecular Dynamics Simulation Based Prediction of Deleterious Angiogenin Mutations Causing Amyotrophic Lateral Sclerosis

Aditya K. Padhi, B. Jayaram , James Gomes

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Computational approach for optimizing inhibitors of 1HWK (HMG-CoA reductase)

A. Ramakrishna , V. Uma

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Computational study of substrates and mediators features of lacasses

Azar Delavari, Juan J. Perez

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Conformational analysis of processivity clamps in solution demonstrates that protein structure does not correlate with dynamics

Penny J. Beuning , Philip Nevin, Jing Fang, Visvaldas Kairys, Česlovas Venclovas, John R. Engen

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Discovery of potent KdsA inhibitors of Leptospira interrogans through homology modeling, docking and molecular dynamics simulations

Dibyabhaba Pradhan, Vani Priyadarshini, Manne Munikumar, Sandeep Swargam, Amineni Umamaheswari

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Dominant Forces in Protein Folding

Arieh Ben-Naim

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Enhanced sampling of peptides and proteins with a new biasing replica exchange method

Katja Ostermeir, Martin Zacharias,

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Extracting Dynamics Information from Multiple Structures

Robert L. Jernigan, Jie Liu, Kannan Sankar, Kejue Jia, Michael T. Zimmermann

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GMPC model and the helix-coil transition in biopolymers

V. F. Morozov, Sh. A. Tonoyan, L. V. Melkonyan, N. L. Poghosyan, Sh. A. Sargsyan

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Going Beyond ‘Lamarckism’ in Protein Tertiary Structure Prediction

Priyanka Dhingra , Avinash Mishra, Rahul Kaushik, M. Hassan, Prashant Rana, Aditya Mittal, B. Jayaram

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Identification of Intein Inhibitors as Novel Anti-microbials with Relevance to Tuberculosis

Seth Pearson , Brian Callahan, Georges Belfort, Marlene Belfort

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Millisecond-Long Molecular Dynamics Simulations of Proteins on a Special-Purpose Machine

David E. Shaw

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Network properties of decoy and CASP predicted models: A comparison with native protein structures

S. Chatterjee, Soma Ghosh, Saraswathi Vishveshwara

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NMR study of RQC domain of BLM protein

Vee Vee Cheong, Brahim Heddi, Anh Tuân Phan

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Novel Methods to Identify and Quantify Protein Kinetic stability in different Systems

Ke Xia, Wilfredo Colón

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Polymorphic assembly of computationally designed hydrophobic-rich collagen peptides

Kenneth N. McGuinness , Vikas Nanda

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Protein Domains - A thermodynamic definition

Lauren L. Porter, George D. Rose

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Protein Structure Prediction with limited data

Alberto Perez, Justin MacCallum, Ken Dill

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Role of Conserved water molecular triad in the recognition of IMP, NAD+ with Asp 274, Asn 303, Arg 322 and Asp 364 in both the isoform of hIMPDH

Deepak K. Mishra, Hridoy R. Bairagya, Bishnu P. Mukhopadhyay

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Role of free Cysteines in leptin receptor

R.Karthick , Gokul Raghunath, Sharmila Anishetty, R.Malathi

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Self-association prompts proteins for new function: The role of altered dynamic properties

Shoshana J. Wodak, Michael Garton , Anatoly Malevanets, Stephen McKinnon

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Structure based engineering to generate high affinity immunotherapy for the drug of abuse

Shraddha Thakkar, Nisha Nanaware-Kharade, Guillermo Gonzalez III, Reha Celikel, Eric Peterson, Kottayil I. Varughese

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Structure based virtual screening towards identification of potential FabH inhibitors

Vani Priyadarshini, Dibyabhaba Pradhan, Manne Munikumar, Sandeep Swargam, Amineni Umamaheswari

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T-cell vaccine design for Streptococcus pneumoniae: an in silico approach

Manne Munikumar , Vani Priyadarshini, Dibyabhaba Pradhan, Sandeep Swargam, Amineni Umamaheswari

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Targeting “Beta lactamase-C” in development of novel anti-tuberculosis therapeutics

Saugata Hazra , John S. Blanchard

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Impact of cancer mutations on protein binding and activity

Anna Panchenko

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Integrating Structural and Systems Biology: Structure-based Prediction of Protein-Protein Interactions on a Genome-Wide Scale

Qiangfeng Cliff Zhang, , Donald Petrey , Barry Honig

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Integrative analysis of gene expression and protein-protein interaction networks in Glioblastoma

Seema Mishra

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Investigating the mode of action of an essential OBG GTPase, CgtA in bacteria

Ananya Chatterjee , Partha P. Datta

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Isolation and partial characterization of a general hormone transporting blood protein complex

Margarita I. Garipova , Rita R. Usmanova

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Small molecule identification against novel MDRA protein of Mycobacterium tuberculosis

M. Kiran Kumar, M. Vasavi, C. Venkataramana Reddy, V. Uma

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Vascular Endothelial Growth Factor Receptor-2 (VEGFR2): Structure and Functional relationship

Jhansi Rani Nathan, Shilpi Shika , Malathi Ragunathan

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Molecular Dynamics and Ligand based studies for the validation of potential inhibitors for SrtA against Bacillus anthracis

Sanjeev Kumar Singh , Chandrabose Selvaraj

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Plucking the High Hanging Fruit: A Systematic Approach for Targeting Protein Interfaces

Paramjit S. Arora

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Point mutations in the yeast Pma1 H+-ATPase affect polyphosphate (PolyP) distribution

Alexandr A. Tomashevski , Valery V. Petrov

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Structural articulation of biochemical reactions using altered bonds and iterative topology switching

Swati R. Manjari, Nilesh K. Banavali

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Structures and Interactions of Proteins Involved in ER-associated Protein Degradation

Udo Heinemann, Anup Arumughan, Jennifer Hanna, Yvette Roske, Anja Schütz, Erich E. Wanker

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The Peculiarities of Regulation of Yarrowia lipolytica Yeast and Citric Acid Overproduction

Igor G. Morgunov , Svetlana V. Kamzolova

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Using CG Modeling in Exploring The Role of Dynamical Effects in Catalysis And in Simulating Biological Molecular Machines

Arieh Warshel

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Showing 101 to 200 of 219 items.  Page: 2