300:, Samudrala's research group developed a series of algorithms and web server modules to predict protein structure, function, and interactions known as Protinfo. The group then applied these methods to organismal proteomes, creating a framework known as the Bioverse for exploring the relationships among the atomic, molecular, genomic, proteomic, systems, and organismal worlds. The Bioverse framework performs analyses and predictions based on genomic sequence data to annotate and understand the interaction of protein sequence, structure, and function, both at the single molecule as well as at the systems levels. The framework was used to annotate the finished rice genome sequence published in 2005.
307:, resulting in the Computational Analysis of Novel Drug Opportunities (CANDO) platform which ranks therapeutics for all indications by analysis and comparison of structural compound-proteome interaction signatures. A combination of novel docking methods and/or its use in the CANDO platform has led to prospectively validated predictions of putative drugs against dengue, dental caries, herpes, lupus, and malaria along with indication-specific collaborators.
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Philosophy, which predicted how the ease of copying and transmitting digital information by the
Internet would lead to unprecedented violations of copyright laws and new models of distribution for music and other digital media. His work in this area was reported as early as 1997 by diverse media
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protein structure prediction challenges since their inception. His work with Moult and Levitt are among the first improvements of blinded protein structure prediction in both comparative and template free modelling categories. With Moult, he was the first to develop and apply probabilistic and
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Other areas of application include predicting HIV drug resistance/susceptibility; nanobiotechnology, where small multifunctional peptides that bind to inorganic substrates are designed computationally; and interactomics of several organisms, including the
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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,
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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.
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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.
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McDermott J, Guerquin M, Frazier Z, Chang AN, Samudrala R. BIOVERSE: Enhancements to the framework for structural, functional, and contextual annotations of proteins and proteomes.
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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.
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graph-theoretic methods to accurately predict interactions for comparative modelling of protein structures. With Levitt, he developed a combined hierarchical approach for
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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.
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Wang K, Horst J, Cheng G, Nickle D, Samudrala R. Protein meta-functional signatures from combining sequence, structure, evolution and amino acid property information.
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Minie M, Chopra G, Sethi G, Horst J, White G, Roy A, Hatti K, Samudrala R. CANDO and the infinite drug discovery frontier. "Drug
Discovery Today" 19: 1353-1363, 2014.
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Samudrala R, Levitt M. Decoys 'R' Us: A database of incorrect protein conformations to improve protein structure prediction. Protein
Science 9: 1399-1401, 2000.
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which recognizes "outstanding scientists and engineers who show exceptional potential for leadership at the frontiers of knowledge". In 2008, he received the
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Sethi G, Chopra G, Samudrala R. Multiscale modelling of relationships between protein classes and drug behavior across all diseases using the CANDO platform.
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Oren EE, Tamerler C, Sahin D, Hnilova M, Seker UOS, Sarikaya M, Samudrala R. A novel knowledge-based approach for designing inorganic binding peptides.
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Liu T, Horst J, Samudrala R. A novel method for predicting and using distance constraints of high accuracy for refining protein structure prediction.
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Samudrala R, Moult J. A graph-theoretic algorithm for comparative modelling of protein structure. Journal of
Molecular Biology 279: 287-302, 1998.
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Jenwitheesuk E, Wang K, Mittler J, Samudrala R. PIRSpred: A webserver for reliable HIV-1 protein-inhibitor resistance/susceptibility prediction.
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Yu J, Wang J, Lin W, Li S, Li H, Zhou J, ..., McDermott J, Samudrala R, Wang J, Wong GK. The genomes of Oryza sativa: A history of duplications.
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Jenwitheesuk E, Horst JA, Rivas K, Van
Voorhis WC, Samudrala R. Novel paradigms for drug discovery: Computational multitarget screening.
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Samudrala R, Moult J. An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction.
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Kittichotirat W, Guerquin M, Bumgarner R, Samudrala R. Protinfo PPC: A web server for atomic level prediction of protein complexes.
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Samudrala is also a musician who has published and recorded work under the pseudonym TWISTED HELICES. In 1994, he published the
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in 2006. In 2014, he became professor and chief of the
Division of Bioinformatics at the State University of New York, Buffalo.
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Horst JA, Laurenzi A, Bernard B, Samudrala R. Computational multitarget drug discovery. "Polypharmacology "263-301, 2012.
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Samudrala R, Moult J. Handling context-sensitivity in protein structures using graph theory: bona fide prediction.
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Schulman BM. The song heard 'round the world: The copyright implications of MP3s and the future of digital music.
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McDermott J, Samudrala R. BIOVERSE: Functional, structural, and contextual annotation of proteins and proteomes.
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Award which funds exceptional young scientists in 2002 and was named one of the world's top young innovators (
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NIH HEAL Initiative issues awards to UB researchers to develop non-addictive painkillers, September 30 2019.
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Hung L-H, Ngan S-C, Liu T, Samudrala R. PROTINFO: New algorithms for enhanced protein structure prediction.
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Evans JS, Samudrala R, Walsh TR, Oren EE, Tamerler C. Molecular design of inorganic-binding polypeptides.
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structure prediction as well as the Decoys 'R' Us database to evaluate discrimination functions.
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Computational analysis of novel drug opportunities (CANDO) indications and collaborations
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Hung L-H, Samudrala R. PROTINFO: Secondary and tertiary protein structure prediction.
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for the CANDO drug discovery platform. In 2019, Samudrala was presented with a
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under the
Advanced Technology Initiative in Infectious Diseases created by the
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Visiting
Scientist Award and was awarded honorary diplomas from the cities of
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prediction of protein structure using a combined hierarchical approach.
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Profile naming Ram Samudrala one of the world's top young innovators
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ASPIRE Reduction-to-Practice Award grand prize presented in 2022.
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folding, structure, function, interaction, design, and evolution.
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972:"Samudrala, Falls Get Funding for Various Research Projects"
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Computational analysis of novel drug opportunities (CANDO)
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Story of a Revolution: Napster & the Music Industry.
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ASPIRE Design Challenge Award, which was followed by a
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Samudrala's group has also applied these methods to
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252:From 1997-2000, he was a postdoctoral fellow with
237:as a Wesleyan Scholar, and completed his Ph.D. in
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590:Proteins: Structure, Function, and Bioinformatics
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871:10 of Indian Origin in MIT's Technology Review.
346:Alberta Heritage Foundation for Medical Research
225:Samudrala received his undergraduate degrees in
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422:Searle Scholar Award profile for Ram Samudrala
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1069:Reece D. Industry grapples with MP3 dilemma.
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856:Kurian V. 10 Indian innovators in MIT list.
537:Proteins: Structure, Function, and Genetics
520:Proteins: Structure, Function, and Genetics
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1084:Napoli L. Fans of MP3 forced the issue.
531:Samudrala R, Xia Y, Huang ES, Levitt M.
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284:and he has regularly taken part in the
249:in 1997 as a Life Technologies Fellow.
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1128:Nutritious Rice for the World web site
1021:Samudrala R. The future of music, 1997
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845:Nutritious Rice for the World web site
807:International Journal of Oral Sciences
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1049:Harvard Journal of Law and Technology
462:Samudrala Computational Biology Group
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720:Mini Reviews in Medicinal Chemistry
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769:Trends in Pharmacological Sciences
473:Roseth B. Funding forward vision.
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1123:Ram Samudrala's personal web site
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451:Ram Samudrala's personal web site
1226:21st-century American biologists
1196:University of Washington faculty
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743:PLoS Neglected Tropical Diseases
498:Ram Samudrala's curriculum vitae
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337:in 2003, In 2005, he received a
280:Samudrala's research focuses on
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1206:Ohio Wesleyan University alumni
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213:, United States. He researches
1:
1231:University at Buffalo faculty
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313:Nutritious Rice for the World
550:Journal of Molecular Biology
362:NIH Director's Pioneer Award
266:Washington State Legislature
165:Other academic advisors
75:Protein structure prediction
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1216:American bioinformaticians
1201:Stanford University alumni
603:PLoS Computational Biology
209:and bioinformatics at the
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298:University of Washington
262:University of Washington
235:Ohio Wesleyan University
149:University of Washington
114:Director's Pioneer Award
57:Ohio Wesleyan University
858:The Hindu Business Line
793:Trends in Microbiology
668:Nucleic Acids Research
655:Nucleic Acids Research
642:Nucleic Acids Research
629:Nucleic Acids Research
616:Nucleic Acids Research
247:University of Maryland
61:University of Maryland
1010:Free Music Philosophy
977:University at Buffalo
949:University at Buffalo
323:Samudrala received a
239:Computational Biology
211:University at Buffalo
207:computational biology
145:University at Buffalo
135:Computational biology
822:23: 2816-2822, 2007.
670:33: W324-W325, 2005.
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618:37: W519-W525, 2009.
221:Education and career
1181:Bioverse web server
1142:Protinfo web server
1088:, December 16 1998.
952:. February 21, 2023
552:275: 893-914, 1998.
270:associate professor
258:Stanford University
107:Career Award (2005)
65:Stanford University
1086:The New York Times
1056:2012-04-09 at the
924:. October 28, 2021
880:2010-08-23 at the
835:33: 514-518, 2008.
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756:Antiviral Research
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539:S3: 194-198, 1999.
482:2011-06-04 at the
400:The New York Times
391:outlets including
319:Awards and honours
205:is a professor of
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722:, 2015. in press.
522:29S: 43-49, 1997.
438:Technology Review
334:Technology Review
227:Computing Science
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1190:Categories
407:References
388:Free music
282:proteomics
243:John Moult
160:John Moult
81:philosophy
79:free music
41:1972-03-23
1144:modules:
1138:sections)
1071:Billboard
1034:MusicDish
533:Ab initio
394:Billboard
331:) by MIT
1152:PIRSPred
1054:Archived
984:July 21,
956:July 21,
878:Archived
480:Archived
276:Research
231:Genetics
296:At the
291:de novo
245:at the
215:protein
192:compbio
179:Website
1158:PSICSI
1036:, 2000
928:May 5,
397:, and
354:Yautan
131:Fields
116:(2010)
101:(2003)
95:(2002)
86:Awards
1136:video
1132:press
509:1995.
376:NCATS
369:NCATS
350:Casma
329:TR100
241:with
233:from
99:TR100
1146:ABCM
1134:and
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930:2023
436:MIT
358:Peru
352:and
286:CASP
229:and
194:.org
186:.org
35:Born
1176:MFS
1170:PPC
1164:NMR
921:NIH
373:NIH
366:NIH
339:NSF
256:at
184:ram
111:NIH
105:NSF
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974:.
946:.
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428:^
414:^
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356:,
147:,
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63:,
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1173:-
1167:-
1161:-
1155:-
1149:-
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932:.
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