image

  1. Protein structure modeling.

    Schwede T, Sali A, Eswar N, Peitsch MC.
    In Computational Structural Biology. 2008. (Eds: Schwede T, Peitsch MC).
    World Scientific Publishing Co Ltd, Singapore.

  2. Comparative protein structure modeling using MODELLER.

    Eswar N, Webb B, Marti-Renom MA, Madhusudhan MS, Eramian D, Shen MY, Pieper U and Sali A
    In Current Protocols in Protein Science. 2007. (Eds: Coligan JE, Dunn BM, Speicher DW, Wingfield PT). Unit 2.9. pp 2.9.1-31.
    John Wiley & Sons, Inc.

  3. Structure of the mammalian 80S ribosome at 8.7Å resolution.

    Chandramouli P, Topf M*, Ménéret JF*, Eswar N*, Gutell RR, Sali A and Akey CW.
    Structure. 2008. 16:535-548.
    (*These authors contributed equally to this work).

  4. Prediction of enzyme function by combining sequence similarity and protein interactions.

    Espadler J, Eswar N, Querol E, Avilés FX, Sali A, Marti-Renom MA, Oliva B.
    BMC Bioinformatics. 2008. (In press)

  5. Host-pathogen protein interactions predicted by structure.

    Davis FP, Barkan DT, Eswar N, McKerrow JH and Sali A.
    Protein Sci. 2007. 16:1-12.

  6. Protein structure modeling with MODELLER.

    Eswar N, Eramian D, Webb B, Shen MY, Sali A
    In Methods in Molecular Biology: Structural Proteomics - High-throughput Methods. 2007. (Eds: Kobe B, Guss M, Huber T).
    Humana Press Inc, USA.

  7. Comparative modeling of drug target proteins.

    Eswar N and Sali A
    In Comprehensive Medicinal Chemistry II. 2007. (Eds: Taylor JB, Triggle DJ). pp 215-236.
    Elsevier Ltd, Oxford, UK.

  8. DBAli tools: mining the protein structure space.

    Marti-Renom MA, Pieper U, Madhusudhan MS, Rossi A, Eswar N, Davis FP, Al-Shahrour F, Dopazo J and Sali A.
    Nucleic Acids Res. 2007. 35:W393-397.

  9. Comparative protein structure modeling using Modeller.

    Eswar N, Webb B, Marti-Renom MA, Madhusudhan MS, Eramian D, Shen MY, Pieper U and Sali A
    In Current Protocols in Bioinformatics. 2006. (Eds: Baxevanis AD, Petsko GA, Stein LD, Stormo GD). Unit 5.6. pp 5.6.1-30.
    John Wiley & Sons, Inc.

  10. Simple fold composition and modular architecture of the nuclear pore complex.

    Devos D, Dokudovskaya S, Williams R, Alber F, Eswar N, Chait BT, Rout MP, Sali A.
    Proc Natl Acad Sci USA. 2006. 103:2172-2177.

  11. Comparative protein structure modeling.

    Madhusudhan MS, Marti-Renom MA, Eswar N, John B, Pieper U, Karchin R, Shen MY and Sali A
    In The Proteomics Protocols Handbook. 2005. (Ed: Walker JM). pp 831-860.
    Humana Press Inc, USA.

  12. MODBASE: a database of annotated comparative protein structure models and associated resources.

    Pieper U, Eswar N, Davis FP, Braberg H, Madhusudhan MS, Rossi A, Marti-Renom M, Karchin R, Webb BM, Eramian D, Shen MY, Kelly L, Melo F, Sali A.
    Nucleic Acids Res. 2006. 34:D291-295.

  13. The C-type lectin fold as an evolutionary solution for massive sequence variation.

    McMahon SA, Miller JL, Lawton JA, Kerkow DE, Hodes A, Marti-Renom MA, Doulatov S, Eswar N, Sali A, Miller JF, Ghosh P.
    Nat Struct Mol Biol. 2005. 12:886-892.

  14. LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources.

    Karchin R, Diekhans M, Kelly L, Thomas DJ, Pieper U, Eswar N, Haussler D, Sali A.
    Bioinformatics. 2005. 21:2814-2820.

  15. Detecting remotely related proteins by their interactions and sequence similarity.

    Espadaler J, Aragues R, Eswar N, Marti-Renom MA, Querol E, Aviles FX, Sali A, Oliva B.
    Proc Natl Acad Sci USA. 2005. 102:7151-7156.

  16. Structure determination of macromolecular complexes by experiment and computation.

    Alber F*, Eswar N* and Sali A.
    In Practical Bioinformatics. 2004. (Ed: Bujnicki JM). pp 73-96.
    Springer-Verlag, Germany.
    (*These authors contributed equally to this work).

  17. High-throughput computational and experimental techniques in structural genomics.

    Chance MR, Fiser A, Sali A, Pieper U, Eswar N, Xu G, Fajardo JE, Radhakannan T, Marinkovic N.
    Genome Res. 2004. 14:2145-2154.

  18. MODBASE, a database of annotated comparative protein structure models, and associated resources.

    Pieper U, Eswar N, Braberg H, Madhusudhan MS, Davis FP, Stuart AC, Mirkovic N, Rossi A, Marti-Renom MA, Fiser A, Webb B, Greenblatt D, Huang CC, Ferrin TE, Sali A.
    Nucleic Acids Res. 2004. 32:D217-222.

  19. Modeling structure from sequence.

    Marti-Renom MA, Fiser A, Madhusudhan MS, John B, Stuart AC, Eswar N, Pieper U, Mirkovic N, Shen MY and Sali A
    In Current Protocols in Bioinformatics. 2003. (Eds: Baxevanis AD, Petsko GA, Stein LD, Stormo GD). Unit 5.1.
    John Wiley & Sons, Inc.

  20. Study of the structural dynamics of the E coli 70S ribosome using real-space refinement.

    Gao H, Sengupta J, Valle M, Korostelev A, Eswar N, Stagg SM, Van Roey P, Agrawal RK, Harvey SC, Sali A, Chapman MS, Frank J.
    Cell. 2003. 113:789-801.

  21. Stranded in isolation: structural role of isolated extended strands in proteins.

    Eswar N, Ramakrishnan C, Srinivasan N.
    Protein Eng. 2003. 16:331-339.

  22. Tools for comparative protein structure modeling and analysis.

    Eswar N, John B, Mirkovic N, Fiser A, Ilyin VA, Pieper U, Stuart AC, Marti-Renom MA, Madhusudhan MS, Yerkovich B, Sali A.
    Nucleic Acids Res. 2003. 31:3375-3380.

  23. EVA: Evaluation of protein structure prediction servers.

    Koh IY, Eyrich VA, Marti-Renom MA, Przybylski D, Madhusudhan MS, Eswar N, Grana O, Pazos F, Valencia A, Sali A, Rost B.
    Nucleic Acids Res. 2003. 31:3311-3315.

  24. Influence of solvent molecules on the stereochemical code of glycyl residues in proteins.

    Eswar N, Nagarajaram HA, Ramakrishnan C, Srinivasan N.
    Proteins. 2002. 49:326-334.

  25. Structural Genomics at the National Synchrotron Light Source.

    Rajashankar KR, Chance MR, Burley SK, Jiang J, Almo SC, Bresnick A, Dodatko T, Huang R, He G, Chen,H, Sullivan M, Toomey J, Thirumuruhan RA, Franklin WA, Sali A, Pieper U, Eswar N, Ilyin V, McMahan L.
    NSLS Activity Report 2001. 2:28-32.

  26. Structural genomics: a pipeline for providing structures for the biologist.

    Chance MR, Bresnick AR, Burley SK, Jiang JS, Lima CD, Sali A, Almo SC, Bonanno JB, Buglino JA, Boulton S, Chen H, Eswar N, He G, Huang R, Ilyin V, McMahan L, Pieper U, Ray S, Vidal M, Wang LK.
    Protein Sci. 2002. 11:723-738.

  27. MODBASE, a database of annotated comparative protein structure models.

    Pieper U, Eswar N, Stuart AC, Ilyin VA, Sali A.
    Nucleic Acids Res. 2002. 30:255-259.

  28. Structure of the 80S ribosome from Saccharomyces cerevisiae--tRNA-ribosome and subunit-subunit interactions.

    Spahn CM, Beckmann R, Eswar N, Penczek PA, Sali A, Blobel G, Frank J.
    Cell. 2001. 107:373-386.

  29. Architecture of the protein-conducting channel associated with the translating 80S ribosome.

    Beckmann R, Spahn CM, Eswar N, Helmers J, Penczek PA, Sali A, Frank J, Blobel G.
    Cell. 2001. 107:361-372.

  30. Structural genomics of enzymes involved in sterol/isoprenoid biosynthesis.

    Bonanno JB, Edo C, Eswar N, Pieper U, Romanowski MJ, Ilyin V, Gerchman SE, Kycia H, Studier FW, Sali A, Burley SK.
    Proc Natl Acad Sci USA. 2001. 98:12896-12901.

  31. Homology-based annotation yields 1,042 new candidate genes in the Drosophila melanogaster genome.

    Gopal S, Schroeder M, Pieper U, Sczyrba A, Aytekin-Kurban G, Bekiranov S, Fajardo JE, Eswar N, Sanchez R, Sali A, Gaasterland T.
    Nat Genet. 2001. 27:337-340.

  32. Protein structure modeling for structural genomics.

    Sanchez R, Pieper U, Melo F, Eswar N, Marti-Renom MA, Madhusudhan MS, Mirkovic N, Sali A.
    Nat Struct Biol. 2000.7:986-990.

  33. Deterministic features of side-chain main-chain hydrogen bonds in globular protein structures.

    Eswar N, Ramakrishnan C.
    Protein Eng. 2000. 13:227-238.

  34. Non-repetitive structures in proteins: Effects of side-chain and solvent interactions with the backbone.

    Eswar, N.
    Indian Institute of Science, Bangalore, India. 2000; 574.19296 P Thesis G15876.

  35. Occurrences of left-handed α-helical conformations in protein strucure.

    Eswar N and Ramakrishnan C.
    In Perspectives in Structural Biology. 1999. (Eds: Vijayan M, Yathindra N, and Kolaskar AS).
    Universities Press, Hyderabad, India.

  36. Prediction of the maximal stability temperature of monomeric globular proteins solely from amino acid sequence.

    Ganesh C, Eswar N, Srivastava S, Ramakrishnan C, Varadarajan R.
    FEBS Lett. 1999. 454:31-36.

  37. Secondary structures without backbone: an analysis of backbone mimicry by polar side chains in protein structures.

    Eswar N, Ramakrishnan C.
    Protein Eng. 1999. 12:447-455.