Ram Samudrala

Publication Activity (10 Years)

Years Active: 1999-2020
Publications (10 Years): 6

Top Topics

Nuclear Magnetic Resonance

Clustering Result

Open Source Software

Protein Structure

Top Venues

J. Chem. Inf. Model.

IEEE Congress on Evolutionary Computation

Publications

Sapan Mandloi, Zackary Falls, Rong Deng, Ram Samudrala, Peter L. Elkin
Association of C>U RNA Editing with Human Disease Variants. MIE (2020)
Liana Bruggemann, Christopher Hawthorne, Ram Samudrala, Guillermo H. López-Campos
Linking Genome and Exposome: Computational Analysis of Human Variation in Chemical-Target Interactions. MIE (2020)
Jonathan Fine, Janez Konc, Ram Samudrala, Gaurav Chopra
CANDOCK: Chemical Atomic Network-Based Hierarchical Flexible Docking Algorithm Using Generalized Statistical Potentials. J. Chem. Inf. Model. 60 (3) (2020)
William Mangione, Zackary Falls, Gaurav Chopra, Ram Samudrala
cando.py: Open Source Software for Predictive Bioanalytics of Large Scale Drug-Protein-Disease Data. J. Chem. Inf. Model. 60 (9) (2020)
James Schuler, William Mangione, Ram Samudrala, Werner Ceusters
Foundations for a Realism-based Drug Repurposing Ontology. ICBO (2019)
James Schuler, Ram Samudrala
Improvements in Shotgun Drug Repurposing Accuracy: Combining OpenBabel with Bioinformatic Docking Data in the CANDO Platform. AMIA (2018)
Ling-Hong Hung, Ram Samudrala
fast_protein_cluster: parallel and optimized clustering of large-scale protein modeling data. Bioinform. 30 (12) (2014)
Rumana Nazmul, Madhu Chetty, Ram Samudrala, David K. Chalmers
Protein structure prediction based on optimal hydrophobic core formation. IEEE Congress on Evolutionary Computation (2012)
Ling-Hong Hung, Ram Samudrala
Accelerated protein structure comparison using TM-score-GPU. Bioinform. 28 (16) (2012)
Stewart E. Moughon, Ram Samudrala
LoCo: a novel main chain scoring function for protein structure prediction based on local coordinates. BMC Bioinform. 12 (2011)
Jun Wang, Jianguo Zhang, Ruiqiang Li, Hongkun Zheng, Jun Li, Yong Zhang, Heng Li, Peixiang Ni, Songgang Li, Shengting Li, Jingqiang Wang, Dongyuan Liu, Jason E. McDermott, Ram Samudrala, Siqi Liu, Jian Wang, Huanming Yang, Jun Yu, Gane Ka-Shu Wong
Evolutionary Transients in the Rice Transcriptome. Genom. Proteom. Bioinform. 8 (4) (2010)
Jeremy A. Horst, Ram Samudrala
A protein sequence meta-functional signature for calcium binding residue prediction. Pattern Recognit. Lett. 31 (14) (2010)
Weerayuth Kittichotirat, Michal Guerquin, Roger Eugene Bumgarner, Ram Samudrala
Protinfo PPC: A web server for atomic level prediction of protein complexes. Nucleic Acids Res. 37 (Web-Server-Issue) (2009)
Kai Wang, Jeremy A. Horst, Gong Cheng, David C. Nickle, Ram Samudrala
Protein Meta-Functional Signatures from Combining Sequence, Structure, Evolution, and Amino Acid Property Information. PLoS Comput. Biol. 4 (9) (2008)
Ersin Emre Oren, Candan Tamerler, Deniz Sahin, Marketa Hnilova, Urartu Ozgur Safak Seker, Mehmet Sarikaya, Ram Samudrala
A novel knowledge-based approach to design inorganic-binding peptides. Bioinform. 23 (21) (2007)
Ekachai Jenwitheesuk, Ram Samudrala
Identification of potential HIV-1 targets of minocycline. Bioinform. 23 (20) (2007)
Kai Wang, Ram Samudrala
Incorporating background frequency improves entropy-based residue conservation measures. BMC Bioinform. 7 (2006)
Kai Wang, Ram Samudrala
Automated functional classification of experimental and predicted protein structures. BMC Bioinform. 7 (2006)
Aaron N. Chang, Jason E. McDermott, Zachary Frazier, Michal Guerquin, Ram Samudrala
INTEGRATOR: interactive graphical search of large protein interactomes over the Web. BMC Bioinform. 7 (2006)
Kai Wang, Ram Samudrala
FSSA: a novel method for identifying functional signatures from structural alignments. Bioinform. 21 (13) (2005)
Jason E. McDermott, Michal Guerquin, Zachary Frazier, Aaron N. Chang, Ram Samudrala
BIOVERSE: enhancements to the framework for structural, functional and contextual modeling of proteins and proteomes. Nucleic Acids Res. 33 (Web-Server-Issue) (2005)
Jason E. McDermott, Roger Eugene Bumgarner, Ram Samudrala
Functional annotation from predicted protein interaction networks. Bioinform. 21 (15) (2005)
Aaron N. Chang, Jason E. McDermott, Ram Samudrala
An enhanced Java graph applet interface for visualizing interactomes. Bioinform. 21 (8) (2005)
Ling-Hong Hung, Shing-Chung Ngan, Tianyun Liu, Ram Samudrala
PROTINFO: new algorithms for enhanced protein structure predictions. Nucleic Acids Res. 33 (Web-Server-Issue) (2005)
Ling-Hong Hung, Ram Samudrala
PROTINFO: secondary and tertiary protein structure prediction. Nucleic Acids Res. 31 (13) (2003)
Jason E. McDermott, Ram Samudrala
Bioverse: functional, structural and contextual annotation of proteins and proteomes. Nucleic Acids Res. 31 (13) (2003)
Ram Samudrala, Yu Xia, M. Levitt, Enoch S. Huang
A Combined Approach for Ab Initio Construction of Low Resolution Protein Tertiary Structures from Sequence. Pacific Symposium on Biocomputing (1999)