Samudrala Group (CompBio) complete publication list

162 publications total comprising 149 scientific research related publications (including book chapters), 8 more general publications, and 5 patent publications (I am against IP, but there's an explanation for this seeming inconsistency here). See our ongoing research for a list organised by topic.

Scientific publications
149 publications listed; * denotes more significant

• Van Norden M, Falls Z, Mandloi S, Segal BH, Baysal BE, Samudrala R, Elkin PL. The implications of APOBEC3-mediated C-to-U RNA editing for human disease. Communications Biology 2024 7:529, 2024.
• Manish M, Mishra S, Pahuja M, Anand A, Subbarao N, Samudrala R. Computational grafting of epitopes. Methods in Molecular Biology 2673: 111-122, 2023.
• Mangione W, Falls Z, Samudrala R. Effective holistic characterization of small molecule effects using heterogeneous biological networks. Frontiers in Pharmacolology 14: 1113007, 2023. *
• Kumari R, Sharma SD, Kumar A, Ende Z, Mishina M, Wang Y, Falls Z, Samudrala R, Pohl J, Knight PR, Sambhara S. Antiviral approaches against influenza virus. Clinical Microbiology Reviews 36: e0004022, 2023.
• Handelmann CR, Tsompana M, Samudrala R, Buck MJ. The impact of nucleosome structure on CRISPR/Cas9 fidelity. Nucleic Acids Research 51: 2333-2344, 2023.
• Bruggemann L, Falls Z, Mangione W, Schwartz SA, Battaglia S, Aalinkeel R, Mahajan SD, Samudrala R. Multiscale analysis and validation of effective drug combinations targeting driver KRAS mutations in non-small cell lung cancer. International Journal of Molecular Sciences 24: 997, 2023. *
• Mangione W, Falls Z, Samudrala R. Optimal COVID-19 therapeutic candidate discovery using the CANDO platform. Frontiers in Pharmacology 13: 970494, 2022. *
• Moukheiber L, Mangione W, Moukheiber M, Maleki S, Falls Z, Gao M, Samudrala R. Identifying protein features and pathways responsible for toxicity using machine learning and tox21: Implications for predictive toxicology. Molecules 27: 3021, 2022.
• Mammen MJ, Tu C, Morris MC, Richman S, Mangione W, Falls Z, Qu J, Broderick G, Sethi S, Samudrala R. Proteomic network analysis of bronchoalveolar lavage fluid in ex-smokers to discover implicated protein targets and novel drug treatments for chronic obstructive pulmonary disease. Pharmaceuticals 15: 566, 2022. *
• Falls Z, Fine J, Chopra G, Samudrala R. Accurate prediction of inhibitor binding to HIV-1 protease using CANDOCK. Frontiers in Chemistry 9: 775513, 2022.
• Schuler J, Falls Z, Mangione W, Hudson M, Bruggemann L, Samudrala R. Evaluating performance of drug repurposing technologies. Drug Discovery Today 27: 49-64, 2022. *
• Overhoff B, Falls Z, Mangione W, Samudrala R. A deep-learning proteomic-scale approach for drug design. Pharmaceuticals (Basel) 14: 1277, 2021. *
• Dey-Rao R, Smith GR, Timilsina U, Falls Z, Samudrala R, Stavrou S, Melendy T. A fluorescence-based, gain-of-signal, live cell system to evaluate SARS-CoV-2 main protease inhibition. Antiviral Research 195: 105183, 2021.
• Palanikumar L, Karpauskaite L, Al-Sayegh M, Chehade I, Alam M, Hassan S, Maity D, Ali L, Kalmouni M, Hunashal Y, Ahmed J, Houhou T, Karapetyan S, Falls Z, Samudrala R, Pasricha R, Esposito G, Afzal AJ, Hamilton AD, Kumar S, Magzoub M. Protein mimetic amyloid inhibitor potently abrogates cancer-associated mutant p53 aggregation and restores tumor suppressor function. Nature Communications 12: 3962, 2021.
• Hudson ML, Samudrala R. Multiscale virtual screening optimization for shotgun drug repurposing using the CANDO platform. Molecules 26: 2581-2597, 2021.
• Chatrikhi R, Feeney CF, Pulvino MJ, Alachouzos G, MacRae AJ, Falls Z, Rai S, Brennessel WW, Jenkins JL, Walter MJ, Graubert TA, Samudrala R, Jurica MS, Frontier AJ, Kielkopf CL. A synthetic small molecule stalls pre-mRNA splicing by promoting an early-stage U2AF2-RNA complex. Cell Chemical Biology 28: 1145-1157, 2021.
• Bondoc JMG, Gutka HJ, Almutairi MM, Patwell R, Rutter MW, Wolf NM, Samudrala R, Mehboob S, Dementiev A, Abad-Zapatero C, Movahedzadeh F. Rv0100, a proposed acyl carrier protein in Mycobacterium tuberculosis: expression, purification and crystallization. Corrigendum. Acta Crystallograpica F Structural Biology Communications 76: 192-193, 2020.
• Mandloi S, Falls Z, Deng R, Samudrala R, Elkin PL. Association of C>U RNA editing with human disease variants. Studies in Health Technology and Informatics 270: 1205-1206, 2020.
• Bruggemann L, Hawthorne C, Samudrala R, Lopez-Campos GH. Linking genome and exposome: Computational analysis of human variation in chemical-target interactions. Studies in Health Technology and Informatics 270: 1331-1332, 2020.
• Mangione W, Falls Z, Chopra G, Samudrala R. cando.py: Open source software for predictive bioanalytics of large scale drug-protein-disease data. Journal of Chemical Information and Modeling 60: 4131-4136, 2020. *
• Mangione W, Falls Z, Melendy T, Chopra G, Samudrala R. Shotgun drug repurposing biotechnology to tackle epidemics and pandemics. Drug Discovery Today 25: 1126-1128, 2020. *
• Fine J, Konc J, Samudrala R, Chopra G. CANDOCK: Chemical atomic network-based hierarchical flexible docking algorithm using generalized statistical potentials. Journal of Chemical Information and Modeling 60: 1509-1527, 2020. *
• Bondoc JMG, Gutka HJ, Almutairi MM, Patwell R, Rutter MW, Wolf NM, Samudrala R, Mehboob S, Movahedzadeh F. Rv0100, a proposed acyl carrier protein in Mycobacterium tuberculosis: expression, purification and crystallization. Acta Crystallograpica F Structural Biology Communications 75: 646-651, 2019.
• Fine J, Lackner R, Samudrala R, Chopra G. Computational chemoproteomics to understand the role of selected psychoactives in treating mental health indications. Scientific Reports 9, 1315, 2019. *
• Schuler J, Samudrala R. Fingerprinting CANDO: Increased accuracy with structure and ligand based shotgun drug repurposing. ACS Omega 4: 17393-17403, 2019. *
• Schuler J, Mangione W, Samudrala R, Ceusters W. Foundations for a realism-based drug repurposing ontology. Proceedings of the 10th International Conference on Biomedical Ontology, 2019.
• Falls Z, Mangione W, Schuler J, Samudrala R. Exploration of interaction scoring criteria in the CANDO platform. BMC Research Notes 12: 318, 2019. *
• Mangione W, Samudrala R. Identifying protein features responsible for improved drug repurposing accuracies using the CANDO platform: Implications for drug design. Molecules 24: 167, 2019. *
• Schuler J, Hudson M, Schwartz D, Samudrala R. A systematic review of computational drug discovery, development, and repurposing for Ebola Virus Disease treatment. Molecules 22: E1777, 2017.
• Hung L-H, Samudrala R. Rice protein models from the Nutritious Rice for the World Project. bioRxiv 091975; doi: https://doi.org/10.1101/091975, 2016.
• Chopra C, Kaushik S, Elkin PL, Samudrala R. Combating Ebola with repurposed therapeutics using the CANDO platform. Molecules 21: 1537, 2016. *
• Craig JK, Risler JK, Loesch KA, Dong W, Baker D, Barrett LK, Subramanian S, Samudrala R, Van Voorhis WC. Mycobacterium cytidylate kinase appears to be an undruggable target. Journal of Biomolecular Design 21: 695-700, 2016.
• Chopra G, Samudrala R. Exploring polypharmacology in drug discovery and repurposing using the CANDO platform. Current Pharmaceutical Design 22: 3109-3123 2016.
• Manocheewa S, Mittler JE, Samudrala R, Mullins JI. Composite sequence-structure stability models as screening tools for identifying vulnerable targets for HIV drug and vaccine development. Viruses 7: 5718-5735, 2015.
• Sethi G, Chopra G, Samudrala R. Multiscale modelling of relationships between protein classes and drug behavior across all diseases using the CANDO platform. Mini Reviews in Medicinal Chemistry 15: 705-717, 2015.
• Matasci N, Hung L-H, Yan Z, Carpenter EJ, Wickett NJ, Mirarab S, Nguyen N, Warnow T, Ayyampalayam S, Barker M, Burleigh JG, Gitzendanner MA, Wafula E, Der JP, dePamphilis CW, Roure B, Philippe H, Ruhfel BR, Miles NW, Graham SW, Mathews S, Surek B, Melkonian M, Soltis DE, Soltis PS, Rothfels C, Pokorny L, Shaw JA, DeGironimo L, Stevenson DW, Villarreal JC, Chen T, Kutchan TM, Rolf M, Baucom RS, Deyholos MK, Samudrala R, Tian Z, Wu X, Sun X, Zhang Y, Wang J, Leebens-Mack J, Wong GSK. Data access for the 1,000 Plants (1KP) project. Gigascience 3: 17, 2014.
• Minie M, Chopra G, Sethi G, Horst JA, White G, Roy A, Hatti K, Samudrala R. CANDO and the infinite drug discovery frontier. Drug Discovery Today 19: 1353-1363, 2014. *
• Hung L-H, Samudrala R. fast_protein_cluster: parallel and optimized clustering of large scale protein modeling data. Bioinformatics 30: 1774-1776, 2014.
• Minie M. Samudrala R. The promise and challenge of digital biology. Journal of Bioengineering and Biomedical Sciences 3: e118, 2013. editorial.
• Lertkiatmongkol P, Assawamakin A, White G, Chopra G, Rongnoparut P, Samudrala R, Tongsima S. Distal effect of amino acid substitutions in CYP2C9 polymorphic variants causes differences in interatomic interactions against (S)-warfarin. PLoS One 8: e74053, 2013.
• Laurenzi A, Hung L-H, Samudrala R. Structure prediction of partial length protein sequences: applications in foldability prediction and EST annotation. International Journal of Molecular Sciences 214: 14892-14907, 2013.
• Homo-dimerization and ligand binding by the leucine-rich repeat domain at RHG1/RFS2 underlying resistance to two soybean pathogens. Afzal AJ, Srour A, Goil A, Vasudaven S, Liu T, Samudrala R, Dogra N, Kohli P, Malakar A, Lightfoot DA. BMC Plant Biology 13: 43, 2013.
• Self-assembly of filamentous amelogenin requires calcium and phosphate: from dimers via nanoribbons to fibrils. Martinez-Avila O, Wu S, Kim SJ, Cheng Y, Khan F, Samudrala R, Sali A, Horst JA, Habelitz S. Biomacromolecules 13: 3494-502, 2012.
• Strategic protein target analysis for developing drugs to stop dental caries. Horst JA, Pieper U, Sali A, Zhan L, Chopra G, Samudrala R, Featherstone JD. Advances in Dental Research 24: 86-93, 2012. *
• Cementomimetics-constructing a cementum-like biomineralized microlayer via amelogenin-derived peptides. Gungormus M, Oren EE, Horst JA, Fong H, Hnilova M, Somerman MJ, Snead ML, Samudrala R, Tamerler C, Sarikaya M. International Journal of Oral Sciences 2: 69-77, 2012. *
• Goldman AD, Barrows J, Samudrala R. The enzymatic and metabolic capabilities of early life. PLoS One 7: e39912, 2012. *
• Hung L-H, Samudrala R. Accelerated protein structure comparison using TM-score-GPU. Bioinformatics 28: 2191-2192, 2012.
• Goldman AD, Horst JA, Hung L-H, Samudrala R. Evolution of the protein repertoire. Systems Biology: 207-237, 2012. (R Meyers, Editor. Wiley-VCH Wienheim, Germany.)
• Horst JA, Laurenzi A, Bernard B, Samudrala R. Computational multitarget drug discovery. Polypharmacology 263-301, 2012. *
• An P, Li R, Wang JM, Yoshimura T, Takahashi M, Samudrala R, O'Brien SJ, Phair J, Goedert JJ, Kirk GD, Troyer JL, Sezgin E, Buchbinder SP, Donfield S, Nelson GW, Winkler CA. Role of exonic variation in chemokine receptor genes on AIDS: CCRL2 F167Y association with pneumocystis pneumonia. PLoS Genetics 7: e1002328, 2011.
• Moughon S, Samudrala R. LoCo: a new backbone-only scoring function for protein structure prediction. BMC Bioinformatics 12: 368, 2011.
• Hung LH, Guerquin M, Samudrala R. GPU-Q-J, a fast method for calculating root mean square deviation (RMSD) after optimal superposition. BMC Research Notes 4: 97, 2011.
• Horst OV, Horst JA, Samudrala R, Dale BA. Caries induced cytokine network in the odontoblast layer of human teeth. BMC Immunology 12: 9, 2011.
• Cunningham ML, Horst JA, Rieder MJ, Hing AV, Stanaway IB, Park SS, Samudrala R, Speltz ML. IGF1R variants associated with isolated single suture craniosynostosis. The American Journal of Human Genetics 155A: 91-97, 2011. [Accompanying cover.]
• McDermott JE, Corrigan A, Peterson E, Oehmen C, Niemann G, Cambronne ED, Sharp D, Adkins JN, Samudrala R, Heffron F. Computational prediction of type III and IV secreted effectors in Gram-negative bacteria. Infection and Immunity 79: 23-32, 2011.
• Nicholson CO, Costin JM, Rowe DK, Lin L, Jenwitheesuk E, Samudrala R, Isern S, Michael SF. Viral entry inhibitors block dengue antibody-dependent enhancement in vitro. Antiviral Research 89: 71-74, 2010. *
• Wang J, Zhang J, Li R, Zheng H, Li J, Zhang Y, Li H, Ni P, Li S, Li S, Wang J, Liu D, McDermott JE, Samudrala R, Liu S, Wang J, Yang H, Yu J, Wong GK. Evolutionary transients in the rice transcriptome. Genomics Proteomics Bioinformatics 8: 211-228, 2010.
• Notman R, Oren EE, Tamerler C, Sarikaya M, Samudrala R, Walsh TR. Solution study of engineered quartz binding peptides using replica exchange molecular dynamics. Biomacromolecules 11: 3266-3274, 2010.
• Movahedzadeh F, Balasubramanian V, Bernard B, Iyer S, Samudrala R, Franzblau SG, Balganesh TS. Anti-tuberculosis agents: A rational approach for discovery and development. Genomic and computational tools for emerging infectious diseases, 2010.
• Horst JA, Wang K, Horst OV, Cunningham ML, Samudrala R. Disease risk of missense mutations using structural inference from predicted function. Current Protein & Peptide Science 11: 573-588, 2010. *
• Horst JA, Samudrala R. A protein sequence meta-functional signature for calcium binding residue prediction. Pattern Recognition Letters 31: 2103-2112, 2010. *
• Costin JM, Jenwitheesuk E, Lok S-M, Hunsperger E, Conrads KA, Fontaine KA, Rees CR, Rossmann MG, Isern S, Samudrala R, Michael SF. Structural optimization and de novo design of dengue virus entry inhibitory peptides. PLoS Neglected Tropical Diseases 4: e721, 2010. *
• Oren EE, Notman R, Kim IW, Evans J, Walsh T, Samudrala R, Tamerler C, Sarikaya M. Probing the molecular mechanisms of quartz-binding peptides. Langmuir 26: 11003-11009, 2010.
• Borlee BR, Goldman AD, Murakami K, Samudrala R, Wozniak DJ, Parsek MR. Pseudomonas aeruginosa uses a cyclic-di-GMP-regulated adhesin to reinforce the biofilm extracellular matrix. Molecular Microbiology 75: 827-842, 2010. [Accompanying cover.]
• Goldman AD, Samudrala R, Barrows J. The evolution and functional repertoire of translation proteins following the origin of life. Biology Direct 5: 15, 2010. *
• Horst JA, Samudrala R. Diversity of protein structures and difficulties in fold recognition: The curious case of Protein G. F1000 Biology Reports 1: 69, 2009. *
• Goldman AD, Leigh JA, Samudrala R. Comprehensive computational analysis of Hmd enzymes and paralogs in methanogenic Archaea. BMC Evolutionary Biology 9: 199, 2009.
• Liu T, Horst JA, Samudrala R. A novel method for predicting and using distance constraints of high accuracy for refining protein structure prediction. Proteins: Structure, Function, and Bioinformatics 77: 220-234, 2009. *
• Kittichotirat W, Guerquin M, Bumgarner RE, Samudrala R. Protinfo PPC: A web server for atomic level prediction of protein complexes. Nucleic Acids Research 37: W519-W525, 2009. *
• Samudrala R, Heffron F, McDermott JE. Accurate prediction of secreted substrates and identification of a conserved putative secretion signal for type III secretion systems. PLoS Pathogens 5: e1000375, 2009. *
• Bernard B, Samudrala R. A generalized knowledge-based discriminatory function for biomolecular interactions. Proteins: Structure, Function, and Bioinformatics 76: 115-128, 2009. *
• McDermott JE, Ireton R, Montgomery K, Bumgarner R, Samudrala R (editors). Computational systems biology. Methods in Molecular Biology 541: v-ix, 2009. *
• Frazier Z, McDermott JE, Samudrala R. Computational representation of biological systems. Methods in Molecular Biology 541: 535-549, 2009.
• Guerquin M, McDermott JE, Samudrala R. The Bioverse API and Web Application. Methods in Molecular Biology 541: 511-534, 2009.
• Rashid I, McDermott JE, Samudrala R. Inferring molecular interaction pathways from eQTL data. Methods in Molecular Biology 541: 211-223, 2009.
• Wichadakul D, McDermott JE, Samudrala R. Prediction and integration of regulatory and protein-protein interactions. Methods in Molecular Biology 541: 101-143, 2009.
• McDermott JE, Wang J, Yu J, Wong GSK, Samudrala R. In Rao GP, Wagner C, Singh RK, editors. Prediction and annotation of plant protein interaction networks. Application of Genomics and Bioinformatics in Plants (Studium Press) 207-238, 2008.
• Wang K, Horst JA, Cheng G, Nickle D, Samudrala R. Protein meta-functional signatures from combining sequence, structure, evolution and amino acid property information. PLoS Computational Biology 4: e1000181, 2008. *
• Samudrala R, Oren EE, Cheng C, Horst, JA, Bernard B, Gungormus M, Hnilova M, Fong H, Tamerler C, Sarikaya M. Knowledge-based design of inorganic binding peptides. Proceedings of the conference on the Foundations of Nanoscience: Self-Assembled Architectures and Devices, 2008.
• Evans JS, Samudrala R, Walsh TR, Oren EE, Tamerler C. Molecular design of inorganic-binding polypeptides. MRS Bulletin 33: 514-518, 2008. [Accompanying cover and introductory article with biographies on pages 504-512.] *
• Liu T, Guerquin M, Samudrala R. Improving the accuracy of template-based predictions by mixing and matching between initial models. BMC Structural Biology 8: 24, 2008.
• Jenkins C, Samudrala R, Geary S, Djordjevic SP. Structural and functional characterisation of an organic hydroperoxide resistance (Ohr) protein from Mycoplasma gallisepticum. Journal of Bacteriology 190: 2206-2208, 2008.
• Jenwitheesuk E, Horst JA, Rivas KL, Van Voorhis WC, Samudrala R. Novel paradigms for drug discovery: Computational multitarget screening. Trends in Pharmacological Sciences 29: 62-71, 2008. [Accompanying cover.] *
• Ngan S-C, Hung L-H, Liu T, Samudrala R. Scoring functions for de novo protein structure prediction revisited. Methods in Molecular Biology 413: 243-282, 2007.
• Oren EE, Tamerler C, Sahin D, Hnilova M, Seker UOS, Sarikaya M, Samudrala R. A novel knowledge-based approach for designing inorganic binding peptides. Bioinformatics 23: 2816-2822, 2007. *
• Jenwitheesuk E, Samudrala R. Identification of potential HIV-1 targets of minocycline. Bioinformatics 23: 2797-2799, 2007.
• Chevance FFV, Takahashi N, Karlinsey JE, Gnerer J, Hirano T, Samudrala R, Aizawa S-I, Hughes KT. The mechanism of outer membrane penetration by the eubacterial flagellum and implications for spirochete evolution. Genes and Development 21: 2326-2335, 2007.
• McDermott JE, Samudrala R. Bioinformatic characterization of plant networks. Proceedings of the Asia Pacific Conference on Plant Tissue Culture and Agrobiotechnology, 2007.
• Bockhorst J, Lu F, Janes JH, Keebler J, Gamain B, Awadalla P, Su X, Samudrala R, Jojic N, Smith JD. Structural polymorphism and diversifying selection on the pregnancy malaria vaccine candidate VAR2CSA. Molecular and Biochemical Parasitology 155: 103-112, 2007.
• Berube PM, Samudrala R, Stahl DA. Transcription of amoC is associated with the recovery of Nitrosomonas europaea from ammonia starvation. Journal of Bacteriology 89: 3935-3944, 2007.
• Hung L-H, Ngan S-C, Samudrala R. De novo protein structure prediction. In Xu Y, Xu D, Liang J, editors. Computational Methods for Protein Structure Prediction and Modeling 2: 43-64, 2007.
• Hung L-H, Samudrala R. An automated assignment-free Bayesian approach for accurately identifying proton contacts from NOESY data. Journal of Biomolecular NMR 36: 189-198, 2006. *
• Wang K, Samudrala R. Incorporating background frequency improves entropy-based residue conservation measures. BMC Bioinformatics 7: 385, 2006.
• Liu T, Samudrala R. The effect of experimental resolution on the performance of knowledge-based discriminatory functions for protein structure selection. Protein Engineering, Design and Selection 19: 431-437, 2006.
• Korotkova N, Le Trong I, Samudrala R, Korotkov K, Van Loy CP, Bui A-L, Moseley SL, Stenkamp RE. Crystal structure and mutational analysis of the DaaE adhesin of Escherichia coli. Journal of Biological Chemistry 281: 22367-22377, 2006.
• Wang K, Samudrala R. Automated functional classification of experimental and predicted protein structures. BMC Bioinformatics 7: 278, 2006. *
• Howell DPG, Samudrala R, Smith JD. Disguising itself - insights into Plasmodium falciparum binding and immune evasion from the DBL crystal structure. Molecular and Biochemical Parasitology 148: 1-9, 2006.
• Wang K, Mittler J, Samudrala R. Comment on "Evidence for positive epistasis in HIV-1". Science 312:848b, 2006.
• Chang AN, McDermott JE, Guerquin M, Frazier Z, Samudrala R. Integrator: Interactive graphical search of large protein interactomes over the Web. BMC Bioinformatics 7: 146, 2006.
• Ngan S-C, Inouye M, Samudrala R. A knowledge-based scoring function based on residue triplets for protein structure prediction. Protein Engineering, Design and Selection 19: 187-193, 2006.
• Jenwitheesuk E, Samudrala R. Heptad-repeat-2 mutations enhance the stability of the enfuvirtide-resistant HIV-1 gp41 hairpin structure. Antiviral Therapy 10: 893-900, 2005. *
• Cheng G, Qian B, Samudrala R, Baker D. Improvement in protein functional site prediction by distinguishing structural and functional constraints on protein family evolution using computational design. Nucleic Acids Research 33: 5861-5867, 2005. *
• Jenwitheesuk E, Samudrala R. Identification of potential multitarget antimalarial drugs. Journal of the American Medical Association 294: 1490-1491, 2005. *
• Wang W, Zheng H, Yang S, Yu H, Li J, Jiang H, Su J, Yang L, Zhang J, McDermott JE, Samudrala R, Wang J, Yang H, Yu J, Kristiansen K, Wong GK, Wang J. Origin and evolution of new exons in rodents. Genome Research 15: 1258-1264, 2005.
• Liu T, Jenwitheesuk E, Teller D, Samudrala R. Structural insights into the Cellular Retinaldehyde Binding Protein (CRALBP). Proteins: Structure, Function, and Bioinformatics 61: 412-422, 2005.
• McDermott JE, Bumgarner RE, Samudrala R. Functional annotation from predicted protein interaction networks. Bioinformatics 21: 3217-3226, 2005. *
• McDermott JE, Guerquin M, Frazier Z, Chang AN, Samudrala R. BIOVERSE: Enhancements to the framework for structural, functional, and contextual annotations of proteins and proteomes. Nucleic Acids Research 33: W324-W325, 2005. *
• Hung L-H, Ngan S-C, Liu T, Samudrala R. PROTINFO: New algorithms for enhanced protein structure prediction. Nucleic Acids Research 33: W77-W80, 2005. *
• Wang K, Samudrala R. FSSA: A novel method for identifying functional signatures from structural alignments. Bioinformatics 21: 2969-2977, 2005. *
• Jenwitheesuk E, Wang K, Mittler J, Samudrala R. PIRSpred: A webserver for reliable HIV-1 protein-inhibitor resistance/susceptibility prediction. Trends in Microbiology 13: 150-151, 2005. *
• Chang AN, McDermott JE, Samudrala R. An enhanced java graph applet interface for visualizing interactomes. Bioinformatics 21: 1741-1742, 2005.
• Jenwitheesuk E, Samudrala R. Virtual screening of HIV-1 protease inhibitors against human cytomegalovirus protease using docking and molecular dynamics. AIDS 19: 529-533, 2005.
• Jenwitheesuk E, Samudrala R. Prediction of HIV-1 protease inhibitor resistance using a protein-inhibitor flexible docking approach. Antiviral Therapy 10: 157-166, 2005. *
• Yu J, Wang J, Lin W, Li S, Li H, Zhou J, Ni P, Dong W, Hu S, Zeng C, Zhang J, Zhang Y, Li R, Xu Z, Li S, Li X, Zheng H, Cong L, Lin L, Yin J, Geng J, Li G, Shi J, Liu J, Lv H, Li J, Wang J, Deng Y, Ran L, Shi X, Wang X, Wu Q, Li C, Ren X, Wang J, Wang X, Li D, Liu D, Zhang X, Ji Z, Zhao W, Sun Y, Zhang Z, Bao J, Han Y, Dong L, Ji J, Chen P, Wu S, Liu J, Xiao Y, Bu D, Tan J, Yang L, Ye C, Zhang J, Xu J, Zhou Y, Yu Y, Zhang B, Zhuang S, Wei H, Liu B, Lei M, Yu H, Li Y, Xu H, Wei S, He X, Fang L, Zhang Z, Zhang Y, Huang X, Su Z, Tong W, Li J, Tong Z, Li S, Ye J, Wang L, Fang L, Lei T, Chen C, Chen H, Xu Z, Li H, Huang H, Zhang F, Xu H, Li N, Zhao C, Li S, Dong L, Huang Y, Li L, Xi Y, Qi Q, Li W, Zhang B, Hu W, Zhang Y, Tian X, Jiao Y, Liang X, Jin J, Gao L, Zheng W, Hao B, Liu S, Wang W, Yuan L, Cao M, McDermott JE, Samudrala R, Wang J, Wong GK. The genomes of Oryza sativa: A history of duplications. PLoS Biology 3: e38, 2005. *
• Ekwa-Ekok C, Diaza GA, Carlson C, Hasegawad T, Samudrala R, Limf K, Yabug JM, Levya B, Schnapp LM. Genomic organization and sequence variation of the human integrin subunit 8 gene (ITGA8). Matrix Biology 23: 487-496, 2004.
• Wang J, Zhang J, Zheng H, Li J, Liu D, Li H, Samudrala R, Yu J, Wong GK. Mouse transcriptome: Neutral evolution of "non-coding" complementary DNAs. Nature 431, 2004.
• Wang K, Samudrala R, Mittler J. HIV-1 genotypic drug resistance interpretation algorithms need to include hypersusceptibility mutations. Journal of Infectious Diseases 190: 2055-2056, 2004.
• Wang K, Samudrala R, Mittler J. Antivirogram or PhenoSense: a comparison of their reproducibility and an analysis of their correlation. Antiviral Therapy 9: 703-712, 2004.
• Jenwitheesuk E, Wang K, Mittler J, Samudrala R. Improved accuracy of HIV-1 genotypic susceptibility interpretation using a consensus approach. AIDS 18: 1858-1859, 2004.
• Wang K, Fain B, Levitt M, Samudrala R. Improved protein structure selection using decoy-dependent discriminatory functions. BMC Structural Biology 4: 8, 2004. *
• Wang K, Jenwitheesuk E, Samudrala R, Mittler J. Simple linear model provides highly accurate genotypic predictions of HIV-1 drug resistance. Antiviral Therapy 9: 343-352, 2004.
• Wang K, Samudrala R, Mittler J. Weak agreement between predictions of ``reduced susceptibility'' from Antivirogram and PhenoSense assays. Journal of Clinical Microbiology 42: 2353-2354, 2004.
• McDermott JE, Samudrala R. Enhanced functional information from protein networks. Trends in Biotechnology 22: 60-62, 2004. *
• Jenwitheesuk E, Samudrala R. Identifying inhibitors of the SARS coronavirus proteinase. Bioorganic & Medicinal Chemistry Letters 13: 3989-3992, 2003. [Most Cited Paper 2003 - 2006 Award.] *
• McDermott JE, Samudrala R. BIOVERSE: Functional, structural, and contextual annotation of proteins and proteomes. Nucleic Acids Research 31: 3736-3737, 2003. *
• Hung L-H, Samudrala R. PROTINFO: Secondary and tertiary protein structure prediction. Nucleic Acids Research 31: 3296-3299, 2003. *
• Jenwitheesuk E, Samudrala R. Improved prediction of HIV-1 protease-inhibitor binding energies by molecular dynamics simulations. BMC Structural Biology 3: 2, 2003. *
• Hung L-H, Samudrala R. Accurate and automated classification of protein secondary structure with PsiCSI. Protein Science 12: 288-295, 2003. *
• Jenkins C, Samudrala R, Anderson I, Hedlund BP, Petroni G, Michailova N, Pinel N, Overbeek R, Rosati G, Staley JT. Genes for the cytoskeletal protein tubulin in the bacteria genus Prosthecobacter. Proceedings of the National Academy of Sciences 99: 17049-17054, 2002.
• McDermott JE, Samudrala R. The Bioverse: An object-oriented genomic database and webserver written in Python. In Proceedings of the conference on Objects in Bio- & Chem-Informatics, 2002.
• Samudrala R, Levitt M. A comprehensive analysis of 40 blind protein structure predictions. BMC Structural Biology 2: 3-18, 2002. *
• Van Loy CP, Sokurenko EP, Samudrala R, Moseley S. Identification of a DAF binding domain in the Dr adhesin. Molecular Microbiology 45: 439-452, 2002.
• Samudrala R. Modelling genome structure and function. Pure and Applied Chemistry 6: 907-914, 2002.
• Samudrala R. Lessons from blind protein structure prediction experiments. In Grohima M, Selvaraj S, editors. Recent Research Developments in Protein Folding, Stability, and Design 123-139, 2002.
• Xia Y, Huang ES, Levitt M, Samudrala R. Ab initio construction of protein tertiary structures using a hierarchical approach. Journal of Molecular Biology 300: 171-185, 2000. *
• Samudrala R, Levitt M. Decoys 'R' Us: A database of incorrect protein conformations to improve protein structure prediction. Protein Science 9: 1399-1401, 2000. <http://dd.compbio.org>
• Huang ES, Samudrala R, Park BH. Scoring functions for ab initio protein structure prediction. Methods in Molecular Biology 143: 223-245, 2000.
• Samudrala R, Huang ES, Koehl P, Levitt M. Constructing side chains on near-native main chains for ab initio protein structure prediction. Protein Engineering 7: 453-457, 2000.
• Samudrala R, Xia Y, Levitt M, Cotton NJ, Huang ES, Davis R. Probing structure-function relationships of the DNA polymerase alpha-associated zinc-finger protein using computational approaches. In Altman R, Dunker K, Hunter L, Klein T, Lauderdale K, editors. Proceedings of the Pacific Symposium on Biocomputing 179-189, 2000.
• Huang ES, Samudrala R, Ponder JW. Ab initio fold prediction of small helical proteins using distance geometry and knowledge-based scoring functions. Journal of Molecular Biology 290: 267-281, 1999.
• Samudrala R, Xia Y, Huang ES, Levitt M. Ab initio prediction of protein structure using a combined hierarchical approach. Proteins: Structure, Function, and Genetics S3: 194-198, 1999. *
• Samudrala R, Xia Y, Levitt M, Huang ES. A combined approach for ab initio construction of low resolution protein tertiary structures from sequence. In Altman R, Dunker K, Hunter L, Klein T, Lauderdale K, editors. Proceedings of the Pacific Symposium on Biocomputing 505-516, 1999.
• Huang ES, Samudrala R, Ponder JW. Distance geometry generates native-like folds for small helical proteins using the consensus distances of predicted protein structures. Protein Science 7: 1998-2003, 1998.
• Samudrala R, Moult J. Determinants of side chain conformational preferences in protein structures. Protein Engineering 11: 991-997, 1998.
• Samudrala R, Moult J. A graph-theoretic algorithm for comparative modelling of protein structure. Journal of Molecular Biology 279: 287-302, 1998. *
• Samudrala R, Moult J. An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction. Journal of Molecular Biology 275: 893-914, 1998. *
• Samudrala R, Moult J. Handling context-sensitivity in protein structures using graph theory: bona fide prediction. Proteins: Structure, Function, and Genetics 29S: 43-49, 1997. *
• Samudrala R. A graph-theoretic solution to the context-sensitivity problem in protein structure prediction. PhD thesis, 1997.
• Samudrala R, Pedersen JT, Zhou H, Luo R, Fidelis K, Moult J. Confronting the problem of interconnected structural changes in the comparative modelling of proteins. Proteins: Structure, Function, and Genetics 23: 327-336, 1995.

General publications
8 publications listed

• Samudrala R. Book review: Discovering Genomics, Proteomics, and Bioinformatics by A. Malcolm Campbell and Laurie Heyer. Cell Biology Education 2: 222-223, 2003.
• Samudrala R. Book Review: Structural Bioinformatics by Philip E. Bourne and Helge Weissig. Briefings in Bioinformatics 4: 299-301, 2003.
• Samudrala R. Taking the cost out of firewalls. LinuxWorld Magazine 1: 58-59, 2003.
• Samudrala R. Linux Cluster HOWTO, 2003.
• Samudrala R. Installing and using RAID. In Danesh A, Das G, editors. Special Edition Using Linux System Administration, Que Publishing, 2000.
• Samudrala R. Creativity and ownership: where is the balance?. In Blondeau O, Latrive F, editors. Libres Enfants Du Savoir Numérique, 129-140, éditions de l'éclat, 2000.
• Samudrala R. The future of music. In Blondeau O, Latrive F, editors. Libres Enfants Du Savoir Numérique, 447-462, éditions de l'éclat, 2000.
• Samudrala R. The free music philosophy. In Blondeau O, Latrive F, editors. Libres Enfants Du Savoir Numérique, 463-478, éditions de l'éclat, 2000.

Patent publications
5 listed; 4 more provisional applications or disclosures submitted

• Mangione W, Falls Z, Samudrala R. Coronavirus treatment compositions and methods. Priority/filing date: December 1, 2021. Publication date: June 2, 2022.
• Oren EE, Tamerler C, Sarikaya M, Samudrala R. Method and system for designing polypeptides and polypeptide-like polymers with specific chemical and physical characteristics. Priority/filing date: September 17, 2008. Publication date: March 18, 2010.
• Michael SF, Isern S, Costin J, Jenwitheesuk E, Samudrala R. Optimized dengue virus entry inhibitory peptide (1OAN1). Priority/filing date: July 13, 2008. Publication date: July 21, 2011.
• Jenwitheesuk E, Michael SF, Isern S, Garry R, Costin J, Samudrala R. Dengue virus entry inhibitory peptide (DN81). Priority/filing date: July 11, 2007. Publication date: May 12, 2011.
• Jenwitheesuk E, Lagunoff M, Van Voorhis W, Samudrala R. Compositions and methods for predicting inhibitors of protein targets. Priority/filing date: July 6, 2007. Publication date: June 7, 2012.