| 301 | -- | 0 | Piotr Berman, Bhaskar DasGupta, Jie Liang. Foreword |
| 303 | -- | 327 | Amarda Shehu, Cecilia Clementi, Lydia E. Kavraki. Sampling Conformation Space to Model Equilibrium Fluctuations in Proteins |
| 329 | -- | 342 | Guojun Li, Zhijie Liu, Jun-tao Guo, Ying Xu. An Algorithm for Simultaneous Backbone Threading and Side-Chain Packing |
| 343 | -- | 362 | Vicky Choi, Navin Goyal. An Algorithmic Approach to the Identification of Rigid Domains in Proteins |
| 363 | -- | 374 | Songjian Lu, Fenghui Zhang, Jianer Chen, Sing-Hoi Sze. Finding Pathway Structures in Protein Interaction Networks |
| 375 | -- | 397 | Nidhal Bouaynaya, Dan Schonfeld. Protein Communication System: Evolution and Genomic Structure |
| 399 | -- | 412 | Bill Jackson, Tibor Jordán. Rigid Components in Molecular Graphs |
| 413 | -- | 432 | Sebastian Böcker, Zsuzsanna Lipták. A Fast and Simple Algorithm for the Money Changing Problem |
| 433 | -- | 438 | Leonidas J. Guibas, Yusu Wang. Toward Unsupervised Segmentation of Semi-Rigid Low-Resolution Molecular Surfaces |