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Book of Abstracts: Albany 2011

category image Albany 2011
Conversation 17
June 14-18 2011
©Adenine Press (2010)
Showing 1 to 100 of 210 items.  Page: 1 3

Computational Microscopy

Klaus Schulten

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Computational Investigation of the Free Energy Landscape of the four stereomers of Ac-L-Pro-c3Phe-NHMe (c3Phe=2,3-methanophenylalanine) in explicit and implicit Solvent

Juan J. Perez, Alex Rodriguez, and Francesc Corcho

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Computer Simulation of Plastocyanin Diffusion and Interaction with Its Reaction Partners

Ilya Kovalenko, Alexandra Diakonova, Olga Knyazeva, Anna Abaturova, Galina Riznichenko, Andrei Rubin

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Computer Simulations of Protein–Protein Complex Formation on Graphics Processing Units

Ilya Kovalenko, Alexandra Diakonova, Sergey Khrushchev, Anna Abaturova, Galina Riznichenko, Andrei Rubin, Sergey Trifonov, Ivan Morozov, Yaroslav Kholodov, Valeri Barsegov

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Efficient Explicit Solvent Simulations of Molecular Association Kinetics

Matthew C. Zwier, Joseph W. Kaus, and Lillian T. Chong

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Exploring Fast Protein Folding Funnel Using Replica Exchange Molecular Dynamics at Different Temperature Ranges

Vinod Jani, Shruti Koulgi, Uddhavesh Sonavane, Rajendra Joshi

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Exploring Folding Funnel of Villin Headpiece Using Replica Exchange Molecular Dynamics and Amber United Atom Model

Vinod Jani, Uddhavesh Sonavane, and Rajendra Joshi

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Exploring the Role of Protein-Protein Interactions in the Mechanical Unfolding of Protein Assemblies

Ruxandra I. Dima

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Flexibility and Modulations in Protein-Protein Interactions: Mechanistic Insights from Molecular Dynamics Simulations of MDM2 and p53

Shubhra Ghosh Dastidar

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Homology Modeling and Molecular Dynamics Simulations of RNA Polymerases

Ivan Barvik, Vlastimil Zima, Kamil Malac

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Method of Molecular Dynamics for Proteins in the Ionization-Conformation Phase Space at Equilibrium Conditions at Constant pH

Y.N. Vorobjev

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Molecular Dynamics Simulations on Structural Heterogeneity States of Protein

Jihua Wang , Liling Zhao , Zanxia Cao

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Molecular Simulations Unravel Key Amino Acid Interactions Regulating Stability and Aggregation of Human Lens γD-crystallin

Payel Das, Jonathan A. King, and Ruhong Zhou

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Phase transition from α-helices to β-sheets in fibrinogen coiled coils

Artem Zhmuro, Andre Brown, Rustem I. Litvinov, Ruxandra I. Dima, John W. Weisel, and Valeri Barsegov

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Resolving fibrinogen nanomechanics using dynamic force measurements in vitro and in silico

Artem Zhmurov, Andre Brown, Rustem I. Litvino, Ruxandra I. Dima, John W. Weisel, and Valeri Barsegov

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Self Assembly Study of the Human GPCR Protein β2-Adrenergic Receptor Using Coarse Grained Molecular Dynamics Technique

Anirban Ghosh, Uddhavesh B. Sonavane, and Rajendra Joshi

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Swarm intelligence: Cooperative replica methods for prediction of protein structure

Neil J. Bruce, and Richard A. Bryce

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The Nucleosome Simulator: 100 Nucleosomes; 2 Microseconds and Counting

Rajib Mukherjee, Hideki Fujioka, Abhinav Thota, Shantenu Jha, Thomas C. Bishop

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Thermodynamics of Waters Sequestered inside Macromolecules.

Mihaly Mezei

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Molecular Motions of Proteins Play Crucial Role in Their Function

Shu-Qun Liu, Shi-Xi Liu Zhao-Hui Meng, Yan Tao, Ke-Qin Zhang, & Yun-Xin Fu

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Role of Disulfide Bonds in Structural Stability and Flexibility of Cuticle-degrading proteases from nematophagous fungi ⎯ a molecular dynamics simulation study

Lian-Ming Liang, Ke-Qin Zhang, Shu-Qun Liu

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Evidence for Initial Non-specific Polypeptide Chain Collapse during the Refolding of the SH3 Domain of PI3 Kinase

Amrita Dasgupta, Jayant B. Udgaonkar

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Folding Globular Proteins: Collapse Kinetics and Chevron Plots

D. Thirumalai

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Origins of the Mechanical Stability of the C2 Domains in Human Synaptotagmin 1

Li Duan , Artem Zhmurov, Valeri Barsegov, Ruxandra I. Dima

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Simulations of the Folding Unfolding of Proteins Under Different Solvent Condition

Deepak R. Canchi, Camilo Jimenez-Cruz, Angel E. Garcia

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Single-molecule Fluorescence Maps the Folding Landscape of a Large Protein

Menahem Pirchi

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The role of central pore residues of p97/VCP on substrate unfolding and translocation: A computational model

Sam Tonddast-Navaei, George Stan

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Thinking into Mechanism of Protein Folding and Molecular Binding

Xing-Lai Ji, Shu-Qun Liu

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Universality of the spatial distribution of the backbones and a narrow band of amino acid stoichiometries amidst the structural and functional diversity of folded proteins

B. Jayaram, A. Mittal

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Largescale Protein Properties: Crystallization, Amyloid Formation, and the Stability of The Proteome

Ken A Dill, Kings Ghosh, Jeremy Schmit

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SANJEEVINI-A Lead Molecule Design Software

Goutam Mukherjee, Tanya Singh, B. Jayaram

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Inferred Biomolecular Interaction Server--A Method and a Server to Analyze and Predict Protein Interacting Partners and Binding Sites

Benjamin A. Shoemaker, Dachuan Zhang , Ratna R. Thangudu, Manoj Tyagi, Jessica H. Fong, Aron Marchler-Bauer, Stephen H. Bryant, Thomas Madej, Anna R. Panchenko

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Integrating CADD Methodologies for the Design of Novel COMT Inhibitors

Nidhi Jatana, Aditya Sharma, N. Latha

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Liquid state NMR spectroscopy as a tool to obtain structural and binding information of drug molecules metabolized by P450BM3 enzymes

A.J. Kolkman, V. Rea, J. Draaisma, M. Tessari, E.V. Vottero, K.A.M. Ampt, J.N.M. Commandeur, H. Irth, N.P.E. Vermeulen, M. Honing, and S.S. Wijmenga

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Reconstructing an enzyme-inhibitor binding process by molecular dynamics simulations

Gianni De Fabritiis

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Structure-function Investigation of Metalloproteinases Provides Novel Insights into Drug Design

Netta Sela-Passwell, Alla Trahtenhercts, and Irit Sagi

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Virtual Screening and Theoretical Activity Prediction of Idenopyrazole Derivatives of CDK2 Inhibitors: A QPLD and MM-GBSA Approach

Sanjeev Kumar Singh , Sunil Kumar Tripathi

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Using Cylindrical Coordinates to Represent Rod-Shaped and Other Fibrous Protein 3D Structures: Potential Advantages and Applications

Srujana Cheguri , Vicente M. Reyes

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A Database/Webserver for Size-Independent Quantification of Ligand Binding Site Burial Depth in Receptor Proteins: Implications on Protein Dynamics

Srujana Cheguri , Vicente M. Reyes

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Cancer Meets the “Omics”: A Comprehensive Cancer Biotherapy Database with Links to Multiple Bioinformatics Websites/WebServers - Facilitating the Search for Anticancer Biological Agents

Preety Priya , Vicente M. Reyes

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Towards a Spherical Coordinate System Metric for Quantitative Comparison of Protein 3D Structures

James DeFelice , Vicente M. Reyes

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Using Cartographic Techniques to Project Protein 3D Surfaces onto the 2D Plane: Potential Applications and Implications

Vicente M. Reyes

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Computer-Aided Pathway to Increasing the Thermostability of Small Proteins

Maxim Kondratyev, Artem Kabanov, Alexander Samchenko, Vladislav Komarov , Nikolay Khechinashvili

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Conserved Water Mediated H-bonding Dynamics of Carboxamide group in NAD to Catalytic Asp 274 and His 93 in Human IMPDH

Hridoy Ranjan Bairagya, Bishnu P Mukhopadhyay1 #, Payel Mallik, Archana K. Srivastava

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Generating Conformational Ensembles for Flexible Protein-Ligand Docking by Elastic Network Model Guided Molecular Dynamics Simulations: Application to Beta 2 Adrenergic Receptor

Basak Isin, Guillermina Estiu, Olaf Wiest, Zoltan N. Oltvai

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Homologous and Heterologous Crystallin Interactions in Cataract

Priya R. Banerjee , Jayanti Pande

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Improving in Digestion and Antioxidant Activity of β-lactoglobulin using Newly designed Copper Complexes as Artificial Proteases

Adeleh Divsalar , Sajedeh Ebrahim-Damavandi, Ali Akbar Saboury, Hassan Mansouri-Torshizi

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Point mutation in M9-M10 loop of the yeast Pma1 H+-ATPase affects both ATPase functioning and polyphosphate (PolyP) distribution

Alexander A. Tomashevsky, and Valery V. Petrov

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Protein Structure Modelling on the Indo-US Cancer Research Grid

Amit Saxena, Anirban Ghosh, George A. Komatsoulis, Hemant Darbari, Anil Srivastava, Ravi Madduri, P.K. Sinha, and Rajendra Joshi, ,

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Role of Conserved Water Molecules in Binding of Thyroxin and Analogs Inhibitors to Human Transthyretin: A Study On Water-Mimic Inhibitor Design.

Avik Banerjee, Hridoy R Bairagya, Bishnu P Mukhopadhyay#, Tapas K Nandi

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Role of M5-M6 loop in the biogenesis and function of the yeast Pma1 H+-ATPase

Valery V. Petrov

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Structure and Topology of Phospholamban Monomer and Pentamer by a Hybrid Solution and Solid-State NMR Method

Nathaniel J. Traaseth, Raffaello Verardi, Lei Shi, and Gianluigi Veglia

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Structures and Dynamics of the Complete Protein Kinase Catalytic Cycle of CDK2/CyclinA

Matthew A. Young, Douglas M. Jacobsen, Zhao-Qin Bao

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The Solution and Binding Behavior of the Intrinsically Disordered FG Nups Determined by in cell NMR

Loren E. Hough, Kaushik Dutta, Jaclyn Tetenbaum-Novatt, Michael Rout, David Cowburn

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Computational Generation of Inhibitor-bound Conformers of p38 MAP Kinase and Comparison with Experiments

Ahmet Bakan , Ivet Bahar

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Dynamics of AMPA-subtype Glutamate Receptor using Elastic Network Models

Indira Shrivastava, Anindita Dutta, and Ivet Bahar

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Protein flexibility methods to compare protein structure predictions

Alberto Perez, Justin L. MacCallum, Yang Zhang, Ivet Bahar, Ken A. Dill

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Protonation of Glutamate-208 Induces the Release of Agmatine in an Outward-Facing Conformation of Arginine/Agmatine Antiporter

Elia Zomot, and Ivet Bahar

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Transition Pathways of Enzymes Explored by Combining the Anisotropic Network Model, Molecular Dynamics Simulations and a Monte Carlo Sampling of Conformational Space

Mert Gur , Ivet Bahar

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Modeling Three Dimensional Structures of Complete PKS Modules for Understanding Inter-Domain Interactions

Swadha Anand , Debasisa Mohanty

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Computational Modeling of Allostery-Driven Unfolding and Translocation of Substrate Proteins

George Stan , Andrea Kravats, Sam Tonddast-Navaei, and Manori Jayasinghe

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Energetically Favourable Communication Pathways in Pyrrolysyl-tRNA Synthetase

Moitrayee Bhattacharyya, Saraswathi Vishveshwara

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Intrinsic Dynamics and Allostery: Learning from Theory, Computations and Experiments

Ivet Bahar

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Linking Allostery In Chaperonins To Protein Folding

Amnon Horovitz

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Molecular Dynamics Simulations of Protein Unfolding and Translocation Resulting from Allosteric Motions of ClpY

Andrea Kravats, Manori Jayasinghe, George Stan

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Perturbation Response Scanning Method for Identifying Allosteric Transitions and Utilizing in Flexible Docking

Z. N. Gerek, A. Bolia, S. B. Ozkan

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Disordered proteins in Parkinson's and Alzheimer's Disease: Linking structural transformations to function, aggregation and toxicity.

David Eliezer

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Evolution of Structure and Dynamics for a Family of Intrinsically Disordered Proteins

Gary W. Daughdrill, Wade Borcherds, Hongwei Wu, Bin Xue, Vladimir Uversky

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Tau change is a key for understanding brain aging and Alzheimer disease

Akihiko Takashima

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Understanding The Molecular Basis Of Pathogenicity or Lack Thereof Of Serum Amyloid A Isoforms

Sai Praveen Srinivasan , Yun Wang, Zhuqiu Ye, Marimar Lopez, Wilfredo Colón

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DNA: Not Merely the Secret of Life

Nadrian C. Seeman

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The Label-Free Unambiguous Detection and Symbolic Display of Single Nucleotide Polymorphisms on DNA Origami

Hari K. K. Subramanian, Banani Chakraborty, Ruojie Sha, Nadrian C. Seeman

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Topological Bonding of DNA Nanostructures

Yoel Ohayon, Ruojie Sha, Ortho Flint, , Nadrian C. Seeman1View Abstract

A Controlled DNA Biped Walker on a DX Track

Dadong Li, Ruojie Sha, James Canary, Nadrian C. Seeman

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A DNA Crystal Designed to Contain Two Molecules per Asymmetric Unit with Fluorescent Dyes

Tong Wang , Ruojie Sha, Jens J. Birktoft, Jianping Zheng, Chengde Mao, Nadrian C. Seeman

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A Toolkit for Site-Specific DNA Interstrand Crosslinks

Miao Ye, Johan Guillaume, Yu Liu, Ruojie Sha, Risheng Wang, Nadrian C. Seeman, James W. Canary

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Amyloid Fibrils Captured inside Twenty-Helix DNA Nanotubes

Anuttara Udomprasert , Marie Bongiovanni, Ruojie Sha, William B. Sherman, Monica Menzenski, Paramjit Arora, James W. Canary, Sally L. Gras, and Nadrian C. Seeman

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Biosensor design using DNA tile lattices

Lauren Hakker, Kimberly A. Harris, Thom H. LaBean, Paul F. Agris

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Crystalline Two-Dimensional DNA-Origami Arrays

Wenyan Liu, Hong Zhong, Risheng Wang, and Nadrian C. Seeman,

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Deoxyribozyme Sensors for Nucleic Acid Analysis

Dmitry M. Kolpashchikov , Yulia V. Gerasimova, Evan Cornett

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DNA Nanoarchitechtures and Mechanical Devices

Kurt V. Gothelf

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Molecular Dynamics Simulations of DNA Holliday Junctions: Conformational Stability and Transitions

Elizabeth G. Wheatley, Susan Pieniazek, David L. Beveridge

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Multi-Step Energy Transfer as a Communication Tool in Nanoscale DNA Assemblies

Jonas K. Hannestad, Bo Albinsson

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Nucleic acid-based molecular devices

Friedrich C. Simmel

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Programming Curvature in DNA Nanotubes

Graham D. Hamblin, Hanadi F. Sleiman

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Rationalizing the Outcome of One-Pot DNA Nano-Assemblies

Erik P. Lundberg, Calin Plesa, L. Marcus Wilhelmsson, Per Lincoln, Tom Brown, Bengt Nordén

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Structure of DNA Four-Way Junctions: Effect of Ions and Proteins

C. Iulia Vitoc, Olga Buzovetsky, Jacob Litke, Yan Li , Ishita Mukerji

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Towards origin of life and... what is life, after all?

Edward N. Trifonov

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Characterization of DNA and RNA Secondary Structures in Anhydrous Media

Irena Mamajanov, Aaron E. Engelhart, Heather D. Bean, Nicholas V. Hud

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Evolutionary Model of Cancer Progression: Understanding the Role Of Passenger Mutations In Cancer Progression

Christopher D. McFarland , Shamil Sunyaev , Leonid Mirny

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Formation and Chiroptical Properties of Amino Acids in Interstellar Ice Analogues

Uwe J. Meierhenrich, Jean-Jacques Filippi, Cornelia Meinert, Jan Hendrik Bredehöft, Jun-ichi Takahashi, Laurent Nahon, Nykola C. Jones, Soeren V. Hoffmann

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Intercalation-Mediated Assembly and the Origin of Nucleic Acids

Aaron E. Engelhart, Ragan Buckley, Eric D. Horowitz , Nicholas V. Hud

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RNA, a Precursor to the Origin of Life

James P. Ferris, Prakash C. Joshi, Michael F. Aldersley, John W. Delano

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Spontaneous Generation of RNA in Water

Giovanna Costanzo , Samanta Pino, Fabiana Ciciriello, Ernesto Di Mauro

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Towards the Design and Synthesis of an Artificial Cell

Jack W. Szostak

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Anticodon loop modifications modulate structural flexibility in E. coli tRNAArg1,2 that lacks a U-turn conformation in solution

William A. Cantara, Yann Bilbille, Jia Kim, Andrzej Malkiewicz, Paul F. Agris

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Structural characteristics of E. coli YrdC suggest a role in the enzymatic biosynthesis of the tRNA modification N6-threonylcarbamoyladenosine

Kimberly A. Harris, Victoria Jones, Yann Bilbille, and Paul F. Agris

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A Structural Method With Single Atom Resolution for Investigating the Secondary Structure of RNA: the Deuterium Kinetic Isotope Effect/Hydroxyl Radical Cleavage Experiment

Shakti Ingle, Robert Azad, and Thomas D. Tullius

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Insight into Transition States in Protein-RNA Recognition through MD Simulations

Lena Dang¹, Susan Pieniazek¹, Anne M. Baranger², David L. Beveridge¹

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RNASTEPS, An Online Database of Sequence-dependent Deformability of RNA Helical Regions

Mauricio Esguerra, Wilma K. Olson

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Showing 1 to 100 of 210 items.  Page: 1 3