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Albany 2015:Book of Abstracts

Albany 2015
Conversation 19
June 9-13 2015
©Adenine Press (2012)
Showing 101 to 200 of 215 items.  Page: 2

Ion-π interactions in biomolecular systems

Luigi D'Ascenzo , Pascal Auffinger

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Modifications Modulate Anticodon Loop Dynamics and Codon Recognition in E. coli tRNAArg1,2

Kathryn L. Sarachan , William A. Cantara, Jessica L. Spears, Hasan Dimirci, Frank V. Murphy IV, Srivathsan Ranganathan, Alan Chen, Paul F. Agris

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Stabilization effects induced by modified nucleotides in tRNA T-loop motifs

Dominique Sydow, Filip Leonarski, Luigi D’Ascenzo , Pascal Auffinger

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Molecular basis for nucleo-cytoplasmic transport of tRNA by Exportin-t

Asmita Gupta , Manju Bansal

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Structural dynamics of a mobile group II intron ribonucleoprotein complex

Guosheng Qu , Xiaolong Dong, Carol Lyn Piazza, Jia Wang, Hongwei Wang, Marlene Belfort

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Origin and evolution of adaptive immunity systems

Eugene V Koonin

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Pseudo-Lamarckian Spacer Adaptation by Type I CRISPR-Cas System

Konstantin Severinov, Kirill Datsenko, Ekaterina Savitskaya, Ekaterina Semenova

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Shaping CRISPR repeat RNA for Cleavage by Cas6 endoribonucleases

Yaming Shao, Hong Li

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Structural insights into the RAD51 paralog complexes reveal molecular details of disease causing mutations

Gareth J. Williams, Soumita SilDas, Aditya Anand, David Schild, John A. Tainer

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Structures Guided Insight into Mechanisms of RNA-guided Surveillance of Foreign DNA

Blake Wiedenheft

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Aprataxin and the threat of RNA contamination in DNA

R. Scott Williams

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Cytosine demethylation through off-target base excision repair

Anton Endutkin, Dmitry Zharkov

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The Road to Genome Expansion is Paved with Good Intentions: When DNA Repair goes Awry

Sarah Delaney,

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Binding Dynamics of Yeast MutS Homologs Msh4-Msh5 with the Holliday Junction

Sudipta Lahiri, Manju Hingorani, Ishita Mukerji

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Structurally Distinct Ubiquitin- and SUMO-Modified PCNA: Implications for their Distinct Roles in the DNA Damage Response

Susan E. Tsutakawa, Chunli Yan, Xiaojun Xu, Zhihao Zhuang, M. Todd Washington, John A. Tainer , Ivaylo Ivanov

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Analysis of SNP containing sites in human genome using text complexity estimates

Nataly S. Safronova, Vladimir N. Babenko , Yuriy L. Orlov

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Building up an integrated picture of the dynamic DSB repair super complex, one component and interaction at a time.

Michal Hammel

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Energetics of damaged bases recognition by DNA glycosylases

Olga S. Fedorova , Nikita A. Kuznetsov

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Integrating Multi-Scale Data on Homologous Recombination into a New Recognition Mechanism based on Simulations of the RecA-ssDNA/dsDNA Structure

Darren Yang, Benjamin Boyer, Chantal Prévost, Claudia Danilowicz, Mara Prentiss

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RecA Mediated Homology Recognition Offers Lessons for Sequence Dependent Protein Recognition, Protein Folding, and Artificial Self-Assembly

Darren Yang, Claudia Danilowicz, Benjamin Boyer, Chantal Prevost , Mara Prentiss

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Structral insights into the mechanism of homologous recombination

Benjamin Boyer , Darren Yang, Claudia Danilowicz, Mara Prentiss, Chantal Prevost

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The mechanism of the specific protein-DNA interactions during DNA lesion search and damaged base recognition by Endonuclease VIII

N. A. Kuznetsov , O. A. Kladova, A. A. Kuznetsova , O. S. Fedorova

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V(D)J recombination targeted in cis by transcription induced DNA supercoiling

Mihai Ciubotaru

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Application of viscometric methods for studying the interaction of various porphyrins with DNA

Vigen G. Barkhudaryan , Gayane V. Ananyan

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Formation of Local TAT Base-Triplets in DNA Pseudoknots with Stem-Loop Complementarity

Calliste Reiling-Steffensmeier, Luis A. Marky

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Large Antiviral Polyamide-DNA Interactions

Elena Vasilieva, Yang Song, Kevin J. Koeller, G. Davis Harris, James K. Bashkin, Cynthia M. Dupureur

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The Comparative Study of H2TOEPyP4 and CoTOEPyP4 Porphyrins with A-DNA

A. Avetisyan , Y. Dalyan

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The features of complexformation of poly(dI-dC) 2 with porphyrins

Gayane V. Ananyan, Nelli H. Karapetyan, Samvel G. Haroutiunian, Yeva B. Dalyan

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Influence of 1,3-diazaadamantane Derivative on the Strand Exchange between Short Oligonucleotides

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

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2'-Deoxyguanine analogs which enhance hybridization oligonucleotides with complementary DNA

Mark Lukin , Tatiana Zaliznyak, Leyla Shakirzyanova , Carlos de los Santos

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Analysis of structure and thermodynamics of modified DNA duplexes using molecular dynamics simulation

Alexander A. Lomzov, Vitaly V. Gorelov, Victor M. Golyshev, Tatiana V. Abramova , Dmitrii V. Pyshnyi

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Attacking mechanism of H and OH radicals to DNA base pair: DFT calculations in water

Naoko Okutsu, Eisuke Shimizu, Victor I. Danilov, Sergiy Shulga , Noriyuki Kurita

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B - Z transition in poly (dG-dC) in the presence of mitoxantrone

Armen T. Karapetyan, Margairta A.Torosyan , Yuri S. Babayan

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Convergence and reproducibility of the DNA duplex d(GCACGAACGAACGAACGC) using molecular dynamics simulations

Rodrigo Galindo-Murillo , Thomas E. Cheatham III

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Interaction of Doxorubicin with Tumor DNA, Irradiated by Electromagnetic Millimetric Non-thermal Waves

Sergey H. Hakobyan, Yuri S. Babayan

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Modeling the DNA bubbles dynamics

Andrey A. Grinevich, Artem A. Ryasik, Ludmila V. Yakushevich

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Spectral Characteristics of DNA-EtBr and DNA-MB Complexes

Poghos O.Vardevanyan, Mariam A. Shahinyan, Ara P. Antonyan, Marine A.Parsadanyan, Mikayel V. Minasyants

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The Binding Mechanisms of Methylene Blue with DNA

Ara P. Antonyan, Lilit A. Hambardzumyan, Marine A. Parsadanyan, Poghos O. Vardevanyan

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The Cold Melting Effect of Complexes DNA with Two Different Ligands Using Different Binding Mechanisms

Zareh A.Grigoryan , Armen T.Karapetyan

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The consistent description of diffusion and kinetic states of the adsorption of ligands on DNA immobilized molecules

Valeri B. Arakelyan, Zaven E. Navoyan, Gohar G. Hovhannisyan, Poghos O. Vardevanyan

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The Influence of Non-Thermal Coherent Millimeter Electromagnetic Waves on the Thermal Expansion Coefficients of DNA Solutions

Ani A. Tadevosyan, Sergey N. Hakobyan, Ruzan S. Ghazaryan, Gayane L. Kanaryan

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Novel Smart C2-Symmetrical NDI Derivatives as G-Quadruplex Stabilizing Ligand with a Potential to Differentiate between Topological Structures

VibhaTandon

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Advanced computational studies of G-quadruplex folding and topological preferences

Jiri Sponer

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Covalence, not Resonance-Assistance, behind Cooperative Hydrogen and Halogen bonds in Quadruplexes

C. Fonseca Guerra

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NMR based Structure and Stabilization of G quadruplex d-(TTGGGGT)4 due to binding with an alkaloid Coralyne

Padmapriya Kumar , Ritu Barthwal

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NMR study of interaction of mitoxantrone to G-quadruplex sequences leading to stabilization and inhibition of telomerase enzyme

Ritu Barthwal, Sweta Tripathi , Tarikere Palakshan Pradeep

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Optimizing charge transfer through G-quadruplex

Rosa Di Felice

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Selective G-Quadruplex Recognition by a Novel Cyanine Dye

Pallavi Chilka, Prathap Reddy Patlolla, Bhaskar Datta

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The "physiological" behaviour of DNA/RNA structural motifs in gas phase

Massimiliano Porrini , Valentina D'Atri , Josephine Abi-Ghanem , Frédéric Rosu , Valérie Gabelica

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Polymorphism within Complex DNA Topologies

Sarah Harris

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Role of Dynamic Base Pair Polymorphism in the Central Dogma of Molecular Biology

Isaac J. Kimsey , Huiqing Zhou, Heidi Alvey , Hashim M. Al-Hashimi

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The Distribution of Water and Ions around Nucleic Acids

David A. Case

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Conformational Behavior of Short Peptides in Explicit Solvent Simulations

Juan Jesus Perez

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The Role of Solvent Mobility in Protein Dynamics

Qiong Yang, Peng Sang, Shu-Qun Liu

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Water near Proteins and Interfaces: A New Molecular Perspective

Shekhar Garde

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Inertial microfluidics for biofluid processing

Aram J. Chung

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Molecular Dynamics Studies of HTLV-1 Rex Responsive Element Aptamer Recognition

Zachary J. Fallon, Shane M. Bernard, Wesley T. Hodges, Megan T. Hoffman, Maria C. Nagan

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Molecular Mechanism of Long-range Proton Translocation by Bacteriorhodopsin

Xiaoxia Ge , Marilyn R. Gunner

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Molten globule behavior of Apicomplexan protein P2 from Plasmodium falciparum and Toxoplasma Gondii

Pushpa Mishra , Shobhona Sharma , Ramakrishna V. Hosur

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Two different hormone transporting systems in human blood Features of peptide hormone transport in human blood

Margarita I. Garipova, Sergey A. Bashkatov, Olesya I. Dazko, Anna A. Kosova, Maria E. Migunova

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Bridging the islands of protein families in sequence space using artificial sequences

N. Srinivasan , R. Mudgal, G. Kumar, N.R. Chandra, R. Sowdhamini, S. Sandhya

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Statistical fluctuations, Dynamics, and De Novo Enzyme Catalysis

Teresa Head-Gordon

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Mutations in membrane and extracytosolic domains of the yeast Pma1 ATPase cause different distribution of polyphosphates

Alexandr A. Tomashevski , Valery V. Petrov

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Mutations in the yeast Pma1 H+-ATPase regulatory domain affect polyphosphate metabolism

Alexandr A. Tomashevski , Valery V. Petrov

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Dynamics of The Metabolic Pathway- An Approximate Study of The Krebs Cycle

Chanchal K Mitra , Kalyani Korla

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Inhibition of Isocitrate Lyase Shifts Metabolism Toward the Isocitrate Overproduction in Yeast Yarrowia lipolytica

Svetlana V. Kamzolova, Igor G. Morgunov

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Metabolism of Biodiesel-derived Waste in the Yeast Yarrowia lipolytica – Producers of Citric- and Isocitric Acids

Igor G. Morgunov, Svetlana V. Kamzolova

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Model-aided anaerobic metabolic gene knockout of malate dehydrogenase (mdh) gene predicts increased succinate production in Escherichia coli

Bashir Sajo Mienda, Mohd Shahir Shamsir

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Physico-chemical characterization of amylases of L. decemlineata and their inhibitors from plants

Vyacheslav O. Tsvetkov, Irina A. Shpirnaya, Karina I. Valiakhmetova, Rinat I. Ibragimov

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Stapled-peptides targeting the protein-binding interface of eukaryotic Translation Initiation Factor 4E (eIF4E) protein

Dilraj Lama , Soo T Quah, Christopher J Brown, David P Lane , Chandra S Verma

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Classification of protein sequences with special references to multi-domain systems

Prachi Mehrotra, Ramachandra M. Bhaskara, Mutharasu Gnanavel , Ramaswamy Rakshambikai, Juliette Martin, Narayanaswamy Srinivasan

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Computational Analysis and Prediction of Proteins that undergo domain swapping

Prashant Shingate, Atul Upadhyay, Shameer Khader , Ramanathan Sowdhamini

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Determination of the Size of Folding Nuclei of Protofibrils from the Concentration Dependence of the Rate and Lag-time of Their Formation

Oxana V. Galzitskaya, Nikita V. Dovidchenko, Olga M. Selivanova, Maria Yu. Suvorina, Alexey K. Surin, , Alexey V. Finkelstein

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Influence of Homo-Repeats on Functions and Aggregation Propensities of Protein Chains

Oxana V. Galzitskaya , Mikhail Lobanov

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Mechanism of Protein Evolution: Conformational Dynamics and Allostery

Taisong Zou , Avishek Kumar, Brandon M Butler , S.Banu Ozkan

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Pathway Enrichment Analysis of Acute Myeloid Leukemia Pathogenesis: A Focus on JAK-STAT signalling pathway

Jhumur Pani , Kumar Gautam Singh , Anjani Kumar Singh , Fanish Kumar Pandey , Himanshu Narayan Singh

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Differences of the Active Site Structure as Revealed by Sequence Analysis of Slow and Fast Bacterial Luciferases

Anna A. Deeva, Evgenia A. Temlyakova, Elena V. Nemtseva, Anatoly A. Sorokin, Valentina A. Kratasyuk

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Topological variance in protein structure: An insight from kinetics and functional study

Taushif Khan, Indira Ghosh

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Transformation of Sequences from Random into Functional in Primary Living Units

Vladimir N. Kompanichenko

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In Silico Discovery of Novel HIV-1 Entry Inhibitors Based on Potent and Broad Neutralizing Antibody VRC01

Alexander M. Andrianov , Ivan A. Kashyn , Alexander V. Tuzikov2

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Molecular Dynamics Simulations of the Structure of Human Antibody 10E8 Fab in Complex with Membrane-Proximal External Region of the HIV-1 GP41 Protein

Ivan A. Kashyn , Alexander V. Tuzikov2, Alexander M. Andrianov

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Towards the high-resolution, ab initio modeling of peptide-mediated interactions

Nawsad Alam, Assaf Lavi, Nir London, Barak Raveh, Dima Kozakov , Ora Schueler-Furman

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Virtual Screening of Novel Anti-HIV-1 Agents Targeting CD4-Binding Site of the Envelope GP120 Protein

Alexander M. Andrianov , Ivan A. Kashyn , Alexander V. Tuzikov2

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Drug resistance: Crystallography of drug-resistant HIV-1 protease mutant

Tushar Raskar, Amit Das , M. V. Hosur

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In silico studies show effective inhibition of HIV-1 Reverse Transcriptase activity by an antiviral herbal compound (5E)-3-(2-aminoethyl)-5-benzylidene-1,3-thiazolidine-2,4-dione

C Seniya , Nand K Sah

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Molecular recognition between active site contour maps and ligand pharmacophoric sites predicts the future leads of HTLV-PR inhibitors

Sanjeev Kumar SinghChandrabose Selvaraj

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Probing the Conformational Control Mechanism of HIV-1 gp120: A Molecular Simulation Study

Peng Sang , Shu-Qun Liu

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Reverse Transcription Driven Uncoating of Mature HIV Capsids

Ioulia Rouzina , Robijn Bruinsma

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Helix-Coil Transitions in heteropolymers. The constrained annealing approach

Shushanik A. Tonoyan, Arevik V. Asatryan, Aram K. Andriasyan, Yevgeni Sh. Mamasakhlisov, Vladimir F. Morozov

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How insulin binds: structure of a micro-receptor complex and implications for analog design

Michael A. Weiss

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The helix-coil transition in two-component solvent in the frames of GMPC. Ligands effects on the characteristics of the transition

Arevik V. Asatryan, Shushanik A. Tonoyan, Saadat Mirtavoosi, Yevgeni Sh. Mamasakhlisov, Vladimir F. Morozov

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Effect of template selection on the construction of atomistic models of GPCRs by homology modeling

Cecylia S. Lupala, Bahareh Rasaeifar, Patricia Gomez-Gutierrez , Juan J. Perez

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Designing Non-Toxic Ligands against TB using Data Intensive Genome Level Analysis

Divneet Kaur , S. K. Brahmachari

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Effect of ligand-binding on specific interactions between DNA and regulatory protein: molecular simulations based on MD and ab initio fragment MO methods

K. Shimamura , Y. Matsushita, M. Oishi, , T. Ohyama , N. Kurita

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On the origin and completeness of ligand binding pockets with applications to drug discovery

Jeffrey Skolnick

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Antiinflamatory Activity of Phenolic Compounds Extracted from Uruguayan Propolis and Grape

Elena Alvareda , Pablo Miranda , Victoria Espinosa4, Helena Pardo, Sara Aguilera, Margot Paulino Zunini

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Combination of e-pharmacophore modeling, multiple docking strategies and molecular dynamic simulations to discover of novel antagonists of BACE1

Natarajan Pradeep , Manne Munikumar, Sandeep Swargam, Kanipakam Hema, Katari Sudheer Kumar , Amineni Umamaheswari

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Discovery of potential inhibitors of BMX non-receptor tyrosine kinase through e-pharmacophore based virtual screening

Dibyabhaba Pradhan , Vani Priyadarshini , Shweta Aggrawal, Natarajan Pradeep, Arnab Nayek, Arun kumar Jain, Amineni Umamaheswari

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Dual Allosteric Inhibitors Jointly Modulate Structure and Dynamics in the Hepatitis C Virus Polymerase

Jodian A. Brown , Ian F. Thorpe

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In silico design and virtual screening of inulinase immobilization ligands with highest affinity

Maxim S. Kondratyev , Marina G. Kholyavka , Artem V. Kabanov , Anatoly A. Sorokin , Alexander A. Samchenko , Valery G. Artyukhov

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Showing 101 to 200 of 215 items.  Page: 2