Ram Samudrala PhD
Ram Samudrala
PhD
Professor and Chief, Division of Bioinformatics
Department of Biomedical Informatics
Jacobs School of Medicine & Biomedical Sciences
Specialty/Research Focus
Artificial Intelligence; Bioinformatics; Biomedical Informatics; Biophysical Modeling; Computational Biology; Computational Chemistry; Computational Drug Discovery; Drug Design; Drug Development; Drug Discovery; Genomics and proteomics; Molecular and Cellular Biology; Nanotechnology; Protein Folding; Protein Function and Structure; Proteomics; Structural Biology; Translational Research
Professional Summary:
My group performs research to understand, through multiscale modelling, how organismal metagenomes specify their behavior and characteristics in conjunction with their environments. We accomplish this by developing novel computational biology and bioinformatics algorithms for predicting protein and proteome structure, function, interaction, design and evolution. We apply these basic science techniques to important practical problems in medicine, genetic and genomic engineering and nanobiotechnology.
I received the 2010 National Institutes of Health (NIH) Director‘s Pioneer Award to develop the Computational Analysis of Novel Drug Opportunities (CANDO) platform (http://protinfo.org/cando/) for multiscale therapeutic drug discovery, repurposing, and design. Our integrated informatics platform determines interactions between and among all drugs/compounds and higher scale entities (proteins, RNA, pathways, cells, tissues, etc.) to generate multiscale interaction signatures. The multiscale signatures are weighted using pharmacological, physiological and chemoinformatics data and compared and analyzed to predict the likelihood of the corresponding compounds being efficacious for any indication, in effect inferring homology of drug/compound behavior at proteomic/interactomic scales.
Using this approach, we made predictions for all the indications that our library of drugs maps to, with benchmarking accuracies that are orders of magnitude better than what is observed when using random controls. We have performed prospective validations of our predictions, demonstrating comparable or better in vitro inhibition than existing drugs approved for clinical use in indications such as COVID-19, dengue, dental caries, diabetes, hepatitis B, herpes, lupus, malaria and tuberculosis. We have implemented drug design capabilities in our platform to generate compounds beyond what is already known for indications such as opioid use disorder and overdose and non-small cell lunger cancer. We have further extended our platform to incorporate genotypic and phenotypic variations to enable precision medicine.
We also applied our computational techniques to design peptides for vaccines, antibacterial activity and inorganic substrate adhesion and model the structures, functions and interactions of all tractable proteins encoded by several rice genomes. A consistent theme in our research is the combination of in virtuale simulation and homology inference, followed by in vitro and in vivo verification and application, directed toward holistic multiscale modelling of complex biological systems. All this is accomplished in close collaboration with researchers across the world and primarily with Dr. Zackary Falls, also a faculty in the Bioinformatics Division.
Education and Training:
- Fellowship, Computational Biology, Stanford University (2000)
- PhD, Computational Biology, University of Maryland (1997)
- BA, Computing Science and Genetics, Ohio Wesleyan University (1993)
Employment:
- Co-Director Informatics Core, Clinical and Translational Sciences Institute, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo (2024-present)
- Chief, Division of Bioinformatics, Biomedical Informatics, University at Buffalo (2014-present)
- Professor, Biomedical Informatics, University at Buffalo Jacobs School of Medicine & Biomedical Sciences (2014-present)
- Associate Professor, Microbiology, University of Washington (2006–2014)
- Assistant Professor, Microbiology, University of Washington (2001–2006)
- Post Doctoral Fellow, Stanford University Medicine (1997–2001)
- Fellow, University of Maryland Center for Advanced Research in Biotechnology (1993–1997)
Awards and Honors:
- 2023 Wiki Science Competition International Prize (2024)
- Individual Development Award (2024)
- Clinical Research Achievement Award Finalist (2023)
- Ohio Wesleyan University Distinguished Achievement Citation (2023)
- NIH NCATS ASPIRE Reduction-to-Practice Challenge (2022)
- 2021 Wiki Science Competition International Prize (2022)
- 2019 Wiki Science Competition National Finalist (2020)
- NIH NCATS ASPIRE Design Challenge (2019)
- University at Buffalo Exceptional Scholar (2019)
- MacArthur Foundation 100&Change Competition Top 50 (2016)
- Individual Development Award (2016)
- NIH Director's Pioneer Award (2010)
- Best Undergraduate Research Mentor Award (2010)
- Alberta Heritage Foundation Medical Research Visiting Scientist Award (2008)
- Honorary diplomas from the cities of Casma and Yautan, Peru (2008)
- NSF CAREER Award (2005)
- University of Washington New Investigator Science in Medicine Lecture (2004)
- Outstanding Young Innovator Award (TR100) (2003)
- Searle Scholar (2002)
- NSF Program in Mathematics and Molecular Biology/Burroughs Wellcome Fund Fellowship (1997)
- Life Technologies Fellowship (1993)
- Zain-ul-Abedin Memorial Scholarship for Outstanding Graduate Studies in Molecular and Cell Biology (1993)
- Howard Hughes Internship Award (1992)
- Wesleyan Scholar (1990)
Research Expertise:
- Multiscale computational biology; bioinformatics; protein and proteome structure, function, interaction, evolution, and design; translational science; small molecule analysis and engineering
Research Centers:
- Center for Computational Research (CCR)
- Clinical and Translational Research Center (CTRC)
- Witebsky Center for Microbial Pathogenesis and Immunology
UB 2020 Strategic Strengths:
- Artistic Expression and Performing Arts.
- Civic Engagement and Public Policy
- Extreme Events: Mitigation and Response
- Health and Wellness Across the Lifespan
- Information and Computing Technology
- Integrated Nanostructured Systems
- Molecular Recognition in Biological Systems and Bioinformatics
Grants and Sponsored Research:
- August 2021–January 2030
NIH NCATS ASPIRE Reduction-to-Practice Award
NCATS
Role: Co-Principal Investigator
$1,220,000 - September 2019–January 2030
NIH NCATS ASPIRE Design Award
NIH
Role: Principal Investigator
$100,000 - September 2022–August 2027
Buffalo Research Innovation in Genomic and Healthcare Technology (BRIGHT) Short-Term Training and Education
NIH
Role: Principal Investigator
$672,596 - July 2017–June 2027
Buffalo Research Innovation in Genomic and Healthcare Technology (BRIGHT) Training and Education
NIH/NLM
Role: Co-Investigator
$4,546,884 - December 2019–December 2024
Buffalo Clinical and Translational Research Center Clinical and Translational Science Award (CTSA)
National Center for Advancing Translational Sciences (NCATS)/National Institutes of Health
Role: Co-Investigator
$20,178,410 - September 2023–July 2024
Designing nonaddictive pain relievers using artificial intelligence to confront the opioid crisis.
University at Buffalo Center for Advanced Technology
Role: Principal Investigator
$42,236 - November 2022–October 2023
High performance computing drug discovery initiative
NIST
Role: Principal Investigator
$1,000,000 - February 2021–December 2022
Computational Analysis of Novel Drug Opportunities (CANDO)
Buffalo Innovation Accelerator Fund
Role: Principal Investigator
$80,000 - April 2020–March 2021
Retrospective cohort study on opioid-related drug-drug interactions
UB, prime NIH
Role: Principal Investigator
$35,000 - June 2020–November 2020
SBIR Phase I: Accelerating understanding of COVID-19 biology and treatment via scaled medical record and biosimulation analytics
Onai, Inc. Prime: NSF
Role: Co-Investigator
$10,000 - September 2010–April 2017
Novel Paradigms for Drug Discovery: Computational Multitarget Screening
National Institute of Health
Role: Principal Investigator
$4,200,000 - February 2001–October 2014
UW Startup: Modelling proteomes
WA State Advanced Technology Initiative
Role: Principal Investigator
$925,000 - September 2005–August 2010
Design of inorganic binding proteins
NSF
Role: Co-Investigator
$600,000 - June 2005–May 2010
Automated protein structure prediction
NSF
Role: Principal Investigator
$414,640 - August 2002–July 2007
Modelling the rice proteome
NSF
Role: Principal Investigator
$1,896,908 - May 2003–April 2006
Protein structure from theory & experiment
NIH
Role: Principal Investigator
$900,979 - July 2002–June 2005
Modelling genome structure and function
Searle Scholars Program
Role: Principal Investigator
$240,000
Patents:
- Optimized dengue virus entry inhibitory peptide (1OAN1) (2008)
- Optimized dengue virus entry inhibitory peptide (DN81) (2007)
Journal Articles:
- Bruggemann L, Falls Z, Overhoff B, Schwarz S, Mahajan S, Samudrala R. (1900) Utilizing deep-Learning methods at the proteomic-scale for superior non-small cell lung cancer drug design. To be published (Jan)
- Keeper JH, Seto J, Oren EE, Horst OV, Hung L-H, Samudrala R. (2024) Accurate informatic modeling of tooth enamel pellicle interactions by training substitution matrices with Mat4Pep. Frontiers in Materials (Dec), 11(1436379): 1-11.
- Van Norden M, Mangione W, Falls Z, Samudrala R. (2024) Strategies for robust, accurate, and generalizable benchmarking of drug discovery platforms. bioRxiv : the preprint server for biology (Dec). doi:10.1101/2024.12.10.627863
- Van Norden M, Falls Z, Mandloi S, Segal BH, Baysal BE, Samudrala R, Elkin PL. (2024) The implications of APOBEC3-mediated C-to-U RNA editing for human disease. Communications biology (May), 7(1): 529. doi:10.1038/s42003-024-06239-w
- Manish M, Mishra S, Pahuja M, Anand A, Subbarao N, Samudrala R. (2023) Computational Grafting of Epitopes. Methods in molecular biology (Clifton, N.J.) (Aug), 2673: 111-122.
- Van Norden M, Falls Z, Mandloi S, Segal B, Baysal B, Samudrala R, Elkin PL. (2023) The Role of C-to-U RNA Editing in Human Biodiversity. bioRxiv : the preprint server for biology (Jul). doi:10.1101/2023.07.31.550344
- Handelmann CR, Tsompana M, Samudrala R, Buck MJ. (2023) The impact of nucleosome structure on CRISPR/Cas9 fidelity. Nucleic acids research (Mar), 51(5): 2333-2344. doi:10.1093/nar/gkad021
- Mangione W, Falls Z, Samudrala R. (2023) Effective holistic characterization of small molecule effects using heterogeneous biological networks. Frontiers in pharmacology (Jan), 14: 1113007. doi:10.3389/fphar.2023.1113007
- Kumari R, Sharma SD, Kumar A, Ende Z, Mishina M, Wang Y, Falls Z, Samudrala R, Pohl J, Knight PR, Sambhara S. (2023) Antiviral Approaches against Influenza Virus. Clinical microbiology reviews (Jan)e0004022.
- Bruggemann L, Falls Z, Mangione W, Schwartz SA, Battaglia S, Aalinkeel R, Mahajan SD, Samudrala R. (2023) Multiscale Analysis and Validation of Effective Drug Combinations Targeting Driver KRAS Mutations in Non-Small Cell Lung Cancer. International journal of molecular sciences (Jan), 24(2) doi:10.3390/ijms24020997
- Mammen MJ, Tu C, Morris MC, Richman S, Mangione W, Falls Z, Qu J, Broderick G, Sethi S, Samudrala R. (2022) 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 (Basel, Switzerland) (May), 15(5) doi:10.3390/ph15050566
- Moukheiber L, Mangione W, Moukheiber M, Maleki S, Falls Z, Gao M, Samudrala R. (2022) Identifying Protein Features and Pathways Responsible for Toxicity Using Machine Learning and Tox21: Implications for Predictive Toxicology. Molecules (Basel, Switzerland) (May), 27(9) doi:10.3390/molecules27093021
- Mangione W, Falls Z, Samudrala R. (2022) Optimal COVID-19 therapeutic candidate discovery using the CANDO platform. Frontiers in pharmacology (Jan), 13: 970494. doi:10.3389/fphar.2022.970494
- Schuler J, Falls Z, Mangione W, Hudson ML, Bruggemann L, Samudrala R. (2022) Evaluating the performance of drug-repurposing technologies. Drug discovery today (Jan), 27(1): 49-64.
- Overhoff B, Falls Z, Mangione W, Samudrala R. (2021) A Deep-Learning Proteomic-Scale Approach for Drug Design. Pharmaceuticals (Basel, Switzerland) (Dec), 14(12) doi:10.3390/ph14121277
- Dey-Rao R, Smith GR, Timilsina U, Falls Z, Samudrala R, Stavrou S, Melendy T. (2021) A fluorescence-based, gain-of-signal, live cell system to evaluate SARS-CoV-2 main protease inhibition. Antiviral research (Nov), 195: 105183. doi:10.1016/j.antiviral.2021.105183
- 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. (2021) A synthetic small molecule stalls pre-mRNA splicing by promoting an early-stage U2AF2-RNA complex. Cell chemical biology (Aug), 28(8): 1145-1157.e6. doi:10.1016/j.chembiol.2021.02.007
- 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. (2021) Protein mimetic amyloid inhibitor potently abrogates cancer-associated mutant p53 aggregation and restores tumor suppressor function. Nature communications (Jun), 12(1): 3962. doi:10.1038/s41467-021-23985-1
- Hudson ML, Samudrala R. (2021) Multiscale Virtual Screening Optimization for Shotgun Drug Repurposing Using the CANDO Platform. Molecules (Basel, Switzerland) (Apr), 26(9) doi:10.3390/molecules26092581
- Falls Z, Fine J, Chopra G, Samudrala R. (2021) Accurate Prediction of Inhibitor Binding to HIV-1 Protease Using CANDOCK. Frontiers in chemistry (Jan), 9: 775513. doi:10.3389/fchem.2021.775513
- Mangione W, Falls Z, Chopra G, Samudrala R. (2020) cando.py: Open Source Software for Predictive Bioanalytics of Large Scale Drug-Protein-Disease Data. Journal of chemical information and modeling (Sep), 60(9): 4131-4136. doi:10.1021/acs.jcim.0c00110
- Mangione W, Falls Z, Melendy T, Chopra G, Samudrala R. (2020) Shotgun drug repurposing biotechnology to tackle epidemics and pandemics. Drug Discovery Today (Jul), 25(7): 1126-1128. doi:10.1016/j.drudis.2020.05.002
- Bruggemann L, Hawthorne C, Samudrala R, Lopez-Campos GH. (2020) Linking Genome and Exposome: Computational Analysis of Human Variation in Chemical-Target Interactions. Studies in health technology and informatics (Jun), 270: 1331-1332.
- Mandloi S, Falls Z, Deng R, Samudrala R, Elkin PL. (2020) Association of C>U RNA Editing with Human Disease Variants. Studies in health technology and informatics (Jun), 270: 1205-1206.
- Bondoc JMG, Gutka HJ, Almutairi MM, Patwell R, Rutter MW, Wolf NM, Samudrala R, Mehboob S, Dementiev A, Abad-Zapatero C, Movahedzadeh F. (2020) Rv0100, a proposed acyl carrier protein in Mycobacterium tuberculosis: expression, purification and crystallization. Corrigendum. Acta crystallographica. Section F, Structural biology communications (Apr), 76(Pt 4): 192-193. doi:10.1107/S2053230X2000271X
- Fine J, Konc J, Samudrala R, Chopra G. (2020) CANDOCK: Chemical Atomic Network-Based Hierarchical Flexible Docking Algorithm Using Generalized Statistical Potentials. Journal of chemical information and modeling (Mar), 60(3): 1509-1527.
- Schuler J, Samudrala R. (2019) Fingerprinting CANDO: Increased Accuracy with Structure- and Ligand-Based Shotgun Drug Repurposing. ACS omega (Oct), 4(17): 17393-17403. doi:10.1021/acsomega.9b02160
- Bondoc JMG, Gutka HJ, Almutairi MM, Patwell R, Rutter MW, Wolf NM, Samudrala R, Mehboob S, Movahedzadeh F. (2019) Rv0100, a proposed acyl carrier protein in Mycobacterium tuberculosis: expression, purification and crystallization. Acta crystallographica. Section F, Structural biology communications (Oct), 75(Pt 10): 646-651. doi:10.1107/S2053230X19012652
- Fine J, Lackner R, Samudrala R, Chopra G. (2019) Computational chemoproteomics to understand the role of selected psychoactives in treating mental health indications. Scientific reports (Sep), 9(1): 13155. doi:10.1038/s41598-019-49515-0
- Falls Z, Mangione W, Schuler J, Samudrala R. (2019) Exploration of interaction scoring criteria in the CANDO platform. BMC research notes (Jun), 12(1): 318. doi:10.1186/s13104-019-4356-3
- Mangione W, Samudrala R. (2019) Identifying Protein Features Responsible for Improved Drug Repurposing Accuracies Using the CANDO Platform: Implications for Drug Design. Molecules (Basel, Switzerland) (Jan), 24(1) doi:10.3390/molecules24010167
- Schuler J, Hudson ML, Schwartz D, Samudrala R. (2017) A Systematic Review of Computational Drug Discovery, Development, and Repurposing for Ebola Virus Disease Treatment. Molecules (Basel, Switzerland) (Oct), 22(10) doi:10.3390/molecules22101777
- Chopra G, Kaushik S, Elkin PL, Samudrala R. (2016) Combating Ebola with Repurposed Therapeutics Using the CANDO Platform. Molecules (Basel, Switzerland) (Nov), 21(12) doi:10.3390/molecules21121537
- Craig JK, Risler JK, Loesch KA, Dong W, Baker D, Barrett LK, Subramanian S, Samudrala R, Van Voorhis WC. (2016) Mycobacterium Cytidylate Kinase Appears to Be an Undruggable Target. J Biomol Screen (Aug), 21(7): 695-700.
- Chopra G, Samudrala R. (2016) Exploring Polypharmacology in Drug Discovery and Repurposing Using the CANDO Platform. Curr Pharm Des (Jan), 22(21): 3109-3123.
- Manocheewa S, Mittler JE, Samudrala R, Mullins JI. (2015) Composite Sequence-Structure Stability Models as Screening Tools for Identifying Vulnerable Targets for HIV Drug and Vaccine Development. Viruses (Nov), 7(11): 5718-5735.
- Sethi G, Chopra G, Samudrala R. (2015) Multiscale modelling of relationships between protein classes and drug behavior across all diseases using the CANDO platform. Mini Rev Med Chem (Jan), 15(8): 705-717.
- Matasci N, Hung LH, 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 GK. (2014) Data access for the 1,000 Plants (1KP) project. Gigascience (Oct), 3: 17-17.
- Minie M, Chopra G, Sethi G, Horst J, White G, Roy A, Hatti K, Samudrala R. (2014) CANDO and the infinite drug discovery frontier. Drug Discov Today (Sep), 19(9): 1353-1363.
- Hung LH, Samudrala R. (2014) fast_protein_cluster: parallel and optimized clustering of large-scale protein modeling data. Bioinformatics (Jun), 30(12): 1774-1776.
- Lertkiatmongkol P, Assawamakin A, White G, Chopra G, Rongnoparut P, Samudrala R, Tongsima S. (2013) Distal effect of amino acid substitutions in CYP2C9 polymorphic variants causes differences in interatomic interactions against (S)-warfarin. PLoS One (Sep), 8(9): 74053-74053.
- Laurenzi A, Hung LH, Samudrala R. (2013) Structure prediction of partial-length protein sequences. Int J Mol Sci (Jul), 14(7): 14892-14907.
- Afzal AJ, Srour A, Goil A, Vasudaven S, Liu T, Samudrala R, Dogra N, Kohli P, Malakar A, Lightfoot DA. (2013) Homo-dimerization and ligand binding by the leucine-rich repeat domain at RHG1/RFS2 underlying resistance to two soybean pathogens. BMC Plant Biol (Mar), 13: 43-43.
- Minie ME, Samudrala R. (2013) The Promise and Challenge of Digital Biology. Journal of bioengineering & biomedical science (Jan), 3(3) doi:10.4172/2155-9538.1000e118
- Martinez-Avila O, Wu S, Kim SJ, Cheng Y, Khan F, Samudrala R, Sali A, Horst JA, Habelitz S. (2012) Self-assembly of filamentous amelogenin requires calcium and phosphate: from dimers via nanoribbons to fibrils. Biomacromolecules (Nov), 13(11): 3494-3502.
- Horst JA, Pieper U, Sali A, Zhan L, Chopra G, Samudrala R, Featherstone JD. (2012) Strategic protein target analysis for developing drugs to stop dental caries. Adv Dent Res (Sep), 24(2): 86-93.
- Goldman AD, Baross JA, Samudrala R. (2012) The enzymatic and metabolic capabilities of early life. PLoS One (Sep), 7(9): 39912-39912.
- Hung LH, Samudrala R. (2012) Accelerated protein structure comparison using TM-score-GPU. Bioinformatics (Aug), 28(16): 2191-2192.
- Gungormus M, Oren EE, Horst JA, Fong H, Hnilova M, Somerman MJ, Snead ML, Samudrala R, Tamerler C, Sarikaya M. (2012) Cementomimetics-constructing a cementum-like biomineralized microlayer via amelogenin-derived peptides. Int J Oral Sci (Jun), 4(2): 69-77.
- Moughon SE, Samudrala R. (2011) LoCo: a novel main chain scoring function for protein structure prediction based on local coordinates. BMC Bioinformatics (Sep), 12: 368-368.
- Hung LH, Guerquin M, Samudrala R. (2011) GPU-Q-J, a fast method for calculating root mean square deviation (RMSD) after optimal superposition. BMC Res Notes (Apr), 4: 97-97.
- Cunningham ML, Horst JA, Rieder MJ, Hing AV, Stanaway IB, Park SS, Samudrala R, Speltz ML. (2011) IGF1R variants associated with isolated single suture craniosynostosis. Am J Med Genet A (Jan), 155A(1): 91-97.
- Horst OV, Horst JA, Samudrala R, Dale BA. (2011) Caries induced cytokine network in the odontoblast layer of human teeth. BMC Immunol (Jan), 12: 9-9.
- McDermott JE, Corrigan A, Peterson E, Oehmen C, Niemann G, Cambronne ED, Sharp D, Adkins JN, Samudrala R, Heffron F. (2011) Computational prediction of type III and IV secreted effectors in gram-negative bacteria. Infect Immun (Jan), 79(1): 23-32.
- Nicholson CO, Costin JM, Rowe DK, Lin L, Jenwitheesuk E, Samudrala R, Isern S, Michael SF. (2011) Viral entry inhibitors block dengue antibody-dependent enhancement in vitro. Antiviral Res (Jan), 89(1): 71-74.
- Notman R, Oren EE, Tamerler C, Sarikaya M, Samudrala R, Walsh TR. (2010) Solution study of engineered quartz binding peptides using replica exchange molecular dynamics. Biomacromolecules (Dec), 11(12): 3266-3274.
- 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 J, Samudrala R, Liu S, Wang J, Yang H, Yu J, Wong GK. (2010) Evolutionary transients in the rice transcriptome. Genomics Proteomics Bioinformatics (Dec), 8(4): 211-228.
- Horst JA, Wang K, Horst OV, Cunningham ML, Samudrala R. (2010) Disease risk of missense mutations using structural inference from predicted function. Curr Protein Pept Sci (Nov), 11(7): 573-588.
- Horst JA, Samudrala R. (2010) A protein sequence meta-functional signature for calcium binding residue prediction. Pattern Recognit Lett (Oct), 31(14): 2103-2112.
- Oren EE, Notman R, Kim IW, Evans JS, Walsh TR, Samudrala R, Tamerler C, Sarikaya M. (2010) Probing the molecular mechanisms of quartz-binding peptides. Langmuir (Jul), 26(13): 11003-11009.
- Costin JM, Jenwitheesuk E, Lok SM, Hunsperger E, Conrads KA, Fontaine KA, Rees CR, Rossmann MG, Isern S, Samudrala R, Michael SF. (2010) Structural optimization and de novo design of dengue virus entry inhibitory peptides. PLoS Negl Trop Dis (Jun), 4(6): 721-721.
- Goldman AD, Samudrala R, Baross JA. (2010) The evolution and functional repertoire of translation proteins following the origin of life. Biol Direct (Apr), 5: 15-15.
- Borlee BR, Goldman AD, Murakami K, Samudrala R, Wozniak DJ, Parsek MR. (2010) Pseudomonas aeruginosa uses a cyclic-di-GMP-regulated adhesin to reinforce the biofilm extracellular matrix. Mol Microbiol (Feb), 75(4): 827-842.
- Liu T, Horst JA, Samudrala R. (2009) A novel method for predicting and using distance constraints of high accuracy for refining protein structure prediction. Proteins (Oct), 77(1): 220-234.
- Horst J, Samudrala R. (2009) Diversity of protein structures and difficulties in fold recognition: the curious case of protein G. F1000 Biol Rep (Sep), 1: 69-69.
- Goldman AD, Leigh JA, Samudrala R. (2009) Comprehensive computational analysis of Hmd enzymes and paralogs in methanogenic Archaea. BMC Evol Biol (Aug), 9: 199-199.
- Bernard B, Samudrala R. (2009) A generalized knowledge-based discriminatory function for biomolecular interactions. Proteins (Jul), 76(1): 115-128.
- Kittichotirat W, Guerquin M, Bumgarner RE, Samudrala R. (2009) Protinfo PPC: a web server for atomic level prediction of protein complexes. Nucleic Acids Res (Jul), 37(Web S): 519-525.
- Samudrala R, Heffron F, McDermott JE. (2009) Accurate prediction of secreted substrates and identification of a conserved putative secretion signal for type III secretion systems. PLoS Pathog (Apr), 5(4): 1000375-1000375.
- Frazier Z, McDermott J, Guerquin M, Samudrala R. (2009) Computational representation of biological systems. Methods Mol Biol (Jan), 541: 535-549.
- Rashid I, McDermott J, Samudrala R. (2009) Inferring molecular interactions pathways from eQTL data. Methods Mol Biol (Jan), 541: 211-223.
- Wichadakul D, McDermott J, Samudrala R. (2009) Prediction and integration of regulatory and protein-protein interactions. Methods Mol Biol (Jan), 541: 101-143.
- Guerquin M, McDermott J, Frazier Z, Samudrala R. (2009) The Bioverse API and web application. Methods Mol Biol (Jan), 541: 511-534.
- Wang K, Horst JA, Cheng G, Nickle DC, Samudrala R. (2008) Protein meta-functional signatures from combining sequence, structure, evolution, and amino acid property information. PLoS Comput Biol (Sep), 4(9): 1000181-1000181.
- Liu T, Guerquin M, Samudrala R. (2008) Improving the accuracy of template-based predictions by mixing and matching between initial models. BMC Struct Biol (May), 8: 24-24.
- Jenkins C, Samudrala R, Geary SJ, Djordjevic SP. (2008) Structural and functional characterization of an organic hydroperoxide resistance protein from Mycoplasma gallisepticum. J Bacteriol (Mar), 190(6): 2206-2216.
- Jenwitheesuk E, Horst JA, Rivas KL, Van Voorhis WC, Samudrala R. (2008) Novel paradigms for drug discovery: computational multitarget screening. Trends Pharmacol Sci (Feb), 29(2): 62-71.
- Ngan SC, Hung LH, Liu T, Samudrala R. (2008) Scoring functions for de novo protein structure prediction revisited. Methods Mol Biol (Jan), 413: 243-281.
- Oren EE, Tamerler C, Sahin D, Hnilova M, Seker UO, Sarikaya M, Samudrala R. (2007) A novel knowledge-based approach to design inorganic-binding peptides. Bioinformatics (Nov), 23(21): 2816-2822.
- Jenwitheesuk E, Samudrala R. (2007) Identification of potential HIV-1 targets of minocycline. Bioinformatics (Oct), 23(20): 2797-2799.
- Bockhorst J, Lu F, Janes JH, Keebler J, Gamain B, Awadalla P, Su XZ, Samudrala R, Jojic N, Smith JD. (2007) Structural polymorphism and diversifying selection on the pregnancy malaria vaccine candidate VAR2CSA. Mol Biochem Parasitol (Oct), 155(2): 103-112.
- Chevance FF, Takahashi N, Karlinsey JE, Gnerer J, Hirano T, Samudrala R, Aizawa S, Hughes KT. (2007) The mechanism of outer membrane penetration by the eubacterial flagellum and implications for spirochete evolution. Genes Dev (Sep), 21(18): 2326-2335.
- Berube PM, Samudrala R, Stahl DA. (2007) Transcription of all amoC copies is associated with recovery of Nitrosomonas europaea from ammonia starvation. J Bacteriol (Jun), 189(11): 3935-3944.
- Hung LH, Samudrala R. (2006) An automated assignment-free Bayesian approach for accurately identifying proton contacts from NOESY data. J Biomol NMR (Nov), 36(3): 189-198.
- Liu T, Samudrala R. (2006) The effect of experimental resolution on the performance of knowledge-based discriminatory functions for protein structure selection. Protein Eng Des Sel (Sep), 19(9): 431-437.
- Wang K, Samudrala R. (2006) Incorporating background frequency improves entropy-based residue conservation measures. BMC Bioinformatics (Aug), 7: 385-385.
- Korotkova N, Le Trong I, Samudrala R, Korotkov K, Van Loy CP, Bui AL, Moseley SL, Stenkamp RE. (2006) Crystal structure and mutational analysis of the DaaE adhesin of Escherichia coli. J Biol Chem (Aug), 281(31): 22367-22377.
- Howell DP, Samudrala R, Smith JD. (2006) Disguising itself--insights into Plasmodium falciparum binding and immune evasion from the DBL crystal structure. Mol Biochem Parasitol (Jul), 148(1): 1-9.
- Wang K, Samudrala R. (2006) Automated functional classification of experimental and predicted protein structures. BMC Bioinformatics (Jun), 7: 278-278.
- Wang K, Mittler JE, Samudrala R. (2006) Comment on "Evidence for positive epistasis in HIV-1". Science (May), 312(5775): 848-848.
- Ngan SC, Inouye MT, Samudrala R. (2006) A knowledge-based scoring function based on residue triplets for protein structure prediction. Protein Eng Des Sel (May), 19(5): 187-193.
- Chang AN, McDermott J, Frazier Z, Guerquin M, Samudrala R. (2006) INTEGRATOR: interactive graphical search of large protein interactomes over the Web. BMC Bioinformatics (Mar), 7: 146-146.
- Liu T, Jenwitheesuk E, Teller DC, Samudrala R. (2005) Structural insights into the cellular retinaldehyde-binding protein (CRALBP). Proteins (Nov), 61(2): 412-422.
- Cheng G, Qian B, Samudrala R, Baker D. (2005) Improvement in protein functional site prediction by distinguishing structural and functional constraints on protein family evolution using computational design. Nucleic Acids Res (Oct), 33(18): 5861-5867.
- Wang W, Zheng H, Yang S, Yu H, Li J, Jiang H, Su J, Yang L, Zhang J, McDermott J, Samudrala R, Wang J, Yang H, Yu J, Kristiansen K, Wong GK, Wang J. (2005) Origin and evolution of new exons in rodents. Genome Res (Sep), 15(9): 1258-1264.
- Jenwitheesuk E, Samudrala R. (2005) Identification of potential multitarget antimalarial drugs. JAMA (Sep), 294(12): 1490-1491.
- McDermott J, Bumgarner R, Samudrala R. (2005) Functional annotation from predicted protein interaction networks. Bioinformatics (Aug), 21(15): 3217-3226.
- Wang K, Samudrala R. (2005) FSSA: a novel method for identifying functional signatures from structural alignments. Bioinformatics (Jul), 21(13): 2969-2977.
- McDermott J, Guerquin M, Frazier Z, Chang AN, Samudrala R. (2005) BIOVERSE: enhancements to the framework for structural, functional and contextual modeling of proteins and proteomes. Nucleic Acids Res (Jul), 33(Web S): 324-325.
- Hung LH, Ngan SC, Liu T, Samudrala R. (2005) PROTINFO: new algorithms for enhanced protein structure predictions. Nucleic Acids Res (Jul), 33(Web S): 77-80.
- Chang AN, McDermott J, Samudrala R. (2005) An enhanced Java graph applet interface for visualizing interactomes. Bioinformatics (Apr), 21(8): 1741-1742.
- Jenwitheesuk E, Wang K, Mittler JE, Samudrala R. (2005) PIRSpred: a web server for reliable HIV-1 protein-inhibitor resistance/susceptibility prediction. Trends Microbiol (Apr), 13(4): 150-151.
- Jenwitheesuk E, Samudrala R. (2005) Virtual screening of HIV-1 protease inhibitors against human cytomegalovirus protease using docking and molecular dynamics. AIDS (Mar), 19(5): 529-531.
- 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 J, Samudrala R, Wang J, Wong GK, Yang H. (2005) The Genomes of Oryza sativa: a history of duplications. PLoS Biol (Feb), 3(2): 38-38.
- Jenwitheesuk E, Samudrala R. (2005) Prediction of HIV-1 protease inhibitor resistance using a protein-inhibitor flexible docking approach. Antivir Ther (Jan), 10(1): 157-166.
- Jenwitheesuk E, Samudrala R. (2005) Heptad-repeat-2 mutations enhance the stability of the enfuvirtide-resistant HIV-1 gp41 hairpin structure. Antivir Ther (Jan), 10(8): 893-900.
- Wang K, Samudrala R, Mittler JE. (2004) HIV-1 genotypic drug-resistance interpretation algorithms need to include hypersusceptibility-associated mutations. J Infect Dis (Dec), 190(11): 2055-2056.
- Ekwa-Ekoka C, Diaz GA, Carlson C, Hasegawa T, Samudrala R, Lim KC, Yabu JM, Levy B, Schnapp LM. (2004) Genomic organization and sequence variation of the human integrin subunit alpha8 gene (ITGA8). Matrix Biol (Nov), 23(7): 487-496.
- Wang J, Zhang J, Zheng H, Li J, Liu D, Li H, Samudrala R, Yu J, Wong GK. (2004) Mouse transcriptome: neutral evolution of 'non-coding' complementary DNAs. Nature (Oct), 431(7010): 1-1.
- Wang K, Samudrala R, Mittler JE. (2004) Antivirogram or phenosense: a comparison of their reproducibility and an analysis of their correlation. Antivir Ther (Oct), 9(5): 703-712.
- Jenwitheesuk E, Wang K, Mittler JE, Samudrala R. (2004) Improved accuracy of HIV-1 genotypic susceptibility interpretation using a consensus approach. AIDS (Sep), 18(13): 1858-1859.
- Wang K, Fain B, Levitt M, Samudrala R. (2004) Improved protein structure selection using decoy-dependent discriminatory functions. BMC Struct Biol (Jun), 4: 8-8.
- Wang K, Jenwitheesuk E, Samudrala R, Mittler JE. (2004) Simple linear model provides highly accurate genotypic predictions of HIV-1 drug resistance. Antivir Ther (Jun), 9(3): 343-352.
- Wang K, Samudrala R, Mittler J. (2004) Weak agreement between Antivirogram and Phenosense assays in predicting reduced susceptibility to antiretroviral drugs. J Clin Microbiol (May), 42(5): 2353-2354.
- McDermott J, Samudrala R. (2004) Enhanced functional information from predicted protein networks. Trends Biotechnol (Feb), 22(2): 60-62.
- Jenwitheesuk E, Samudrala R. (2003) Identifying inhibitors of the SARS coronavirus proteinase. Bioorg Med Chem Lett (Nov), 13(22): 3989-3992.
- McDermott J, Samudrala R. (2003) Bioverse: Functional, structural and contextual annotation of proteins and proteomes. Nucleic Acids Res (Jul), 31(13): 3736-3737.
- Hung LH, Samudrala R. (2003) PROTINFO: Secondary and tertiary protein structure prediction. Nucleic Acids Res (Jul), 31(13): 3296-3299.
- Jenwitheesuk E, Samudrala R. (2003) Improved prediction of HIV-1 protease-inhibitor binding energies by molecular dynamics simulations. BMC Struct Biol (Apr), 3: 2-2.
- Hung LH, Samudrala R. (2003) Accurate and automated classification of protein secondary structure with PsiCSI. Prot Sci (Feb), 12(2): 288-295.
- Jenkins C, Samudrala R, Anderson I, Hedlund BP, Petroni G, Michailova N, Pinel N, Overbeek R, Rosati G, Staley JT. (2002) Genes for the cytoskeletal protein tubulin in the bacterial genus Prosthecobacter. Proc Natl Acad Sci U S A (Dec), 99(26): 17049-17054.
- Samudrala R, Levitt M. (2002) A comprehensive analysis of 40 blind protein structure predictions. BMC Struct Biol (Aug), 2: 3-3.
- Van Loy CP, Sokurenko EV, Samudrala R, Moseley SL. (2002) Identification of amino acids in the Dr adhesin required for binding to decay-accelerating factor. Mol Microbiol (Jul), 45(2): 439-452.
- Samudrala R, Levitt M. (2000) Decoys 'R' Us: a database of incorrect conformations to improve protein structure prediction. Protein Sci (Jul), 9(7): 1399-1401.
- Samudrala R, Huang ES, Koehl P, Levitt M. (2000) Constructing side chains on near-native main chains for ab initio protein structure prediction. Protein Eng (Jul), 13(7): 453-457.
- Xia Y, Huang ES, Levitt M, Samudrala R. (2000) Ab initio construction of protein tertiary structures using a hierarchical approach. J Mol Biol (Jun), 300(1): 171-185.
- Samudrala R, Xia Y, Levitt M, Cotton NJ, Huang ES, Davis R. (2000) Probing structure-function relationships of the DNA polymerase alpha-associated zinc-finger protein using computational approaches. Pac Symp Biocomput (Jan)179-190.
- Huang ES, Samudrala R, Park BH. (2000) Scoring functions for ab initio protein structure prediction. Methods Mol Biol (Jan), 143: 223-245.
- Huang ES, Samudrala R, Ponder JW. (1999) Ab initio fold prediction of small helical proteins using distance geometry and knowledge-based scoring functions. J Mol Biol (Jul), 290(1): 267-281.
- Samudrala R, Xia Y, Huang E, Levitt M. (1999) Ab initio protein structure prediction using a combined hierarchical approach. Proteins (Jan), Suppl: 194-198.
- Samudrala R, Xia Y, Levitt M, Huang ES. (1999) A combined approach for ab initio construction of low resolution protein tertiary structures from sequence. Pac Symp Biocomput (Jan)505-516.
- Samudrala R, Moult J. (1998) Determinants of side chain conformational preferences in protein structures. Protein Eng (Nov), 11(11): 991-997.
- Huang ES, Samudrala R, Ponder JW. (1998) Distance geometry generates native-like folds for small helical proteins using the consensus distances of predicted protein structures. Protein Sci (Sep), 7(9): 1998-2003.
- Samudrala R, Moult J. (1998) A graph-theoretic algorithm for comparative modeling of protein structure. J Mol Biol (May), 279(1): 287-302.
- Samudrala R, Moult J. (1998) An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction. J Mol Biol (Feb), 275(5): 895-916.
- Samudrala R, Moult J. (1997) Handling context-sensitivity in protein structures using graph theory: bona fide prediction. Proteins (Jan), Suppl: 43-49.
- Samudrala R, Pedersen JT, Zhou HB, Luo R, Fidelis K, Moult J. (1995) Confronting the problem of interconnected structural changes in the comparative modeling of proteins. Proteins (Nov), 23(3): 327-336.
- Xu S, Jiang L, Zhang Z, Luo X, Wu W, Wu H, Huang Z, Falls Z, Samudrala R, Tan Z. (1900) Deciphering bisphenol A (BPA)-elicited osteoarthritis mechanisms through network toxicology, and advancing de novo therapeutic design. To be submitted (Jan)
- Xu S, Mangione W, Van Norden M, Hu Y, Falls Z, Samudrala R. (1900) Multiscale analysis and optimal glioma therapeutic candidate discovery using the CANDO platform. (Jan)
- Elefteriou K, Xu S, Falls Z, Samudrala R. (1900) Discovery of putative drug candidates against pancreatic cancer using the CANDO platform. To be submitted (Jan)
Books and Book Chapters:
- Bruggemann L, Qayum S, Ma Q, Ocque A, Aalinkeel R, Samudrala R, Morse GD, Schwartz SA, Mahajan SD. (2024) Chapter 33 - Predicting the effectiveness of combination treatment of dolutegravir and fluoxetine for depressive disorders in HIV. In: HIV-Associated Neurocognitive Disorders. Elsevier, 577-566.
Presentations:
- "CANDO and the infinite drug discovery frontier" PhD Program in Biomedical Sciences introduction (2024)
- "Multiscale analysis and validation of effective drug combinations targeting driver KRAS mutations in non-small cell lung cancer." Buffalo Translational Consortium - Clinical Research Achievement Awards finalist (2024)
- "CANDO and the infinite drug discovery frontier." Louisiana Biomedical Research Network Annual Meeting. (2024)
- "Multiscale small molecule interactomics using the CANDO platform." MRS Fall Meeting: Molecular Biomimetics—Biology Meets Materials Science and Artificial Intelligence at the Molecular Dimensions. (2023)
- "CANDO and the infinite drug discovery frontier." Ideation session at Sensorium Therapeutics. (2023)
- "Prediction of co-prescription induced drug events using the CANDO platform." University at Buffalo Clinical and Translational Sciences Institute Pilot Studies Colloquium. (2022)
- "How healthcare data will change the world." University at Buffalo Distinctive Dialogues. (2022)
- "Proteomusic: converting protein structures to complex music patterns." Sigma Xi STEM Art and Film Festival. (2021)
- "Recent developments in bioinformatics." National Library of Medicine/National Center for Biotechnology Information workshop. (2021)
- "Broad spectrum coronavirus therapeutic discovery using the CANDO platform." Louisiana Biomedical Research Network Annual Meeting. (2021)
- "Computational Analysis of Novel Drug Opportunities (CANDO)." International Conference on Protein and RNA Structure Prediction. (2019)
- "Optimum analgesic discovery by multiscale interactomic profiling." NIH NCATS ASPIRE Design Challenge Winners Conference. (2019)
- "Computational Analysis of Novel Drug Opportunities (CANDO)." Center for Leading Innovation & Collaboration (CLIC) Un-meeting. (2019)
- "The comprehensive solution to characterise and treat disease" Louisiana Biomedical Research Network Annual Meeting. (2019)
- "AI-based shotgun drug discovery, repurposing, and design." Research Areas Ready for Acceleration and Growth. (2018)
- "AI-based shotgun drug discovery to characterise and treat disease." SUNY Germination Space Artificial Intelligence Program. (2018)
- "Grant application strategies." Research fundamentals workshop. (2018)
- "Interactomics: Computational Analysis of Novel Drug Opportunities. International conference on Clinical Sciences and Drug Discovery." (2015)
- "Multiscale modelling of relationships between protein classes and drug behavior across all diseases using the cando platform." International Conference on Protein Engineering (2015)
- "Interactome based drug discovery." Intelligent Systems in Molecular Biology. (2015)
- "Interactomics: Computational Analysis of Novel Drug Opportunities." Significant Advances in Bioengineering. (2015)
- "Interactomics: Computational Analysis of Novel Drug Opportunities." NIH Common Fund High-Risk High-Reward Symposium. (2014)
- "Interactomics: Atomic systems biology translated to drug discovery. From High-throughput Structural Bioinformatics to Integrative Systems Biology." Network Tools and Applications in Biology Conference (2014)
- "Interactomics: Computational Analysis of Novel Drug Opportunities." Michael Levitt Nobel Memorial Symposium. (2014)
- "Interactomics: Computational Analysis of Novel Drug Opportunities." Systems Biology of Infectious Diseases. (2014)
- "Interactomics: Computational Analysis of Novel Drug Opportunities. Intelligent Systems in Molecular Biology" (2014)
- "Drug design against NSCLC" ACS BIOT 2025 Annual Meeting
Service Activities:
- Clinical and Translational Sciences Institute; Co-Director Informatics (2024–present)
- SUNY Empire Innovation Program; Reviewer (2024)
- New Innovator Award Distinguished Member of the Editorial Board; Distinguished Reviewer (2024)
- Heliyon; Advisory board member (2024)
- Kuwait University; Grant reviewer (2024)
- UB-Empire-AI commiteee; Member (2024)
- Drug Screening and Pharmacology Summit.; Organising Committee Member (2023)
- Grant reviewer for Kuwait University; Reviewer (2023)
- Natural Sciences and Engineering Research Council of Canada (NSERC); Reviewer (2023–2024)
- JSMBS Awards Committee; Member (2023–present)
- BRIGHT short-term training program; Program director/mentor (2022–2028)
- Faculty and administrator hiring search committees; member (2022)
- Frontiers in Chemistry; Associate Editor (2022–present)
- PhD Program in Biomedical Sciences (PPBS); Steering committee member (2022–present)
- 18th IEEE International Conference on Computational Intelligence in Bioinformatics and Computational Biology. Victoria, Australia.; International Advisory Committee Member (2021)
- Promotion and tenure committee; Dossier reviewer (2020–2023)
- Biology; Editorial board member (2020–present)
- CLIMB UP for Summer Research; reviewer (2019)
- Clinical Translational Sciences Institute; Pilot studies grant reviewer (2019–present)
- Drug Development Core, UB Clinical and Translational Research Center; Scientific leadership committee member (2017–2020)
- Louisiana Biomedical Research Network; External Advisory Committee member (2017–present)
- PhD Program in Biomedical Sciences (PPBS); Admissions committee member (2016–present)
- Faculty council; Alternate member (2016–present)
- MD/PhD admissions committee; Reviewer (2016–present)
- Faculty Opinons; Faculty (2002–present)
- Bioinformatics, BMC Bioinformatics, BMC Structural Biology, Drug Discovery Today, Frontiers in Chemistry, Frontiers in Pharmacology, Journal of Molecular Biology, Nucleic Acids Research, Proteins: Structure, Function, and Bioinformatics, Protein Science, Science Advances, and several others; Reviewer (1995–present)