A Combined Approach for Ab Initio Construction of Low Resolution Protein Tertiary Structures from Sequence. - Ram Samudrala; Yu Xia 002; M. Levitt; Enoch S. Huang (Pacific Symposium on Biocomputing, 1999)

PROTINFO: secondary and tertiary protein structure prediction. - Ling-Hong Hung; Ram Samudrala (Nucleic Acids Res., 2003)

Bioverse: functional, structural and contextual annotation of proteins and proteomes. - Jason E. McDermott; Ram Samudrala (Nucleic Acids Res., 2003)

An enhanced Java graph applet interface for visualizing interactomes. - Aaron N. Chang; Jason E. McDermott; Ram Samudrala (Bioinform., 2005)

Functional annotation from predicted protein interaction networks. - Jason E. McDermott; Roger Eugene Bumgarner; Ram Samudrala (Bioinform., 2005)

FSSA: a novel method for identifying functional signatures from structural alignments. - Kai Wang; Ram Samudrala (Bioinform., 2005)

PROTINFO: new algorithms for enhanced protein structure predictions. - Ling-Hong Hung; Shing-Chung Ngan; Tianyun Liu; Ram Samudrala (Nucleic Acids Res., 2005)

BIOVERSE: enhancements to the framework for structural, functional and contextual modeling of proteins and proteomes. - Jason E. McDermott; Michal Guerquin; Zachary Frazier; Aaron N. Chang; Ram Samudrala (Nucleic Acids Res., 2005)

INTEGRATOR: interactive graphical search of large protein interactomes over the Web. - Aaron N. Chang; Jason E. McDermott; Zachary Frazier; Michal Guerquin; Ram Samudrala (BMC Bioinform., 2006)

Automated functional classification of experimental and predicted protein structures. - Kai Wang 063; Ram Samudrala (BMC Bioinform., 2006)

Incorporating background frequency improves entropy-based residue conservation measures. - Kai Wang 063; Ram Samudrala (BMC Bioinform., 2006)

Identification of potential HIV-1 targets of minocycline. - Ekachai Jenwitheesuk; Ram Samudrala (Bioinform., 2007)

A novel knowledge-based approach to design inorganic-binding peptides. - Ersin Emre Oren; Candan Tamerler; Deniz Sahin; Marketa Hnilova; Urartu Ozgur Safak Seker; Mehmet Sarikaya; Ram Samudrala (Bioinform., 2007)

Protein Meta-Functional Signatures from Combining Sequence, Structure, Evolution, and Amino Acid Property Information. - Kai Wang 063; Jeremy A. Horst; Gong Cheng; David C. Nickle; Ram Samudrala (PLoS Comput. Biol., 2008)

Protinfo PPC: A web server for atomic level prediction of protein complexes. - Weerayuth Kittichotirat; Michal Guerquin; Roger Eugene Bumgarner; Ram Samudrala (Nucleic Acids Res., 2009)

Evolutionary Transients in the Rice Transcriptome. - Jun Wang 004; Jianguo Zhang; Ruiqiang Li; Hongkun Zheng; Jun Li 051; Yong Zhang 036; Heng Li 002; Peixiang Ni; Songgang Li; Shengting Li; Jingqiang Wang; Dongyuan Liu; et al. (Genom. Proteom. Bioinform., 2010)

A protein sequence meta-functional signature for calcium binding residue prediction. - Jeremy A. Horst; Ram Samudrala (Pattern Recognit. Lett., 2010)

LoCo: a novel main chain scoring function for protein structure prediction based on local coordinates. - Stewart E. Moughon; Ram Samudrala (BMC Bioinform., 2011)

Protein structure prediction based on optimal hydrophobic core formation. - Rumana Nazmul; Madhu Chetty; Ram Samudrala; David K. Chalmers (IEEE Congress on Evolutionary Computation, 2012)

Accelerated protein structure comparison using TM-score-GPU. - Ling-Hong Hung; Ram Samudrala (Bioinform., 2012)

fast_protein_cluster: parallel and optimized clustering of large-scale protein modeling data. - Ling-Hong Hung; Ram Samudrala (Bioinform., 2014)

Improvements in Shotgun Drug Repurposing Accuracy: Combining OpenBabel with Bioinformatic Docking Data in the CANDO Platform. - James Schuler; Ram Samudrala (AMIA, 2018)

Foundations for a Realism-based Drug Repurposing Ontology. - James Schuler; William Mangione; Ram Samudrala; Werner Ceusters (ICBO, 2019)

Linking Genome and Exposome: Computational Analysis of Human Variation in Chemical-Target Interactions. - Liana Bruggemann; Christopher Hawthorne; Ram Samudrala; Guillermo H. López-Campos (MIE, 2020)

Association of C>U RNA Editing with Human Disease Variants. - Sapan Mandloi; Zackary Falls; Rong Deng; Ram Samudrala; Peter L. Elkin (MIE, 2020)

CANDOCK: Chemical Atomic Network-Based Hierarchical Flexible Docking Algorithm Using Generalized Statistical Potentials. - Jonathan Fine; Janez Konc; Ram Samudrala; Gaurav Chopra (J. Chem. Inf. Model., 2020)

cando.py: Open Source Software for Predictive Bioanalytics of Large Scale Drug-Protein-Disease Data. - William Mangione; Zackary Falls; Gaurav Chopra; Ram Samudrala (J. Chem. Inf. Model., 2020)