Ram Samudrala

28 papers B 1Misc 2Journal 22Unranked 3
YearRankTypeTitle / Venue / Authors
2025 J jnl
Strategies for robust, accurate, and generalizable benchmarking of drug discovery platforms.
Bioinform.
Melissa Van Norden, William Mangione, Zackary Falls, Ram Samudrala
2020 — conf
Association of C>U RNA Editing with Human Disease Variants.
MIE
Sapan Mandloi, Zackary Falls, Rong Deng, Ram Samudrala, Peter L. Elkin
2020 J jnl
CANDOCK: Chemical Atomic Network-Based Hierarchical Flexible Docking Algorithm Using Generalized Statistical Potentials.
J. Chem. Inf. Model.
Jonathan Fine, Janez Konc, Ram Samudrala, Gaurav Chopra
2020 — conf
Linking Genome and Exposome: Computational Analysis of Human Variation in Chemical-Target Interactions.
MIE
Liana Bruggemann, Christopher Hawthorne, Ram Samudrala, Guillermo H. López-Campos
2020 J jnl
cando.py: Open Source Software for Predictive Bioanalytics of Large Scale Drug-Protein-Disease Data.
J. Chem. Inf. Model.
William Mangione, Zackary Falls, Gaurav Chopra, Ram Samudrala
2019 — conf
Foundations for a Realism-based Drug Repurposing Ontology.
ICBO
James Schuler, William Mangione, Ram Samudrala, Werner Ceusters
2018 Misc conf
Improvements in Shotgun Drug Repurposing Accuracy: Combining OpenBabel with Bioinformatic Docking Data in the CANDO Platform.
AMIA
James Schuler, Ram Samudrala
2014 J jnl
fast_protein_cluster: parallel and optimized clustering of large-scale protein modeling data.
Bioinform.
Ling-Hong Hung, Ram Samudrala
2012 J jnl
Accelerated protein structure comparison using TM-score-GPU.
Bioinform.
Ling-Hong Hung, Ram Samudrala
2012 B conf
Protein structure prediction based on optimal hydrophobic core formation.
IEEE Congress on Evolutionary Computation
Rumana Nazmul, Madhu Chetty, Ram Samudrala, David K. Chalmers
2011 J jnl
LoCo: a novel main chain scoring function for protein structure prediction based on local coordinates.
BMC Bioinform.
Stewart E. Moughon, Ram Samudrala
2010 J jnl
A protein sequence meta-functional signature for calcium binding residue prediction.
Pattern Recognit. Lett.
Jeremy A. Horst, Ram Samudrala
2010 J jnl
Evolutionary Transients in the Rice Transcriptome.
Genom. Proteom. Bioinform.
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
2009 J jnl
Protinfo PPC: A web server for atomic level prediction of protein complexes.
Nucleic Acids Res.
Weerayuth Kittichotirat, Michal Guerquin, Roger Eugene Bumgarner, Ram Samudrala
2008 J jnl
Protein Meta-Functional Signatures from Combining Sequence, Structure, Evolution, and Amino Acid Property Information.
PLoS Comput. Biol.
Kai Wang, Jeremy A. Horst, Gong Cheng, David C. Nickle, Ram Samudrala
2007 J jnl
A novel knowledge-based approach to design inorganic-binding peptides.
Bioinform.
Ersin Emre Oren, Candan Tamerler, Deniz Sahin, Marketa Hnilova, Urartu Ozgur Safak Seker, Mehmet Sarikaya, Ram Samudrala
2007 J jnl
Identification of potential HIV-1 targets of minocycline.
Bioinform.
Ekachai Jenwitheesuk, Ram Samudrala
2006 J jnl
Automated functional classification of experimental and predicted protein structures.
BMC Bioinform.
Kai Wang, Ram Samudrala
2006 J jnl
INTEGRATOR: interactive graphical search of large protein interactomes over the Web.
BMC Bioinform.
Aaron N. Chang, Jason E. McDermott, Zachary Frazier, Michal Guerquin, Ram Samudrala
2006 J jnl
Incorporating background frequency improves entropy-based residue conservation measures.
BMC Bioinform.
Kai Wang, Ram Samudrala
2005 J jnl
An enhanced Java graph applet interface for visualizing interactomes.
Bioinform.
Aaron N. Chang, Jason E. McDermott, Ram Samudrala
2005 J jnl
BIOVERSE: enhancements to the framework for structural, functional and contextual modeling of proteins and proteomes.
Nucleic Acids Res.
Jason E. McDermott, Michal Guerquin, Zachary Frazier, Aaron N. Chang, Ram Samudrala
2005 J jnl
FSSA: a novel method for identifying functional signatures from structural alignments.
Bioinform.
Kai Wang, Ram Samudrala
2005 J jnl
Functional annotation from predicted protein interaction networks.
Bioinform.
Jason E. McDermott, Roger Eugene Bumgarner, Ram Samudrala
2005 J jnl
PROTINFO: new algorithms for enhanced protein structure predictions.
Nucleic Acids Res.
Ling-Hong Hung, Shing-Chung Ngan, Tianyun Liu, Ram Samudrala
2003 J jnl
Bioverse: functional, structural and contextual annotation of proteins and proteomes.
Nucleic Acids Res.
Jason E. McDermott, Ram Samudrala
2003 J jnl
PROTINFO: secondary and tertiary protein structure prediction.
Nucleic Acids Res.
Ling-Hong Hung, Ram Samudrala
1999 Misc conf
A Combined Approach for Ab Initio Construction of Low Resolution Protein Tertiary Structures from Sequence.
Pacific Symposium on Biocomputing
Ram Samudrala, Yu Xia, M. Levitt, Enoch S. Huang