Computing Protein Structures from Electron Density Maps: The Missing Fragment Problem. - Itay Lotan; Henry van den Bedem; Ashley Deacon; Jean-Claude Latombe (WAFR, 2004)

Efficient Algorithms to Explore Conformation Spaces of Flexible Protein Loops. - Ankur Dhanik; Peggy Yao; Nathan Marz; Ryan Propper; Charles Kou; Guanfeng Liu 001; Henry van den Bedem; Jean-Claude Latombe (WABI, 2007)

Modeling Structural Heterogeneity in Proteins from X-Ray Data. - Ankur Dhanik; Henry van den Bedem; Ashley Deacon; Jean-Claude Latombe (WAFR, 2008)

Efficient Algorithms to Explore Conformation Spaces of Flexible Protein Loops. - Peggy Yao; Ankur Dhanik; Nathan Marz; Ryan Propper; Charles Kou; Guanfeng Liu 001; Henry van den Bedem; Jean-Claude Latombe; Inbal Halperin-Landsberg; Russ B. Altman (IEEE ACM Trans. Comput. Biol. Bioinform., 2008)

KGSrna: Efficient 3D Kinematics-Based Sampling for Nucleic Acids. - Rasmus Fonseca; Henry van den Bedem; Julie Bernauer (RECOMB, 2015)

Exposing Hidden Alternative Backbone Conformations in X-ray Crystallography Using qFit. - Daniel A. Keedy; James S. Fraser; Henry van den Bedem (PLoS Comput. Biol., 2015)

Nullspace Sampling with Holonomic Constraints Reveals Molecular Mechanisms of Protein Gαs. - Dimitar V. Pachov; Henry van den Bedem (PLoS Comput. Biol., 2015)

Probing RNA Native Conformational Ensembles with Structural Constraints. - Rasmus Fonseca; Henry van den Bedem; Julie Bernauer (J. Comput. Biol., 2016)

Fast, clash-free RNA conformational morphing using molecular junctions. - Amélie Héliou; Dominik Budday; Rasmus Fonseca; Henry van den Bedem (Bioinform., 2017)

Collision-free poisson motion planning in ultra high-dimensional molecular conformation spaces. - Rasmus Fonseca; Dominik Budday; Henry van den Bedem (J. Comput. Chem., 2018)

Kinematic Flexibility Analysis: Hydrogen Bonding Patterns Impart a Spatial Hierarchy of Protein Motion. - Dominik Budday; Sigrid Leyendecker; Henry van den Bedem (J. Chem. Inf. Model., 2018)

Sequence-guided protein structure determination using graph convolutional and recurrent networks. - Po-Nan Li; Saulo Henrique Pires de Oliveira; Soichi Wakatsuki; Henry van den Bedem (BIBE, 2020)

An efficient graph generative model for navigating ultra-large combinatorial synthesis libraries. - Aryan Pedawi; Pawel Gniewek; Chaoyi Chang; Brandon M. Anderson; Henry van den Bedem (NeurIPS, 2022)

Kinematic Vibrational Entropy Assessment and Analysis of SARS CoV-2 Main Protease. - Xiyu Chen; Sigrid Leyendecker; Henry van den Bedem (J. Chem. Inf. Model., 2022)

AtomNet PoseRanker: Enriching Ligand Pose Quality for Dynamic Proteins in Virtual High-Throughput Screens. - Kate A. Stafford; Brandon M. Anderson; Jon Sorenson; Henry van den Bedem (J. Chem. Inf. Model., 2022)