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2020 – today
- 2020
[j21]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): 1509-1527 (2020)- [j20]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): 4131-4136 (2020) - [c6]Sapan Mandloi, Zackary Falls, Rong Deng, Ram Samudrala, Peter L. Elkin:
Association of C>U RNA Editing with Human Disease Variants. MIE 2020: 1205-1206 - [c5]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: 1331-1332
2010 – 2019
- 2019
- [c4]James Schuler, William Mangione, Ram Samudrala, Werner Ceusters:
Foundations for a Realism-based Drug Repurposing Ontology. ICBO 2019: 1-8 - 2018
- [c3]James Schuler, Ram Samudrala:
Improvements in Shotgun Drug Repurposing Accuracy: Combining OpenBabel with Bioinformatic Docking Data in the CANDO Platform. AMIA 2018 - 2014
- [j19]Ling-Hong Hung, Ram Samudrala:
fast_protein_cluster: parallel and optimized clustering of large-scale protein modeling data. Bioinform. 30(12): 1774-1776 (2014) - 2012
- [j18]Ling-Hong Hung, Ram Samudrala:
Accelerated protein structure comparison using TM-score-GPU. Bioinform. 28(16): 2191-2192 (2012) - [c2]Rumana Nazmul, Madhu Chetty, Ram Samudrala, David K. Chalmers:
Protein structure prediction based on optimal hydrophobic core formation. IEEE Congress on Evolutionary Computation 2012: 1-9 - 2011
- [j17]Stewart E. Moughon, Ram Samudrala:
LoCo: a novel main chain scoring function for protein structure prediction based on local coordinates. BMC Bioinform. 12: 368 (2011) - 2010
- [j16]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): 211-228 (2010) - [j15]Jeremy A. Horst, Ram Samudrala:
A protein sequence meta-functional signature for calcium binding residue prediction. Pattern Recognit. Lett. 31(14): 2103-2112 (2010)
2000 – 2009
- 2009
- [j14]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): 519-525 (2009) - 2008
- [j13]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) - 2007
- [j12]Ekachai Jenwitheesuk, Ram Samudrala:
Identification of potential HIV-1 targets of minocycline. Bioinform. 23(20): 2797-2799 (2007) - [j11]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): 2816-2822 (2007) - 2006
- [j10]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: 146 (2006) - [j9]Kai Wang, Ram Samudrala:
Automated functional classification of experimental and predicted protein structures. BMC Bioinform. 7: 278 (2006) - [j8]Kai Wang, Ram Samudrala:
Incorporating background frequency improves entropy-based residue conservation measures. BMC Bioinform. 7: 385 (2006) - 2005
- [j7]Aaron N. Chang, Jason E. McDermott, Ram Samudrala:
An enhanced Java graph applet interface for visualizing interactomes. Bioinform. 21(8): 1741-1742 (2005) - [j6]Kai Wang, Ram Samudrala:
FSSA: a novel method for identifying functional signatures from structural alignments. Bioinform. 21(13): 2969-2977 (2005) - [j5]Jason E. McDermott, Roger Eugene Bumgarner, Ram Samudrala:
Functional annotation from predicted protein interaction networks. Bioinform. 21(15): 3217-3226 (2005) - [j4]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): 77-80 (2005) - [j3]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): 324-325 (2005) - 2003
- [j2]Ling-Hong Hung, Ram Samudrala:
PROTINFO: secondary and tertiary protein structure prediction. Nucleic Acids Res. 31(13): 3296-3299 (2003) - [j1]Jason E. McDermott, Ram Samudrala:
Bioverse: functional, structural and contextual annotation of proteins and proteomes. Nucleic Acids Res. 31(13): 3736-3737 (2003)
1990 – 1999
- 1999
- [c1]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: 505-516
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