REFEREED JOURNALS

• T. Kim, J. Lee, and W. Im (2008)
  Molecular Dynamics Studies on Structure and Dynamics of Phospholamban Monomer and Pentamer in Membranes.
  submitted

• J. Lee, S. Ham, and W. Im (2008)
  Beta-Hairpin Restraint Potentials for Calculations of Potentials of Mean Force as a Function of
  Beta-Hairpin Tilt, Rotation, and Distance.
  submitted

• S. Jo, M. Vargyas, J. Vasko-Szedlar, B. Roux, and W. Im (2008)
  PBEQ-Solver for Online Visualization of Electrostatic Potential of Biomolecules.
  Nucl. Acids Res. 36:W270-275

• J. Lee, J. Chen, C.L. Brooks III, and W. Im (2008)
  Application of Solid-state NMR Restraint Potentials in Membrane Protein Modeling.
  J. Magn. Reson. 193:68-76

• J. Lee and W. Im (2008)
  Role of Hydrogen Bonding and Helix-Lipid Interactions in Transmembrane Helix Association.
  J. Am. Chem. Soc. 130:6456-6462

• S. Jo, T. Kim, V.G. Iyer, and W. Im (2008)
  CHARMM-GUI: A Web-based Graphical User Interface for CHARMM.
  J. Comput. Chem. 29:1859-1865

• T. Rathinavelan and W. Im (2008)
  A Novel Strategy to Determine Protein Structures using Exclusively Residual Dipolar Coupling.
  J. Comput. Chem. 29:1640-1649

• S.H. Park, C. Cheong, J. Idoyaga, J.Y. Kim, J-H Choi, Y. Do, H. Lee, J.H. Jo, Y-S Oh, W. Im, R.M. Steinman, and C.G. Park (2008)
  Generation and Application of New Rat Monoclonal Antibodies against Synthetic Tags for Improved Immunodetection.
  J. Immunol. Methods 331:27-38

• J. Lee and W. Im (2008)
  Transmembrane Helix Tilting: Insights from Calculating the Potential of Mean Force.
  Phys. Rev. Lett. 100:018103

• S. Jo, T. Kim, and W. Im (2007)
  Automated Builder and Database of Protein/Membrane Complexes for Molecular Dynamics Simulations.
  PLoS ONE  2(9):e880

• Y. Wang, A.N. Ouellette, C.W. Egan, T. Rathinavelan, W. Im and R.N. De Guzman (2007)
  Differences in the Electrostatic Surfaces of the Type III Secretion Needle Proteins.
  J. Mol. Biol. 371:1304-1314

• J. Lee and W. Im (2007)
  Restrain Potential and Free Energy Decomposition for Helical Tilting.
  Chem. Phys. Lett. 441:132-135

• T. Rathinavelan and W. Im (2007)
  Explicit Treatment of Force Contribution from Alignment Tensor using Overdetermined Linear Equations and Its Application in NMR Structure Determination.
  J. Comput. Chem. 28:1858-1864

• J. Lee and W. Im (2007)
  Implementation and Application of Helix-Helix Distance and Crossing Angle Restraint Potentials.
  J. Comput. Chem. 28:669-680

• L. Bu, W. Im, and C.L. Brooks III (2007)
  Membrane Assembly of Simple Helix Homo-oligomers Studied via Molecular Dynamics Simulations.
  Biophys. J. 92:854-863

• Y. Liu, M. Scolari, W. Im, and H.J. Woo (2006)
  Protein-Protein Interactions in Actin-Myosin Binding and Structural Effects of R405Q Mutation: A Molecular Dynamics Study.
  Proteins 64:156-166 

• J. Chen, W. Im, and C.L. Brooks III (2006)
  Balancing Solvation and Intramolecular Interactions: Towards a Self-Consistent Generalized Born Force Field.
  J. Am. Chem. Soc. 128:3728-3736 

• W. Im, J. Chen, and C.L. Brooks III (2006)
  Peptide and Protein Folding and Conformational Equilibria: Theoretical Treatment of Electrostatics and Hydrogen Bonding with Implicit Solvent Models.
  Adv. Protein Chem. 72: 173-198

• J. Chen, W. Im, and C.L. Brooks III (2005)
  Application of Torsion Angle Molecular Dynamics for Efficient Sampling of Protein Conformation.
  J. Comput. Chem. 26: 1565-1578 

• W. Im and C.L. Brooks III (2005)
  Interfacial Folding and Membrane Insertion of Synthetic Peptides Studied by Molecular Dynamics Simulations.
  Proc. Natl. Acad. Sci. USA 102:6771-6776 

• J. Chen, H. Won, W. Im, H.J. Dyson and C.L. Brooks III (2005)
  Generation of Native-like Models from Limited NMR Data, Modern Force Fields and Advanced Conformational Sampling.
  J. Biomol. NMR 31:59-64 

• J. Chen, W. Im, and C.L. Brooks III (2004)
  Refinement of NMR Structure Using Implicit Solvent and Advanced Sampling Techniques.
  J. Am. Chem. Soc. 126:16038-16047 

• S.Y. Noskov, W. Im, and B. Roux (2004)
  Ion Permeation through the α-Hemolysin Channel: Theoretical Studies based on Brownian Dynamics and Poisson-Nernst-Plank Electrodiffusion Theory.
  Biophys. J. 87:2299-2309 

• B. Roux, T. Allen, S. Berneche, and W. Im (2004)
  Theoretical and Computational Models of Ion Channels.
  Q. Rev. Biophys. 37:15-103 

• W. Im and C.L. Brooks III (2004)
  De Novo Folding of Membrane Proteins: An Exploration of the Structure and NMR Properties of the fd Coat Protein.
  J. Mol. Biol. 337:513-519 

• M. Feig, W. Im, and C.L. Brooks, III (2004)
  Implicit Solvation Based on Generalized Born Theory in Different Dielectric Environment.
  J. Chem. Phys. 120:903-911 

• M. Feig, A. Onufriev, M.S. Lee, W. Im, D.A. Case, and C.L. Brooks III (2004)
  Performance Comparison of Generalized Born and Poisson Methods in the Calculation of Electrostatic Solvation Energies for Protein Structures.
  J. Comput. Chem. 25:265-284 

• W. Im, M. Feig, and C.L. Brooks III (2003)
  An Implicit Membrane Generalized Born Theory for the Study of Structure, Stability, and Interactions of Membrane Proteins.
  Biophys. J. 85:2900-2918 

• W. Im, M.S. Lee, and C.L. Brooks III (2003)
  Generalized Born Model with a Simple Smoothing Function.
  J. Comput. Chem. 24:1691-1702 

• N.K. Banavali, W. Im, and B. Roux (2002)
  Electrostatic Free Energy Calculations using the Generalized Solvent Boundary Potential Method.
  J. Chem. Phys. 117:7381-7388 

• W. Im and B. Roux (2002)
  Ion Permeation and Selectivity of OmpF Porin: A Theoretical Study Based on Molecular Dynamics, Brownian Dynamics, and Continuum Electrodiffusion Theory.
  J. Mol. Biol. 322:851-869 

• W. Im and B. Roux (2002)
  Ions and Counterions in a Biological Channel: A Molecular Dynamics Simulation of OmpF Porin from Escherichia coli in an Explicit Membrane with 1 M KCl Aqueous Salt Solution.
  J. Mol. Biol. 319:1177-1197 

• A. Philippsen, W. Im, A. Engel, T. Schirmer, B. Roux, and D.J. Muller (2002)
  Imaging the Electrostatic Potential of Transmembrane Channels: Atomic Probe Microscopy of OmpF Porin.
  Biophys. J. 82:1667-1676 

• W. Im and B. Roux (2001)
  Brownian Dynamics Simulations of Ions Channels: A General Treatment of the Electrostatic Reaction Field for Molecular Pores of Arbitrary Geometry.
  J. Chem. Phys. 115:4850-4861 

• W. Im, S. Berneche, and B. Roux (2001)
  Generalized Solvent Boundary Potentials for Computer Simulations.
  J. Chem. Phys. 114:2924-2937 

• B. Roux, S. Berneche and W. Im (2000)
  Ion Channels, Permeation, and Electrostatics: Insight into the Function of KcsA.
  Biochemistry 39:13295-13306 

• W. Im, S. Seefeld and B. Roux (2000)
  Grand Canonical Monte Carlo - Brownian Dynamics Algorithm for Simulating Ion Channels.
  Biophys. J. 79:788-801 

• M. Nina, W. Im, and B. Roux (1999)
  Optimized Atomic Radii for Protein Continuum Electrostatics Solvation Forces.
  Biophys. Chem. 78:89-96 

• W. Im, D. Beglov, and B. Roux (1998)
  Continuum Solvation Model: Computation of Electrostatic Forces from Numerical Solutions to the Poisson-Boltzmann Equation.
  Comput. Phys. Comm. 111:59-75 

• W. Im and Y. Won (1994)
  Molecular Dynamics Simulation on Thermodynamic and Structural Properties of Liquid Hydrocarbons : Normal Alkanes.
  bull. Korean Chem. Soc. 15:852-856 

BOOK CHAPTERS & THESIS

• J. Lee and W. Im (2008)
  Formalisms and Applications of Helical Restraint Potentials.
  In Quantum Bio-Informatics: From Quantum Information to Bio-Informatics,
  L. Accardi, W. Freudenberg, and M. Ohya Eds. 21:359-370.

• B. Roux, D. Beglov, and W. Im (1999)
  Generalized Solvent Boundary Potentials for Computer Simulations.
  In Treatments of electrostatics interactions in computer simulations of condensed media, Santa Fe Workshop,
  L.R. Pratt and G. Hummer Eds. 492:473-491.

• W. Im (2002)
  The Role of Electrostatics in Ion Permeation and Selectivity of Biological Membrane Channels.
  Ph.D. Thesis, Cornell University.

• W. Im (1996)
  Molecular Dynamics Simulation on Thermodynamic, Structural, and Dynamic Properties of Liquid Alkanes and Liquid Acetonitrile.
  M. Sc. Thesis, Hanyang University.