Cover image for From physics to biology : the interface between experiment and computation : BIFI 2006 II International Congress,  Zaragoza (Spain), 8-11 February 2006
From physics to biology : the interface between experiment and computation : BIFI 2006 II International Congress, Zaragoza (Spain), 8-11 February 2006
AIP conference proceedings ; v.851
Publication Information:
Melville, NY : American Institute of Physics, 2006


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PSZ JB 30000010138262 QC52 B56 2006 Open Access Book Proceedings, Conference, Workshop etc.

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All papers in this volume were peer-reviewed. The BIFI2006 Conference represents an interactive forum for physicists, chemists, biologists, and mathematicians for sharing ideas as well as adressing recent advances in the frontier between physics and biology. Current challenges in molecular and cell biology, biomedicine, and biotechnology require the interdisciplinary collaborative effort of theoretical and experimental researchers benefiting from the interplay between the latest computational and experimental developments. There were three main topics at the conference: nucleic acids, proteins and peptides, and collective behavior of biomolecules. This volume includes papers on: protein folding, nucleic acid structure, ligand binding, proteomics, network dynamics and topology, cell signaling, collective behavior, biomolecular modeling, systems biology, and biophysical computational methods.

Table of Contents

G. Cavelier and L. M. AmzelM. E. WallC. N. CavasottoS. Cocco and R. MonassonA. Giorgetti and D. Raimondo and A. TramontanoI. Junier and F. RitortP. Tortosa and A. JaramilloJ. J. DannenbergP. Echenique and J. L. Alonso and I. CalvoM. H. ZamanJ. M. Sanchez-RuizJ. A. Hernandez and S. Lopez-Gomollon and S. Pellicer and B. Martin and E. Sevilla and M. T. Bes and M. L. Peleato and M. F. FillatM. Cotallo-Aban and D. Prada-Gracia and J. J. Mazo and P. Buscolini and F. Falo and J. SanchoY. Moreno and L. M. Floria and J. Gomez-GardenesA. Velazquez-CampoyL. Gracia and J. A. Speidel and H. WeinsteinL. Schubert and S. Frago and M. Martinez-Julvez and M. MedinaS. A. Samsonov and E. Nordlund and N. A. Platonova and A. N. Skvortsov and N. V. Tsymbalenko and L. V. PuchkovaN. Basdevant and T. Ha-Duong and D. BorgisJ. A. D'Aquino and D. Ringe
Forewordp. vii
Prefacep. ix
Role of Fluctuations in Quinone Reductase Hydride Transfer: A Combined Quantum Mechanics and Molecular Dynamics Studyp. 1
Ligand Binding, Protein Fluctuations, and Allosteric Free Energyp. 16
Ligand Docking and Virtual Screening in Structure-Based Drug Discoveryp. 34
The Mechanical Opening of DNA and the Sequence Contentp. 50
Structural Bioinformatics: Advances and Applicationsp. 64
Single-Domain Protein Folding: A Multi-Faceted Problemp. 70
Active Sites by Computational Protein Designp. 96
The Effects of H-Bond Cooperativity upon the Secondary Structures of Peptidesp. 102
Effects of Constraints in General Branched Molecules: A Quantitative ab initio Study in HCO-L-Ala-NH[subscript 2]p. 108
Multiscale Modeling of Tumor Cell Migrationp. 117
Variable-Barrier Modeling of Equilibrium Protein Foldingp. 123
FurA from Anabaena PCC 7120: New Insights on Its Regulation and the Interaction with DNAp. 129
Analysis of Apoflavodoxin Folding Behavior with Elastic Network Modelsp. 135
Current Trends in the Modeling of Biological Networksp. 150
Unspecific Cooperative Ligand Binding to One-Dimensional Lattice-Like Macromoleculesp. 162
New Computational Approaches for NMR-Based Drug Design: A Protocol for Ligand Docking to Flexible Target Sitesp. 176
Sequence and Phylogenetic Analysis of FAD Synthetasep. 180
Tissue-Specific Ctrl Gene Expression and in silico Analysis of its Putative Protein Productp. 185
A Particle-Based Implicit Solvent Model for Biomolecular Simulationsp. 192
Mechanisms of Metal Ion Activation of the Diphtheria Toxin Repressor DtxRp. 196
List of Participantsp. 199
Author Indexp. 203