Ram Samudrala

According to our database, Ram Samudrala authored at least 27 papers between 1999 and 2020.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

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

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

Association of C>U RNA Editing with Human Disease Variants.

Sapan Mandloi, Zackary Falls, Rong Deng, Ram Samudrala, Peter L. Elkin

Proceedings of the Digital Personalized Health and Medicine - Proceedings of MIE 2020, Medical Informatics Europe, Geneva, Switzerland, April 28, 2020

Linking Genome and Exposome: Computational Analysis of Human Variation in Chemical-Target Interactions.

Liana Bruggemann, Christopher Hawthorne, Ram Samudrala, Guillermo H. López-Campos

Proceedings of the Digital Personalized Health and Medicine - Proceedings of MIE 2020, Medical Informatics Europe, Geneva, Switzerland, April 28, 2020

2019

Foundations for a Realism-based Drug Repurposing Ontology.

James Schuler, William Mangione, Ram Samudrala, Werner Ceusters

Proceedings of the 10th International Conference on Biomedical Ontology (ICBO 2019), Buffalo, New York, USA, July 30, 2019

2018

Improvements in Shotgun Drug Repurposing Accuracy: Combining OpenBabel with Bioinformatic Docking Data in the CANDO Platform.

James Schuler, Ram Samudrala

Proceedings of the AMIA 2018, 2018

2014

fast_protein_cluster: parallel and optimized clustering of large-scale protein modeling data.

Ling-Hong Hung, Ram Samudrala

Bioinform., 2014

2012

Accelerated protein structure comparison using TM-score-GPU.

Ling-Hong Hung, Ram Samudrala

Bioinform., 2012

Protein structure prediction based on optimal hydrophobic core formation.

Rumana Nazmul, Madhu Chetty, Ram Samudrala, David K. Chalmers

Proceedings of the IEEE Congress on Evolutionary Computation, 2012

2011

LoCo: a novel main chain scoring function for protein structure prediction based on local coordinates.

Stewart E. Moughon, Ram Samudrala

BMC Bioinform., 2011

2010

A protein sequence meta-functional signature for calcium binding residue prediction.

Jeremy A. Horst, Ram Samudrala

Pattern Recognit. Lett., 2010

Evolutionary Transients in the Rice Transcriptome.

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

Genom. Proteom. Bioinform., 2010

2009

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

2008

Protein Meta-Functional Signatures from Combining Sequence, Structure, Evolution, and Amino Acid Property Information.

Kai Wang, Jeremy A. Horst, Gong Cheng, David C. Nickle, Ram Samudrala

PLoS Comput. Biol., 2008

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

Identification of potential HIV-1 targets of minocycline.

Ekachai Jenwitheesuk, Ram Samudrala

Bioinform., 2007

2006

Incorporating background frequency improves entropy-based residue conservation measures.

Kai Wang, Ram Samudrala

BMC Bioinform., 2006

Automated functional classification of experimental and predicted protein structures.

Kai Wang, Ram Samudrala

BMC Bioinform., 2006

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

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

PROTINFO: new algorithms for enhanced protein structure predictions.

Ling-Hong Hung, Shing-Chung Ngan, Tianyun Liu, Ram Samudrala

Nucleic Acids Res., 2005

FSSA: a novel method for identifying functional signatures from structural alignments.

Kai Wang, Ram Samudrala

Bioinform., 2005

Functional annotation from predicted protein interaction networks.

Jason E. McDermott, Roger Eugene Bumgarner, Ram Samudrala

Bioinform., 2005

An enhanced Java graph applet interface for visualizing interactomes.

Aaron N. Chang, Jason E. McDermott, Ram Samudrala

Bioinform., 2005

2003

Bioverse: functional, structural and contextual annotation of proteins and proteomes.

Jason E. McDermott, Ram Samudrala

Nucleic Acids Res., 2003

PROTINFO: secondary and tertiary protein structure prediction.

Ling-Hong Hung, Ram Samudrala

Nucleic Acids Res., 2003

1999

A Combined Approach for Ab Initio Construction of Low Resolution Protein Tertiary Structures from Sequence.

Ram Samudrala, Yu Xia, M. Levitt, Enoch S. Huang

Proceedings of the 4th Pacific Symposium on Biocomputing, 1999