Awards and honours |
Major research resources developed |
Scientific publications |
General publications |
Professional activities |
- Associate Professor, University of Washington, Seattle. July 2006-. (Assistant Professor, February 2001-June 2006.)
- Modelling structure, function, expression, interaction, and
evolution of proteins, RNA, DNA, and small molecules.
- Postdoctoral Fellow, Stanford University. September 1997-January 2001.
- Protein folding, protein structure and function prediction;
computational structural and functional genomics.
- Mentor: Michael Levitt
- Ph.D., Centre for Advanced Research in Biotechnology. Jun 1993-Aug 1997.
- Protein folding and protein structure prediction using computational approaches.
- Mentor: John Moult.
- B.A., Ohio Wesleyan University. January 1990-May 1993.
- Majors: Computing Science and Genetics.
- Minors: Mathematics and Biology.
- NIH Director's Pioneer Award. 2010.
- Undergraduate Research Mentor Award. 2010.
- Honorary diplomas from the cities of Casma and Yautan, Peru; as
well as an official Decree of Thanks from the Peruvian Minister of
Health for research on vaccine discovery. 2008.
- Alberta Heritage Foundation for Medical Research Visiting
Scientist Award. 2008.
Director's Pioneer Award finalist (25/465
applicants selected as finalists). 2006.
- NSF CAREER award. 2005-2010.
New Investigator Science in Medicine Lecture. 2004.
- Named one of the world's top young innovators (TR100 selection)
by MIT Technology Review. 2003.
- Searle Scholar. 2002-2005.
- NSF Program in Mathematics and Molecular Biology/Burroughs
Wellcome Fund Fellow. 1997-2001.
- Centre for Advanced Research in Biotechnology Life Technologies
Graduate Fellow. 1993-1997.
- Zain-ul-Abedin Memorial Scholarship for Outstanding Graduate
Studies in Molecular and Cell Biology. 1993.
- Howard Hughes Internship Award. 1992.
- Dean's List. 1990-1993.
- Wesleyan Scholar and Honours Student at Ohio Wesleyan. 1990-1993.
- Computational analysis of novel drug opportunities (CANDO) platform
The CANDO platform is comprised of a unique computational
multitarget fragment-based docking with dynamics protocol to
implement a comprehensive and efficient drug discovery pipeline with
higher efficiency, lowered cost, and increased success rates,
compared to current approaches. The pipeline is being applied to
evaluate how all FDA approved drugs, phenethylamines, tryptamines
and other physchoactive drugs bind to all known protein structures
in Homo sapiens and several pathogenic species. The binding
studies are combined with pharmacological, physiological, and
cheminformatics data to predict new therapeutics through repurposing
drugs already approved for other indications. The top predictions
are verified in the laboratory and clinic by our collaborators. The
project, funded by a 2010 NIH Director's
Pioneer Award, represents an integration of our group's applied
research on therapeutic discovery, building upon basic protein
structure, function, and interaction prediction research.
- Protinfo structure, function, and interaction prediction web server modules
The web server consists of modules to predict the protein structure
of individual molecules and complexes (ABCM, PPC), integrate limited
or noisy experimental data with our structure prediction algorithms
(PsiCSI, NMR), score protein structure decoys (SCORE), assign
proteins to particular functional categories and predict
functionally important residues (MFS, FSSA); predict protein ion
binding sites, types, affinities, and specificities from structure
(SOAK); and predict HIV-1 drug resistance/susceptibility (PIRSPred).
Currently structure, function, and interaction predictions for up to
100 molecules/day are performed.
- The Bioverse framework
The Bioverse provides a framework for exploring the relationships
among the molecular, genomic, proteomic, systems, and organismal
worlds. Our goal is to perform sophisticated 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 Bioverse currently consists of more than 50 organismal
proteomes and is used by several hundred visitors accessing more
than 1,000 molecules/day. The current Bioverse 2D is being expanded
- ``Nutritious Rice for the World'' project
This project was developed in collaboration with IBM to predict the
structures, functions, and interactions of the rice interactome. More
over 200 media outlets have provided coverage on this project.
110 publications listed, 5 more submitted; * denotes more significant; H-index > 40; 83/104 publications in journals with average impact factor of 5.8 (top 4%)
- 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,
- Hung L-H, Samudrala R. Accelerated protein structure
comparison using TM-score-GPU. Bioinformatics 28:
- 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
2011 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.]
- 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, 2011. *
- 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.
- 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. Evolutionary transients in the rice
transcriptome. Genomics Proteomics Bioinformatics 8:
- 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 J, 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 J, 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,
- 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 J, 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 J, 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 J. 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 J, Ireton R, Montgomery K, Bumgarner R, Samudrala
R (editors). Computational
systems biology. Methods in Molecular Biology 541:
v-ix, 2009. *
- Frazier Z, McDermott J, Samudrala R. Computational representation of
biological systems. Methods in Molecular Biology
541: 535-549, 2009.
- Guerquin M, McDermott J, Samudrala R. The Bioverse API and Web
Application. Methods in Molecular Biology 541:
- Rashid I, McDermott J, Samudrala R. Inferring molecular interaction
pathways from eQTL data. Methods in Molecular
Biology 541: 211-223, 2009.
- Wichadakul D, McDermott J, Samudrala R. Prediction and
integration of regulatory and protein-protein
interactions. Methods in Molecular Biology 541:
- McDermott J, 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 J, 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, J, 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
- 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:
- 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:
- McDermott J, 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
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,
- Chang AN, McDermott J, Guerquin M, Frazier Z, Samudrala
R. Integrator: Interactive
graphical search of large protein
interactomes over the Web. BMC Bioinformatics 7:
- 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,
- 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 J, 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 J, Bumgarner RE, Samudrala R. Functional
annotation from predicted protein interaction networks.
Bioinformatics 21: 3217-3226, 2005. *
- 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. 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,
- Chang AN, McDermott J, 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,
- Jenwitheesuk E, Samudrala R. Prediction of HIV-1
protease inhibitor resistance using a protein-inhibitor flexible
docking approach. Antiviral Therapy 10: 157-166,
- 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. 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:
- 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 J, 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 J, 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:
- McDermott J, 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.
- 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:
- Samudrala R, Xia Y, Levitt M, Cotton NJ, Huang ES, Davis R.
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, Levitt M. Huang ES. 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. Ph.D. 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.
- Samudrala R. Book
review: Discovering Genomics,
Proteomics, and Bioinformatics by A. Malcolm Campbell
and Laurie Heyer. Cell Biology Education 2: 222-223,
- 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,
- 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
Blondeau O, Latrive F, editors. Libres Enfants Du Savoir
Numérique, 447-462, éditions de l'éclat,
- Samudrala R. The free music philosophy.
In Blondeau O, Latrive F, editors. Libres Enfants Du Savoir
Numérique, 463-478, éditions de l'éclat,
- Interactomics. International Workshop on Network Tools and
Application for Biology. Venice, Italy. October 16-18,
- Interactomics. Zing Protein and RNA Structure Prediction
Conference. Xcaret, Mexico. December 1-5, 2013. invited.
Computational analysis of novel drug
opportunities. International Conference on Pattern Recognition
in Bioinformatics (PRIB). Nice, France. June 18,
Computational analysis of novel drug opportunities. Genoa
Computational Biology Workshop. Genoa, Italy. June 14,
International Union of Pure and Applied Chemistry
Conference. Chonburi, Thailand. January 24, 2013. keynote.
- Interactomics. International
Conference on Bioinformatics (InCoB). Bangkok, Thailand. October 4,
2012. keynote; presented by Gaurav Chopra.
Discovering drugs against infectious and neoplastic disease using a
shotgun computational multitargeting approach. Mahidol
International Conference on Infections and Cancers. Bangkok,
Thailand. February 8, 2012. keynote.
- Interactomics. Pacific
Symposium on Biocomputing. Kona, HI. January 5,
analysis of novel drug opportunities (CANDO). Seventh Annual NIH
Director Pioneer's Award Symposium. Bethesda, MD. September 21,
multitarget computational drug discovery. World DNA and Genome
Day. Dalian, China. April 27, 2011. invited.
life at the atomic level. Paws-on-Science Huskies Weekend at the
Pacific Science Center. Seattle, WA. April 9, 2011. exhibit;
presented by 4 undergraduate students.
multitarget computational drug discovery. Pepcon: Emerging
Leaders in Protein and Peptide Science. Beijing, China. March 25,
Vaccine Discovery. World Congress on Vaccines. Beijing,
China. March 23, 2011. invited.
structeomes. Undergraduate Research Program Research Exposed
series. University of Washington, Seattle, WA. January 19,
variants associated with isolated single suture craniosynostosis.
Ninth Critical Assessment of Structure Prediction (CASP9). Asilomar,
CA. December 8, 2010. refereed; presented by Jeremy Horst.
- Research authorship. Biomedical Research Integrity Discussion.
University of Washington, Seattle, WA. August 3, 2010. two
life at the atomic level. Paws-on-Science Huskies
Weekend at the Pacific Science Center. Seattle, WA. April 10,
silico design of solid binding peptides as molecular building
blocks in technology and medicine. ACS 237th National
Meeting. Salt Lake City, UT. March 24, 2009. invited;
presented by Ersin Emre Oren.
structure refinement. Eighth Critical Assessment of Structure
Prediction (CASP8). Asilomar, CA. December 7, 2008. refereed.
folding algorithms. Melbourne, Australia. October 16, 2008. keynote.
interactomes. BioC 2008. Fred Hutchinson Cancer
Research Center, Seattle, WA. July 28, 2008. invited.
the Bartonella interactome. Meeting on discovery of a
vaccine for Bartonella bacilliformis. National Institutes of
Health, Lima, Peru. June 26, 2008. invited.
interactomes. U.S.-India Joint Training Program Workshop on
Global Infectious Diseases. Hyderabad, India. January 22,
interactomes. The 4th Solanaceae Genome Workshop. Jeju Island,
Korea. Sep 10, 2007. invited.
interactomes. 21st Symposium of the Protein Society. Boston,
MA. July 24, 2007. invited.
interactomes. Asia Pacific Conference on Plant Tissue Culture
and Agrobiotechnology. Kuala Lumpur, Malaysia. June 19,
engineering of bionanostructures. Foundations of
Nanoscience: Self-assembled Architectures and Devices
Conference. Snowbird, UT. April 21, 2007. invited.
structural proteomics. Seventh Critical Assessment of Structure
Prediction (CASP7). Asilomar, CA. November 30, 2006. invited.
proteomes. Molecular Biomimetics and Bionanotechnology
conference. Istanbul, Turkey. November 13, 2006. invited.
inorganic binding proteins. First workshop on Molecular
Biomimetics. Friday Harbour, WA. September 6, 2006. invited.
proteomes. Oral Biology Research Symposium. Seattle, WA. October
7, 2005. invited.
proteomes. BioC. Seattle, WA. August 17, 2005. invited.
proteomes: Application to understanding HIV disease progression.
Center for AIDS Research Symposium. Seattle, WA. May 27,
proteomes. Fifth Annual Northwest Gene Expression
Conference. Seattle, WA. May 26, 2005. invited.
engineering of bionanostructures. Foundations of
Nanoscience: Self-assembled Architectures and Devices
Conference. Snowbird, UT. April 25, 2005. invited.
proteomes. Searle Scholars Meeting. Chicago, IL. April 12,
integrated computational framework for systems biology
research. LabAutomation Conference. San Jose, CA. February 3,
New automated methods for CASP6. Sixth Critical Assessment of
Structure Prediction (CASP6). Gaeta, Italy. December 6,
2004. refereed; presented by Ling-Hong Hung.
Bioinformatics. American Crystallographic Association Annual
Meeting. Chicago, IL. July 22, 2004. invited.
proteomes. Fourth Annual Northwest Gene Expression
Conference. Seattle, WA. August 28, 2003. invited.
protein structure from sequence. Biothailand 2003 Post-Congress
Workshop. Bangkok, Thailand. July 22, 2003. invited.
the rice proteome. Conference on Rice Biotechnology
2003. Pattaya, Thailand. July 18, 2003. invited.
comparison and analysis of proteomes from different
organisms. International Conference on Biodiversity and
Bioactive Compounds. Pattaya, Thailand. July 17, 2003. invited.
vs. non-violent approaches to global conflict resolution. Time
of Reflection: The War in Iraq symposium. Seattle, WA. April
proteomes. The International Conference on
Bioinformatics 2002. Bangkok, Thailand. February 8,
Structure Prediction. The International Conference on
Bioinformatics (InCoB). Bangkok, Thailand. February 5,
genome structure and function. Statistical Genetics and
Computational Molecular Biology Symposium. Seattle, WA. December
- Protein structure prediction: progress and prospects. At the
Interface of Biology, Mathematics and Physics Symposium. Tucson,
AZ. March 2001. invited.
- Protein structure prediction: progress and
prospects. Biomedical Computation at Stanford 2000
Symposium. Stanford, CA. October 2000. invited.
- Computational biology: from gene to structure to
function. Intelligent Systems in Molecular Biology. San Diego, CA.
August 2000. invited.
- Computational biology: from gene to structure to
function. Mathematical and Computational Challenges in Molecular and
Cell Biology Symposium. Berkeley, CA. June 2000. invited.
- Probing structure-function relationships of proteins using
computational approaches. Pacific Symposium on
Biocomputing. Honolulu, HI. January 2000. refereed.
- Heterogeneous clusters and computational biology. Mellon
Institute's Developing and Using Clusters as a Biomedical Research
Tool Conference. Pittsburgh, PA. June 1999. invited.
- The triumph of technology: the defeat of copyright law. Second
Annual MP3 Summit. San Diego, CA. June 1999. invited.
- Applying the Cathedral and Bazaar paradigms to the music
industry. Alliance for Converging Technologies Lighthouse
Conference. Berkeley, CA. March 9, 1999. invited.
- Combining an all-atom conditional probability discriminatory
function and exhaustive enumeration techniques for protein structure
prediction. NSF Program in Mathematics and Molecular Biology meeting
VI. Santa Fe, NM. January 1999. invited.
- A combined approach for ab initio construction of low
resolution protein tertiary structures from sequence.
Pacific Symposium on Biocomputing. Kona, HI. January
- Bona fide ab initio prediction of protein structures by
exhaustive enumeration and successive filtering using
knowledge-based scoring functions. Third Critical Assessment of
Structure Prediction. Asilomar, CA, December 16,
- Free Music Philosophy. First Annual MP3 Summit. San Diego, CA.
June 1998. invited.
- An all-atom conditional probability discriminatory
function for protein structure prediction. Burroughs Wellcome
Fund's Doing Science at the Interface. Berkeley, CA. June
- Creativity and ownership: where is the balance? Third Annual
Ethics and Technology Conference. Santa Clara, CA. June
- Confronting the problem of interconnected structural changes in
the comparative modelling of proteins. NSF Program in Mathematics
and Molecular Biology meeting V. Santa Fe, NM. January
- A graph theoretic approach to handle the problem of
interconnectedness in the comparative modelling of proteins.
Second Critical Assessment of Structure Prediction. Asilomar,
CA. December 13, 1996. refereed.
- Comparative modelling of the Histidine-containing
Phosophocarrier protein, the Cellular Retinoic Acid-binding Protein,
and the Eosinophil Derived Neurotoxin. First Critical Assessment of
Structure Prediction. Asilomar, CA, December 5, 1994. refereed.
- Undergraduate Research Symposium moderator, Undergraduate Research
Program, University of Washington, Seattle. May 19, 2011.
- Levinson Scholar Review Committee, Undergraduate Research
Program, University of Washington, Seattle. September 13, 2010.
- Undergraduate Award Committee, Department of Microbiology,
University of Washington, Seattle. 2010-.
- Consulant for the National Centre for Genetic
Engineering and Biotechnology (BIOTEC), Thailand. December, 2009-.
- Chair/member of the Admissions Committee, Department of
Microbiology, University of Washington, Seattle. 2004-2008.
- Adjunct Faculty, Department of Biology, University
of Washington, Seattle.
- Adjunct Faculty, Department of Oral Biology, University
of Washington, Seattle.
- Faculty Member, Structural Biology, Faculty of 1000. June 1,
- Member, Interdisciplinary Program in Pathobiology,
University of Washington, Seattle. 2012-.
- Member, Computational Molecular Biology Program, University of
Washington, Seattle. 2001-.
- Member, Molecular and Cellular Biology Program, University of
Washington, Seattle. 2001-.
- Member, Nanotechnology Program, University of Washington,
- Member, Center for Ecogenetics and Environmental Health,
University of Washington, Seattle.
- Member, Keck Center for Microbial Pathogens, University of
- Member, Bioconductor Advisory Board, Fred Hutchinson Cancer
Research Center, Seattle. 2006-.
- Member, Biocommons Computing Center Advisory Board,
University of Washington, Seattle. 2003-.
- Member, Scientific committee for the International Conference on
Bioinformatics, Bangkok, Thailand. 2002.
- Member, NIH study section (BDMA, BCP) special emphasis
panels: 6/2003, 3/2004, 6/2004, 12/2004, 10/2007, 11/2007, 2/2009,
2/2013 (Pioneer Award).
- Member, NSF review panels: 8/2002, 5/2003, 3/2005, 4/2005,
5/2006, 3/2007, 10/2010, 4/2013 (PDB).
- Ad hoc grant application reviewer for
NIH and NSF (in addition to the above panels) as well as
Agency for Science, Technology and Research (A*STAR) Singapore,
Burroughs Wellcome Fund,
UW Royalty Research Fund,
and several others.
- Editor in Chief, Interactome. 2013-.
- Associate Editor, BMC Systems Biology. 2012-.
- Associate Editor, BMC Bioinformatics. 2010-.
- Editorial Board, Journal of Bioengineering & Biomedical
- Manuscript reviewer for
BMC Structural Biology,
Journal of Molecular Biology,
Nucleic Acids Research,
Proteins: Structure, Function, and Bioinformatics,
and several others.
- Principal Investigator at the University of
Washington of a computational genomics
research group investigating protein structure and
function; bioinformatics/data mining; predicting membrane protein
structure; protein design; docking; evolution; and understanding
higher level organisation of protein pathways in the cell and
simulating their behaviour. February 2001-.
- Postdoctoral Fellow at Stanford University working on methods
to sample main chain conformations
in comparative modelling and ab initio scenarios,
continued development of all-atom discriminatory functions and side
chain prediction methods, comparative modelling and ab initio
prediction for the third and fourth Critical Assessment of
Structure Prediction (CASP3 and 4) experiments, and computational
aspects of structural and functional genomics. With Michael Levitt. September
- Graduate Research Fellow at the Centre for Advanced Research in
Biotechnology working on modelling protein
structure primarily using graph theoretic methods, development of an
all-atom conditional-probability discriminatory function,
development of algorithms for side chain prediction, and comparative
modelling for the first and second Critical Assessment of Structure
Prediction (CASP1 and 2) experiments.
With John Moult. August 1993-August 1997.
- Research Intern at East Carolina University, Greenville, NC
doing theoretical and experimental work on analysing
genetic relationships between the Herpes Simplex Virus and the
Pseudo Rabies Virus. With Nels Pederson. Summer 1992.
- Research Intern at USDA laboratories, Delaware, Ohio performing
computational analysis of the performance of various drugs that
prevent Dutch Elm disease. With Steve Ishita. Spring 1992.
- Programming Languages, Operating Systems, Computer
Architecture, Structured Computer Organisation, Artificial
Intelligence, Algorithms and Data structures, Mathematical Foundations
of Computing Science, Compiler Theory and Design, Linear Algebra,
Numerical Analysis, and Combinatorics and Graph Theory.
- Programming languages: experience with several procedural
languages such as C/C++, FORTRAN, and Perl; functional languages such as
Lisp; and formatting languages such as TeX/LaTeX and SGML/HTML.
- Operating systems: experience with several flavours of Unix
(mainly Linux, Irix, OSF/1, and AIX), networking protocols, and
- Software: I have written several general freeware programs that
are used by the Internet community. As part of my research, I have
written programs that been used extensively in-house, and are
available as a freeware distribution, for prediction of protein
structure and function, both at the single molecule as well as the
- Solved several computing problems working as a computing
consultant for Information Systems, The Writing Resource Centre, and
the Politics and Government Department at Ohio Wesleyan (1990-1993),
and at the Centre for Advanced Research in Biotechnology
(1993-1997). Designed and implemented high-performance Linux-based
computing clusters at Stanford University (1997-2001) and the
University of Washington (2001-present).
- Molecular and Population Genetics, Developmental Biology, Bacterial
Physiology, Plant Structure Function and Systematics, Evolution,
Developmental Biology, Chemistry of Nucleic Acids, Protein Chemistry and Enzymic
Catalysis, Protein Structure and Function, Cell Biology, and
Biophysics and Theoretical/Computational Biology.
- Computational techniques: experience with modelling of DNA, RNA,
protein, and organismal structure, function, and evolution by simulation.
- Experimental techniques: experience with recombinant DNA technology
(cloning, expression, analysis of genetic material).
Box 357242, Department of Microbiology
University of Washington, Seattle, WA 98195-7242