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Ram Samudrala
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Journal Articles
- 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) - 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) - 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) - 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)
Conference and Workshop Papers
- 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 - 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 - 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 - 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
Coauthor Index
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