Ram Samudrala - Publications

Affiliations: 
Microbiology University of Washington, Seattle, Seattle, WA 

113 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Fine J, Konc J, Samudrala R, Chopra G. CANDOCK: Chemical Atomic Network-based Hierarchical Flexible Docking Algorithm using Generalized Statistical Potentials. Journal of Chemical Information and Modeling. PMID 32069042 DOI: 10.1021/acs.jcim.9b00686  0.96
2019 Fine J, Lackner R, Samudrala R, Chopra G. Computational chemoproteomics to understand the role of selected psychoactives in treating mental health indications. Scientific Reports. 9: 13155. PMID 31511563 DOI: 10.1038/s41598-019-49515-0  0.96
2016 Chopra G, Kaushik S, Elkin PL, Samudrala R. Combating Ebola with Repurposed Therapeutics Using the CANDO Platform. Molecules (Basel, Switzerland). 21. PMID 27898018 DOI: 10.3390/molecules21121537  0.96
2016 Craig JK, Risler JK, Loesch KA, Dong W, Baker D, Barrett LK, Subramanian S, Samudrala R, Van Voorhis WC. Mycobacterium Cytidylate Kinase Appears to Be an Undruggable Target. Journal of Biomolecular Screening. PMID 27146385 DOI: 10.1177/1087057116646702  1
2016 Chopra G, Samudrala R. Exploring polypharmacology in drug discovery and repurposing using the CANDO platform. Current Pharmaceutical Design. PMID 27013226  0.96
2015 Manocheewa S, Mittler JE, Samudrala R, Mullins JI. Composite Sequence-Structure Stability Models as Screening Tools for Identifying Vulnerable Targets for HIV Drug and Vaccine Development. Viruses. 7: 5718-35. PMID 26556362 DOI: 10.3390/v7112901  1
2015 Sethi G, Chopra G, Samudrala R. Multiscale modelling of relationships between protein classes and drug behavior across all diseases using the CANDO platform. Mini Reviews in Medicinal Chemistry. 15: 705-17. PMID 25694071  0.96
2015 Sethi G, Chopra G, Samudrala R. Multiscale modelling of relationships between protein classes and drug behavior across all diseases using the CANDO platform Mini-Reviews in Medicinal Chemistry. 15: 705-717.  1
2014 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, ... ... Samudrala R, et al. Data access for the 1,000 Plants (1KP) project. Gigascience. 3: 17. PMID 25625010 DOI: 10.1186/2047-217X-3-17  1
2014 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: 1353-63. PMID 24980786 DOI: 10.1016/j.drudis.2014.06.018  1
2014 Hung LH, Samudrala R. fast_protein_cluster: parallel and optimized clustering of large-scale protein modeling data. Bioinformatics (Oxford, England). 30: 1774-6. PMID 24532722 DOI: 10.1093/bioinformatics/btu098  1
2013 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. PMID 24023924 DOI: 10.1371/journal.pone.0074053  1
2013 Laurenzi A, Hung LH, Samudrala R. Structure prediction of partial-length protein sequences. International Journal of Molecular Sciences. 14: 14892-907. PMID 23867606 DOI: 10.3390/ijms140714892  1
2013 Afzal AJ, Srour A, Goil A, Vasudaven S, Liu T, Samudrala R, Dogra N, Kohli P, Malakar A, Lightfoot DA. Homo-dimerization and ligand binding by the leucine-rich repeat domain at RHG1/RFS2 underlying resistance to two soybean pathogens Bmc Plant Biology. 13. PMID 23497186 DOI: 10.1186/1471-2229-13-43  1
2012 Martinez-Avila O, Wu S, Kim SJ, Cheng Y, Khan F, Samudrala R, Sali A, Horst JA, Habelitz S. Self-assembly of filamentous amelogenin requires calcium and phosphate: from dimers via nanoribbons to fibrils. Biomacromolecules. 13: 3494-502. PMID 22974364 DOI: 10.1021/bm300942c  1
2012 Goldman AD, Baross JA, Samudrala R. The enzymatic and metabolic capabilities of early life. Plos One. 7: e39912. PMID 22970111 DOI: 10.1371/journal.pone.0039912  1
2012 Horst JA, Pieper U, Sali A, Zhan L, Chopra G, Samudrala R, Featherstone JD. Strategic protein target analysis for developing drugs to stop dental caries. Advances in Dental Research. 24: 86-93. PMID 22899687 DOI: 10.1177/0022034512449837  1
2012 Gungormus M, Oren EE, Horst JA, Fong H, Hnilova M, Somerman MJ, Snead ML, Samudrala R, Tamerler C, Sarikaya M. Cementomimetics-constructing a cementum-like biomineralized microlayer via amelogenin-derived peptides. International Journal of Oral Science. 4: 69-77. PMID 22743342 DOI: 10.1038/ijos.2012.40  1
2012 Hung LH, Samudrala R. Accelerated protein structure comparison using TM-score-GPU Bioinformatics. 28: 2191-2192. PMID 22718788 DOI: 10.1093/bioinformatics/bts345  1
2012 Nazmul R, Chetty M, Samudrala R, Chalmers D. Protein structure prediction based on optimal hydrophobic core formation 2012 Ieee Congress On Evolutionary Computation, Cec 2012. DOI: 10.1109/CEC.2012.6256579  1
2012 Horst JA, Laurenzi A, Bernard B, Samudrala R. Computational Multitarget Drug Discovery Polypharmacology in Drug Discovery. 263-301. DOI: 10.1002/9781118098141.ch13  1
2011 Moughon SE, Samudrala R. LoCo: A novel main chain scoring function for protein structure prediction based on local coordinates Bmc Bioinformatics. 12. PMID 21920038 DOI: 10.1186/1471-2105-12-368  1
2011 Horst OV, Horst JA, Samudrala R, Dale BA. Caries induced cytokine network in the odontoblast layer of human teeth. Bmc Immunology. 12: 9. PMID 21261944 DOI: 10.1186/1471-2172-12-9  1
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. American Journal of Medical Genetics. Part A. 155: 91-7. PMID 21204214 DOI: 10.1002/ajmg.a.33781  1
2011 Nicholson CO, Costin JM, Rowe DK, Lin L, Jenwitheesuk E, Samudrala R, Isern S, Michael SF. Viral entry inhibitors block dengue antibody-dependent enhancement in vitro. Antiviral Research. 89: 71-4. PMID 21093488 DOI: 10.1016/j.antiviral.2010.11.008  1
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. PMID 20974833 DOI: 10.1128/IAI.00537-10  1
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. DOI: 10.1186/1756-0500-4-97  1
2010 Wang J, Zhang J, Li R, Zheng H, Li J, Zhang Y, Li H, Ni P, Li S, Li S, Wang J, Liu D, McDermott J, Samudrala R, Liu S, et al. Evolutionary transients in the rice transcriptome. Genomics, Proteomics & Bioinformatics. 8: 211-28. PMID 21382590 DOI: 10.1016/S1672-0229(10)60023-X  1
2010 Notman R, Oren EE, Tamerler C, Sarikaya M, Samudrala R, Walsh TR. Solution study of engineered quartz binding peptides using replica exchange molecular dynamics Biomacromolecules. 11: 3266-3274. PMID 20964422 DOI: 10.1021/bm100646z  1
2010 Horst JA, Wang K, Horst OV, Cunningham ML, Samudrala R. Disease risk of missense mutations using structural inference from predicted function. Current Protein & Peptide Science. 11: 573-88. PMID 20887259 DOI: 10.2174/138920310794109139  1
2010 Horst JA, Samudrala R. A protein sequence meta-functional signature for calcium binding residue prediction. Pattern Recognition Letters. 31: 2103-2112. PMID 20824111 DOI: 10.1016/j.patrec.2010.04.012  1
2010 Costin JM, Jenwitheesuk E, Lok SM, 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. PMID 20582308 DOI: 10.1371/journal.pntd.0000721  1
2010 Oren EE, Notman R, Kim IW, Evans JS, Walsh TR, Samudrala R, Tamerler C, Sarikaya M. Probing the molecular mechanisms of quartz-binding peptides Langmuir. 26: 11003-11009. PMID 20499870 DOI: 10.1021/la100049s  1
2010 Goldman AD, Samudrala R, Baross JA. The evolution and functional repertoire of translation proteins following the origin of life Biology Direct. 5. PMID 20377891 DOI: 10.1186/1745-6150-5-15  1
2010 Borlee BR, Goldman AD, Murakami K, Samudrala R, Wozniak DJ, Parsek MR. Pseudomonas aeruginosa uses a cyclic-di-GMP-regulated adhesin to reinforce the biofilm extracellular matrix. Molecular Microbiology. 75: 827-42. PMID 20088866 DOI: 10.1111/j.1365-2958.2009.06991.x  1
2010 McDermott J, Samudrala R. Plenary presentation: Bioinformatic characterization of plant networks Asia-Pacific Journal of Molecular Biology and Biotechnology. 18: 15-21.  1
2009 Goldman AD, Leigh JA, Samudrala R. Comprehensive computational analysis of Hmd enzymes and paralogs in methanogenic Archaea Bmc Evolutionary Biology. 9. PMID 19671178 DOI: 10.1186/1471-2148-9-199  1
2009 Michino M, Abola E, Brooks CL, Dixon JS, Moult J, Stevens RC. Community-wide assessment of GPCR structure modelling and ligand docking: GPCR Dock 2008. Nature Reviews. Drug Discovery. 8: 455-63. PMID 19461661 DOI: 10.1038/nrd2877  1
2009 Liu T, Horst JA, Samudrala R. A novel method for predicting and using distance constraints of high accuracy for refining protein structure prediction. Proteins. 77: 220-34. PMID 19422061 DOI: 10.1002/prot.22434  1
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. PMID 19420059 DOI: 10.1093/nar/gkp306  1
2009 Samudrala R, Heffron F, McDermott JE. Accurate prediction of secreted substrates and identification of a conserved putative secretion signal for type III secretion systems. Plos Pathogens. 5: e1000375. PMID 19390620 DOI: 10.1371/journal.ppat.1000375  1
2009 Rashid I, McDermott J, Samudrala R. Inferring molecular interactions pathways from eQTL data. Methods in Molecular Biology (Clifton, N.J.). 541: 211-23. PMID 19381546 DOI: 10.1007/978-1-59745-243-4_10  1
2009 Guerquin M, McDermott J, Frazier Z, Samudrala R. The Bioverse API and web application. Methods in Molecular Biology (Clifton, N.J.). 541: 511-34. PMID 19381533 DOI: 10.1007/978-1-59745-243-4_22  1
2009 Frazier Z, McDermott J, Guerquin M, Samudrala R. Computational representation of biological systems. Methods in Molecular Biology (Clifton, N.J.). 541: 535-49. PMID 19381532 DOI: 10.1007/978-1-59745-243-4_23  1
2009 Wichadakul D, McDermott J, Samudrala R. Prediction and integration of regulatory and protein-protein interactions. Methods in Molecular Biology (Clifton, N.J.). 541: 101-43. PMID 19381527 DOI: 10.1007/978-1-59745-243-4_6  1
2009 Bernard B, Samudrala R. A generalized knowledge-based discriminatory function for biomolecular interactions Proteins: Structure, Function and Bioinformatics. 76: 115-128. PMID 19127590 DOI: 10.1002/prot.22323  1
2008 Wang K, Horst JA, Cheng G, Nickle DC, Samudrala R. Protein meta-functional signatures from combining sequence, structure, evolution, and amino acid property information. Plos Computational Biology. 4: e1000181. PMID 18818722 DOI: 10.1371/journal.pcbi.1000181  1
2008 Liu T, Guerquin M, Samudrala R. Improving the accuracy of template-based predictions by mixing and matching between initial models Bmc Structural Biology. 8. PMID 18457597 DOI: 10.1186/1472-6807-8-24  1
2008 Jenkins C, Samudrala R, Geary SJ, Djordjevic SP. Structural and functional characterization of an organic hydroperoxide resistance protein from Mycoplasma gallisepticum Journal of Bacteriology. 190: 2206-2216. PMID 18192392 DOI: 10.1128/JB.01685-07  1
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. PMID 18190973 DOI: 10.1016/j.tips.2007.11.007  1
2008 Samudrala R, Oren EE, Cheng G, Horst J, Bernard B, Gungormus M, Hnilova M, Fong H, Tamerler C, Sarikaya M. Knowledge-based design of inorganic-binding peptides 5th Conference On Foundations of Nanoscience: Self-Assembled Architectures and Devices, Fnano 2008. 75-80.  1
2008 Evans JS, Samudrala R, Walsh TR, Oren EE, Tamerler C. Molecular design of inorganic-binding polypeptides Mrs Bulletin. 33: 514-518.  1
2007 Ngan SC, Hung LH, Liu T, Samudrala R. Scoring functions for de novo protein structure prediction revisited Methods in Molecular Biology. 413: 243-281. PMID 18075169  1
2007 Oren EE, Tamerler C, Sahin D, Hnilova M, Seker UOS, Sarikaya M, Samudrala R. A novel knowledge-based approach to design inorganic-binding peptides Bioinformatics. 23: 2816-2822. PMID 17875545 DOI: 10.1093/bioinformatics/btm436  1
2007 Jenwitheesuk E, Samudrala R. Identification of potential HIV-1 targets of minocycline Bioinformatics. 23: 2797-2799. PMID 17804437 DOI: 10.1093/bioinformatics/btm424  1
2007 Chevance FFV, Takahashi N, Karlinsey JE, Gnerer J, Hirano T, Samudrala R, Aizawa SI, Hughes KT. The mechanism of outer membrane penetration by the eubacterial flagellum and implications for spirochete evolution Genes and Development. 21: 2326-2335. PMID 17761814 DOI: 10.1101/gad.1571607  1
2007 Bockhorst J, Lu F, Janes JH, Keebler J, Gamain B, Awadalla P, Su Xz, 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. PMID 17669514 DOI: 10.1016/j.molbiopara.2007.06.007  1
2007 Berube PM, Samudrala R, Stahl DA. Transcription of all amoC copies is associated with recovery of Nitrosomonas europaea from ammonia starvation. Journal of Bacteriology. 189: 3935-44. PMID 17384196 DOI: 10.1128/JB.01861-06  1
2006 Hung LH, Samudrala R. An automated assignment-free Bayesian approach for accurately identifying proton contacts from NOESY data Journal of Biomolecular Nmr. 36: 189-198. PMID 17016668 DOI: 10.1007/s10858-006-9082-1  1
2006 Wang K, Samudrala R. Incorporating background frequency improves entropy-based residue conservation measures Bmc Bioinformatics. 7. PMID 16916457 DOI: 10.1186/1471-2105-7-385  1
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. PMID 16845128 DOI: 10.1093/protein/gzl027  1
2006 Korotkova N, Le Trong I, Samudrala R, Korotkov K, Van Loy CP, Bui AL, Moseley SL, Stenkamp RE. Crystal structure and mutational analysis of the DaaE adhesin of Escherichia coli Journal of Biological Chemistry. 281: 22367-22377. PMID 16751628 DOI: 10.1074/jbc.M604646200  1
2006 Wang K, Samudrala R. Automated functional classification of experimental and predicted protein structures Bmc Bioinformatics. 7. PMID 16749925 DOI: 10.1186/1471-2105-7-278  1
2006 Wang K, Mittler JE, Samudrala R. Comment on "Evidence for positive epistasis in HIV-1". Science (New York, N.Y.). 312: 848; author reply 84. PMID 16690844 DOI: 10.1126/science.1109904  1
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. PMID 16621067 DOI: 10.1016/j.molbiopara.2006.03.004  1
2006 Chang AN, McDermott J, Frazier Z, Guerquin M, Samudrala R. INTEGRATOR: interactive graphical search of large protein interactomes over the Web. Bmc Bioinformatics. 7: 146. PMID 16542421 DOI: 10.1186/1471-2105-7-146  1
2006 Ngan SC, Inouye MT, Samudrala R. A knowledge-based scoring function based on residue triplets for protein structure prediction Protein Engineering, Design and Selection. 19: 187-193. PMID 16533801 DOI: 10.1093/protein/gzj018  1
2006 Tamerler C, Schwartz D, Samudrala R, Ginger D, Parviz B, Traxler B, Xia Y, Jen A, Baneyx F, Evans J, Sarikaya M. Gepi - Genetically engineered polypeptides for inorganics: Peptide-based molecular tool set 3rd Conference On Foundations of Nanoscience: Self-Assembled Architectures and Devices, Fnano 2006. 182-183.  1
2005 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. PMID 16430194  1
2005 Cheng G, Qian B, Samudrala R, Baker D. Improvement in protein functional site prediction by distinguishing structural and functional constraints on protein family evolution using computational design. Nucleic Acids Research. 33: 5861-7. PMID 16224101 DOI: 10.1093/nar/gki894  1
2005 Jenwitheesuk E, Samudrala R. Identification of potential multitarget antimalarial drugs [4] Journal of the American Medical Association. 294: 1490-1491. PMID 16189361 DOI: 10.1001/jama.294.12.1490  1
2005 Liu T, Jenwitheesuk E, Teller DC, Samudrala R. Structural insights into the cellular retinaldehyde-binding protein (CRALBP). Proteins. 61: 412-22. PMID 16121400 DOI: 10.1002/prot.20621  1
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, et al. Origin and evolution of new exons in rodents. Genome Research. 15: 1258-64. PMID 16109974 DOI: 10.1101/gr.3929705  1
2005 Hung LH, Ngan SC, Liu T, Samudrala R. PROTINFO: New algorithms for enhanced protein structure predictions Nucleic Acids Research. 33: W77-W80. PMID 15980581 DOI: 10.1093/nar/gki403  1
2005 McDermott J, Guerquin M, Frazier Z, Chang AN, Samudrala R. BIOVERSE: enhancements to the framework for structural, functional and contextual modeling of proteins and proteomes. Nucleic Acids Research. 33: W324-5. PMID 15980482 DOI: 10.1093/nar/gki401  1
2005 McDermott J, Bumgarner R, Samudrala R. Functional annotation from predicted protein interaction networks. Bioinformatics (Oxford, England). 21: 3217-26. PMID 15919725 DOI: 10.1093/bioinformatics/bti514  1
2005 Wang K, Samudrala R. FSSA: A novel method for identifying functional signatures from structural alignments Bioinformatics. 21: 2969-2977. PMID 15860561 DOI: 10.1093/bioinformatics/bti471  1
2005 Jenwitheesuk E, Wang K, Mittler JE, Samudrala R. PIRSpred: a web server for reliable HIV-1 protein-inhibitor resistance/susceptibility prediction. Trends in Microbiology. 13: 150-1. PMID 15817383 DOI: 10.1016/j.tim.2005.02.003  1
2005 Jenwitheesuk E, Samudrala R. Virtual screening of HIV-1 protease inhibitors against human cytomegalovirus protease using docking and molecular dynamics Aids. 19: 529-531. PMID 15764860  1
2005 Jenwitheesuk E, Samudrala R. Prediction of HIV-1 protease inhibitor resistance using a protein-inhibitor flexible docking approach Antiviral Therapy. 10: 157-166. PMID 15751773  1
2005 Chang AN, McDermott J, Samudrala R. An enhanced Java graph applet interface for visualizing interactomes. Bioinformatics (Oxford, England). 21: 1741-2. PMID 15613388 DOI: 10.1093/bioinformatics/bti237  1
2004 Ekwa-Ekoka C, Diaz GA, Carlson C, Hasegawa T, Samudrala R, Lim KC, Yabu JM, Levy B, Schnapp LM. Genomic organization and sequence variation of the human integrin subunit α8 gene (ITGA8) Matrix Biology. 23: 487-496. PMID 15579315 DOI: 10.1016/j.matbio.2004.08.005  1
2004 Wang K, Samudrala R, Mittler JE. Antivirogram or phenosense: a comparison of their reproducibility and an analysis of their correlation. Antiviral Therapy. 9: 703-12. PMID 15535407  1
2004 Wang K, Samudrala R, Mittler JE. HIV-1 genotypic drug-resistance interpretation algorithms need to include hypersusceptibility-associated mutations. The Journal of Infectious Diseases. 190: 2055-6; author reply. PMID 15529272 DOI: 10.1086/423489  1
2004 Wang J, Zhang J, Zheng H, Li J, Liu D, Li H, Samudrala R, Yu J, Wong GKS. Mouse transcriptome: neutral evolution of 'non-coding' complementary DNAs. Nature. 431: 1 p following 757; d. PMID 15495343  1
2004 Jenwitheesuk E, Wang K, Mittler JE, Samudrala R. Improved accuracy of HIV-1 genotypic susceptibility interpretation using a consensus approach. Aids (London, England). 18: 1858-9. PMID 15316352 DOI: 10.1097/00002030-200409030-00020  1
2004 Wang K, Jenwitheesuk E, Samudrala R, Mittler JE. Simple linear model provides highly accurate genotypic predictions of HIV-1 drug resistance. Antiviral Therapy. 9: 343-52. PMID 15259897  1
2004 Wang K, Fain B, Levitt M, Samudrala R. Improved protein structure selection using decoy-dependent discriminatory functions. Bmc Structural Biology. 4: 8. PMID 15207004 DOI: 10.1186/1472-6807-4-8  1
2004 Wang K, Samudrala R, Mittler J, Qari S, Heneine W, Hellmann N, Bacheler L. Weak Agreement between Antivirogram and PhenoSense Assays in Predicting Reduced Susceptibility to Antiretroviral Drugs [3] (multiple letters) Journal of Clinical Microbiology. 42: 2353-2354. PMID 15131234 DOI: 10.1128/JCM.42.5.2353-2354.2004  1
2004 McDermott J, Samudrala R, Date SV, Marcotte EM. Enhanced functional information from predicted protein networks Trends in Biotechnology. 22: 60-63. PMID 14757037 DOI: 10.1016/j.tibtech.2003.11.010  1
2003 Jenwitheesuk E, Samudrala R. Identifying inhibitors of the SARS coronavirus proteinase Bioorganic and Medicinal Chemistry Letters. 13: 3989-3992. PMID 14592491 DOI: 10.1016/j.bmcl.2003.08.066  1
2003 McDermott J, Samudrala R. Bioverse: Functional, structural and contextual annotation of proteins and proteomes Nucleic Acids Research. 31: 3736-3737. PMID 12824406 DOI: 10.1093/nar/gkg550  1
2003 Hung LH, Samudrala R. PROTINFO: Secondary and tertiary protein structure Nucleic Acids Research. 31: 3296-3299. PMID 12824311 DOI: 10.1093/nar/gkg541  1
2003 Hung LH, Samudrala R. Accurate and automated classification of protein secondary structure with PsiCSI Protein Science. 12: 288-295. PMID 12538892 DOI: 10.1110/ps.0222303  1
2003 Jenwitheesuk E, Samudrala R. Improved prediction of HIV-1 protease-inhibitor binding energies by molecular dynamics simulations Bmc Structural Biology. 3: 1-9. DOI: 10.1186/1472-6807-3-1  1
2002 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 bacterial genus Prosthecobacter. Proceedings of the National Academy of Sciences of the United States of America. 99: 17049-54. PMID 12486237 DOI: 10.1073/pnas.012516899  1
2002 Samudrala R, Levitt M. A comprehensive analysis of 40 blind protein structure predictions. Bmc Structural Biology. 2: 3. PMID 12150712  1
2002 Van Loy CP, Sokurenko EV, Samudrala R, Moseley SL. Identification of amino acids in the Dr adhesin required for binding to decay-accelerating factor. Molecular Microbiology. 45: 439-52. PMID 12123455 DOI: 10.1046/j.1365-2958.2002.03022.x  1
2002 Samudrala R. Modeling genome structure and function Pure and Applied Chemistry. 74: 907-914.  1
2000 Huang ES, Samudrala R, Park BH. Scoring functions for ab initio protein structure prediction. Methods in Molecular Biology (Clifton, N.J.). 143: 223-45. PMID 11084908 DOI: 10.1385/1-59259-368-2:223  1
2000 Samudrala R, Levitt M. Decoys 'R' Us: a database of incorrect conformations to improve protein structure prediction. Protein Science : a Publication of the Protein Society. 9: 1399-401. PMID 10933507 DOI: 10.1110/ps.9.7.1399  1
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. 13: 453-7. PMID 10906341  1
2000 Samudrala R, Xia Y, Levitt M, Cotton NJ, Huang ES, Davis R. Probing structure-function relationships of the DNA polymerase alpha-associated zinc-finger protein using computational approaches. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 179-90. PMID 10902167  1
2000 Xia Y, Huang ES, Levitt M, Samudrala R. Ab initio construction of protein tertiary structures using a hierarchical approach. Journal of Molecular Biology. 300: 171-85. PMID 10864507 DOI: 10.1006/jmbi.2000.3835  1
1999 Samudrala R, Xia Y, Huang E, Levitt M. Ab initio protein structure prediction using a combined hierarchical approach. Proteins. 194-8. PMID 10526368 DOI: 10.1002/(SICI)1097-0134(1999)37:3+<194::AID-PROT24>3.0.CO;2-F  1
1999 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: 267-81. PMID 10388572 DOI: 10.1006/jmbi.1999.2861  1
1999 Samudrala R, Xia Y, Levitt M, Huang ES. A combined approach for ab initio construction of low resolution protein tertiary structures from sequence. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 505-16. PMID 10380223  1
1998 Samudrala R, Moult J. Determinants of side chain conformational preferences in protein structures Protein Engineering. 11: 991-997. PMID 9876919  1
1998 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 : a Publication of the Protein Society. 7: 1998-2003. PMID 9761481 DOI: 10.1002/pro.5560070916  1
1998 Samudrala R, Moult J. A graph-theoretic algorithm for comparative modeling of protein structure Journal of Molecular Biology. 279: 287-302. PMID 9636717 DOI: 10.1006/jmbi.1998.1689  1
1998 Samudrala R, Moult J. An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction Journal of Molecular Biology. 275: 895-916. PMID 9480776 DOI: 10.1006/jmbi.1997.1479  1
1997 Samudrala R, Moult J. Handling context-sensitivity in protein structures using graph theory: Bona fide prediction Proteins: Structure, Function and Genetics. 29: 43-49. PMID 9485494 DOI: 10.1002/(SICI)1097-0134(1997)1+<43::AID-PROT7>3.0.CO;2-P  1
1995 Samudrala R, Pedersen JT, Zhou HB, Luo R, Fidelis K, Moult J. Confronting the problem of interconnected structural changes in the comparative modeling of proteins Proteins: Structure, Function and Genetics. 23: 327-336. PMID 8710826 DOI: 10.1002/prot.340230307  1
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