Andras Fiser

Summary

Publications

  1. ncbi request reprint ModLoop: automated modeling of loops in protein structures
    Andras Fiser
    Department of Biochemistry and Seaver Foundation Center for Bioinformatics, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY 10461, USA
    Bioinformatics 19:2500-1. 2003
  2. ncbi request reprint Protein structure modeling in the proteomics era
    Andras Fiser
    Department of Biochemistry, Seaver Foundation Center for Bioinformatics, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY 10461, USA
    Expert Rev Proteomics 1:97-110. 2004
  3. pmc Computational analysis and experimental validation of gene predictions in Toxoplasma gondii
    Joseph M Dybas
    Biodefense Proteomics Research Center, Albert Einstein College of Medicine, Bronx, New York, United States of America
    PLoS ONE 3:e3899. 2008
  4. pmc Distinct pose of discodermolide in taxol binding pocket drives a complementary mode of microtubule stabilization
    Marina Khrapunovich-Baine
    Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
    Biochemistry 48:11664-77. 2009
  5. pmc Comprehensive proteomic analysis of membrane proteins in Toxoplasma gondii
    Fa Yun Che
    Department of Pathology, Biodefense Proteomics Research Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
    Mol Cell Proteomics 10:M110.000745. 2011
  6. pmc Post-translational modifications to Toxoplasma gondii alpha- and beta-tubulins include novel C-terminal methylation
    Hui Xiao
    Departments of Pathology, Laboratory for Macromolecular Analysis and Proteomics, Albert Einstein College of Medicine, Bronx, New York 10461, USA
    J Proteome Res 9:359-72. 2010
  7. pmc EPIC-DB: a proteomics database for studying Apicomplexan organisms
    Carlos J Madrid-Aliste
    Biodefense Proteomics Research Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
    BMC Genomics 10:38. 2009
  8. pmc Identification of a functionally critical GXXG motif and its relationship to the folate binding site of the proton-coupled folate transporter (PCFT-SLC46A1)
    Rongbao Zhao
    Depts of Medicine and Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
    Am J Physiol Cell Physiol 303:C673-81. 2012
  9. pmc Hallmarks of molecular action of microtubule stabilizing agents: effects of epothilone B, ixabepilone, peloruside A, and laulimalide on microtubule conformation
    Marina Khrapunovich-Baine
    Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
    J Biol Chem 286:11765-78. 2011
  10. ncbi request reprint Comparative protein structure modeling by combining multiple templates and optimizing sequence-to-structure alignments
    Narcis Fernandez-Fuentes
    Department of Biochemistry and Seaver Center for Bioinformatics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
    Bioinformatics 23:2558-65. 2007

Collaborators

Detail Information

Publications49

  1. ncbi request reprint ModLoop: automated modeling of loops in protein structures
    Andras Fiser
    Department of Biochemistry and Seaver Foundation Center for Bioinformatics, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY 10461, USA
    Bioinformatics 19:2500-1. 2003
    ..For a rapid response, ModLoop runs on a cluster of Linux PC computers...
  2. ncbi request reprint Protein structure modeling in the proteomics era
    Andras Fiser
    Department of Biochemistry, Seaver Foundation Center for Bioinformatics, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY 10461, USA
    Expert Rev Proteomics 1:97-110. 2004
    ..The current state and recent advances in structure modeling approaches are reviewed here, with special emphasis on comparative protein structure modeling techniques...
  3. pmc Computational analysis and experimental validation of gene predictions in Toxoplasma gondii
    Joseph M Dybas
    Biodefense Proteomics Research Center, Albert Einstein College of Medicine, Bronx, New York, United States of America
    PLoS ONE 3:e3899. 2008
    ..An essential step towards understanding molecular mechanisms controlling transitions between the various life stages and identifying candidate drug targets is to accurately characterize the T. gondii proteome...
  4. pmc Distinct pose of discodermolide in taxol binding pocket drives a complementary mode of microtubule stabilization
    Marina Khrapunovich-Baine
    Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
    Biochemistry 48:11664-77. 2009
    ..Also, our results indicate complementary stabilizing effects of Taxol and discodermolide on the microtubules, which may explain the synergy observed between the two drugs in vivo...
  5. pmc Comprehensive proteomic analysis of membrane proteins in Toxoplasma gondii
    Fa Yun Che
    Department of Pathology, Biodefense Proteomics Research Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
    Mol Cell Proteomics 10:M110.000745. 2011
    ..gondii or to the Apicomplexa, providing a set of gene predictions ripe for experimental investigation, and potentially suitable targets for the development of therapeutic strategies...
  6. pmc Post-translational modifications to Toxoplasma gondii alpha- and beta-tubulins include novel C-terminal methylation
    Hui Xiao
    Departments of Pathology, Laboratory for Macromolecular Analysis and Proteomics, Albert Einstein College of Medicine, Bronx, New York 10461, USA
    J Proteome Res 9:359-72. 2010
    ..Methylation, a PTM not previously described on tubulin, was also detected. Methylated tubulins were not detected in the host cells, human foreskin fibroblasts, suggesting that this may be a modification specific to the Apicomplexa...
  7. pmc EPIC-DB: a proteomics database for studying Apicomplexan organisms
    Carlos J Madrid-Aliste
    Biodefense Proteomics Research Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
    BMC Genomics 10:38. 2009
    ..High throughput methods necessitate publicly accessible and easily queried databases for efficiently and logically storing, displaying, and analyzing the large volume of data...
  8. pmc Identification of a functionally critical GXXG motif and its relationship to the folate binding site of the proton-coupled folate transporter (PCFT-SLC46A1)
    Rongbao Zhao
    Depts of Medicine and Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
    Am J Physiol Cell Physiol 303:C673-81. 2012
    ..The functional role of residues around Gly-189 and Gly-192 is consistent with a molecular structural model in which these two residues along with Ieu-188 are accessible to the PCFT aqueous translocation pathway...
  9. pmc Hallmarks of molecular action of microtubule stabilizing agents: effects of epothilone B, ixabepilone, peloruside A, and laulimalide on microtubule conformation
    Marina Khrapunovich-Baine
    Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
    J Biol Chem 286:11765-78. 2011
    ....
  10. ncbi request reprint Comparative protein structure modeling by combining multiple templates and optimizing sequence-to-structure alignments
    Narcis Fernandez-Fuentes
    Department of Biochemistry and Seaver Center for Bioinformatics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
    Bioinformatics 23:2558-65. 2007
    ..Two major bottlenecks in advancing comparative protein structure modeling are the efficient combination of multiple template structures and the generation of a correct input target-template alignment...
  11. pmc M4T: a comparative protein structure modeling server
    Narcis Fernandez-Fuentes
    Department of Biochemistry and Seaver Foundation Center for Bioinformatics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
    Nucleic Acids Res 35:W363-8. 2007
    ..The performance of M4T was benchmarked on CASP6 comparative modeling target sequences and on a larger independent test set and showed a favorable performance to current state-of-the-art methods...
  12. ncbi request reprint MMM: a sequence-to-structure alignment protocol
    Brajesh K Rai
    Department of Biochemistry and Seaver Center for Bioinformatics, Albert Einstein College of Medicine 1300 Morris Park Avenue, Bronx, NY 10461, USA
    Bioinformatics 22:2691-2. 2006
    ..Accurate alignment of a target sequence to a template structure continues to be a bottleneck in producing good quality comparative protein structure models...
  13. pmc Functional roles of the A335 and G338 residues of the proton-coupled folate transporter (PCFT-SLC46A1) mutated in hereditary folate malabsorption
    Daniel Sanghoon Shin
    Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
    Am J Physiol Cell Physiol 303:C834-42. 2012
    ..The data illustrate how alterations in carrier cycling can impact influx K(t) without comparable alterations in substrate binding to the carrier...
  14. pmc Photo-assisted peptide enrichment in protein complex cross-linking analysis of a model homodimeric protein using mass spectrometry
    Funing Yan
    Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
    Proteomics 11:4109-15. 2011
    ..These technical improvements allow this method to be used for investigating protein-protein interactions in complex biological samples...
  15. doi request reprint Improved scoring function for comparative modeling using the M4T method
    Dmitry Rykunov
    Department of Systems and Computational Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY 10461, USA
    J Struct Funct Genomics 10:95-9. 2009
    ..The accuracy of the scoring function was further increased by using BLOSUM mutation table scores...
  16. ncbi request reprint Modeller: generation and refinement of homology-based protein structure models
    Andras Fiser
    Department of Biochemistry and Seaver Foundation Center for Bioinformatics, Albert Einstein College of Medicine, Bronz, New York 10461, USA
    Methods Enzymol 374:461-91. 2003
  17. pmc Role of the fourth transmembrane domain in proton-coupled folate transporter function as assessed by the substituted cysteine accessibility method
    Daniel Sanghoon Shin
    Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
    Am J Physiol Cell Physiol 304:C1159-67. 2013
    ....
  18. pmc A supersecondary structure library and search algorithm for modeling loops in protein structures
    Narcis Fernandez-Fuentes
    Department of Biochemistry and Seaver Foundation Center for Bioinformatics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
    Nucleic Acids Res 34:2085-97. 2006
    ..47 A of r.m.s.d. accuracy, respectively. In a head-to-head comparison on loops extracted from freshly deposited new protein folds the current method outperformed in a approximately 5:1 ratio an earlier developed database search method...
  19. pmc A P425R mutation of the proton-coupled folate transporter causing hereditary folate malabsorption produces a highly selective alteration in folate binding
    Daniel Sanghoon Shin
    Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
    Am J Physiol Cell Physiol 302:C1405-12. 2012
    ..Hence, despite its location, the P425R-PCFT mutation produces a conformational change that fully preserves pemetrexed binding but markedly impairs binding of methotrexate and other folates to the carrier...
  20. ncbi request reprint Multiple mapping method: a novel approach to the sequence-to-structure alignment problem in comparative protein structure modeling
    Brajesh K Rai
    Department of Biochemistry and Seaver Center for Bioinformatics, Albert Einstein College of Medicine, Bronx, New York 10461, USA
    Proteins 63:644-61. 2006
    ..MMM also compared favorably over two alignment meta-servers. The algorithm is computationally efficient; therefore, it is a suitable tool for genome scale modeling studies...
  21. pmc ArchPRED: a template based loop structure prediction server
    Narcis Fernandez-Fuentes
    Department of Biochemistry and Seaver Foundation Center for Bioinformatics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
    Nucleic Acids Res 34:W173-6. 2006
    ..47 A of r.m.s.d. accuracy, respectively. In a head to head comparison on loops extracted from freshly deposited new protein folds the current method outperformed in a approximately 5:1 ratio an earlier developed database search method...
  22. pmc Saturating representation of loop conformational fragments in structure databanks
    Narcis Fernandez-Fuentes
    Department of Biochemistry and Seaver Foundation Center for Bioinformatics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
    BMC Struct Biol 6:15. 2006
    ..The applicability and performance of these approaches depend on the availability of short fragments in structure databanks...
  23. pmc Exchanging murine and human immunoglobulin constant chains affects the kinetics and thermodynamics of antigen binding and chimeric antibody autoreactivity
    Marcela Torres
    Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, United States of America
    PLoS ONE 2:e1310. 2007
    ..These findings suggest that V region conformational changes can be dictated by the C(H) domains through an allosteric effect involving networks of highly connected amino acids...
  24. pmc Protein structure based prediction of catalytic residues
    J Eduardo Fajardo
    Department of Systems and Computational Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
    BMC Bioinformatics 14:63. 2013
    ..Worldwide structural genomics projects continue to release new protein structures at an unprecedented pace, so far nearly 6000, but only about 60% of these proteins have any sort of functional annotation...
  25. pmc Frozen tissue can provide reproducible proteomic results of subcellular fractionation
    Jihyeon Lim
    Laboratory for Macromolecular Analysis and Proteomics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
    Anal Biochem 418:78-84. 2011
    ..This demonstrates the feasibility of analyzing cellular compartment-specific proteins in archived tissue samples with the simple DDF method...
  26. pmc Nonprotein based enrichment method to analyze peptide cross-linking in protein complexes
    Funing Yan
    Department of Biochemistry, and Biodefense Proteomics Research Center, Albert Einstein College of Medicine, Bronx, New York 10461, USA
    Anal Chem 81:7149-59. 2009
    ..These features may make the method suitable to investigate protein-protein interactions in biological samples...
  27. pmc Functional roles of aspartate residues of the proton-coupled folate transporter (PCFT-SLC46A1); a D156Y mutation causing hereditary folate malabsorption
    Daniel Sanghoon Shin
    Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, USA
    Blood 116:5162-9. 2010
    ..Hence, D156 plays a critical role in PCFT protein stability, and D109, located in the first intracellular loop between the second and third transmembrane domains, is absolutely required for PCFT function...
  28. ncbi request reprint Effects of amino acid composition, finite size of proteins, and sparse statistics on distance-dependent statistical pair potentials
    Dmitry Rykunov
    Department of Biochemistry, Seaver Center for Bioinformatics, Albert Einstein College of Medicine, Bronx, New York 10461, USA
    Proteins 67:559-68. 2007
    ..A new definition for reference state, free of the observed systematic errors, is suggested. It has been demonstrated to generate statistical potentials that compare favorably to other publicly available ones...
  29. pmc New statistical potential for quality assessment of protein models and a survey of energy functions
    Dmitry Rykunov
    Department of Systems and Computational Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY 10461, USA
    BMC Bioinformatics 11:128. 2010
    ..Scoring functions, such as molecular mechanic forcefields and statistical potentials are fundamentally important tools in protein structure modeling and quality assessment...
  30. pmc Modeling proteins using a super-secondary structure library and NMR chemical shift information
    Vilas Menon
    Department of Systems and Computational Biology, Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
    Structure 21:891-9. 2013
    ..The current approach opens a venue to address the modeling of larger protein structures for which chemical shifts are available...
  31. pmc The ybeY protein from Escherichia coli is a metalloprotein
    Chenyang Zhan
    New York Structural Genomics Research Consortium NYSGXRC, Albert Einstein College of Medicine, Bronx, New York 10461, USA
    Acta Crystallogr Sect F Struct Biol Cryst Commun 61:959-63. 2005
    ....
  32. doi request reprint Template-based protein structure modeling
    Andras Fiser
    Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, USA
    Methods Mol Biol 673:73-94. 2010
    ..Strategies for template-based structure modeling will be discussed with a focus on comparative modeling, by reviewing techniques available for all the major steps involved in the comparative modeling pipeline...
  33. pmc Functional classification of immune regulatory proteins
    Rotem Rubinstein
    Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
    Structure 21:766-76. 2013
    ..The Brotherhood algorithm is likely to have a significant impact on structural immunology by identifying those proteins and complexes for which structural characterization will be particularly informative...
  34. doi request reprint Predicting disulfide bond connectivity in proteins by correlated mutations analysis
    Rotem Rubinstein
    Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
    Bioinformatics 24:498-504. 2008
    ..Prediction of disulfide bond connectivity facilitates structural and functional annotation of proteins. Previous studies suggest that cysteines of a disulfide bond mutate in a correlated manner...
  35. pmc Identification of linear epitopes in Bacillus anthracis protective antigen bound by neutralizing antibodies
    Nareen Abboud
    Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
    J Biol Chem 284:25077-86. 2009
    ..These results identify the first linear neutralizing epitopes of PA and show that peptides containing epitope sequences can elicit neutralizing antibody responses, a finding that could be exploited for vaccine design...
  36. pmc The functional roles of the His247 and His281 residues in folate and proton translocation mediated by the human proton-coupled folate transporter SLC46A1
    Ersin Selcuk Unal
    Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
    J Biol Chem 284:17846-57. 2009
    ..The His281 residue is not essential for proton coupling but plays an important role in PCFT protonation, which, in turn, augments folate binding to the carrier...
  37. ncbi request reprint The immunoglobulin heavy chain constant region affects kinetic and thermodynamic parameters of antibody variable region interactions with antigen
    Marcela Torres
    Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
    J Biol Chem 282:13917-27. 2007
    ..Furthermore, isotype affected the polyreactivity of V region identical antibodies, implying a role for C region in determining self-reactivity...
  38. ncbi request reprint Cell wall branches, penicillin resistance and the secrets of the MurM protein
    Andras Fiser
    Department of Biochemistry and Seaver Foundation Center for Bioinformatics, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY 10461, USA
    Trends Microbiol 11:547-53. 2003
    ..To understand these surprising observations a 3D-model of MurM was constructed, which helped to put into structural context several of the biochemical and genetic observations made about this protein...
  39. pmc A biochemical mechanism for the oncogenic potential of the p110beta catalytic subunit of phosphoinositide 3-kinase
    Hashem A Dbouk
    Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
    Proc Natl Acad Sci U S A 107:19897-902. 2010
    ..This study shows that the enhanced transforming potential of p110β is the result of its decreased inhibition by p85, due to the disruption of an inhibitory C2-iSH2 domain interface...
  40. pmc High-throughput computational and experimental techniques in structural genomics
    Mark R Chance
    New York Structural Genomics Research Consortium, Albert Einstein College of Medicine, Bronx, New York 10461, USA
    Genome Res 14:2145-54. 2004
    ..This projected resource will provide structural biology information important to understanding the function of most proteins of the cell...
  41. ncbi request reprint Structural genomics of protein phosphatases
    Steven C Almo
    Albert Einstein College of Medicine, Bronx, NY, USA
    J Struct Funct Genomics 8:121-40. 2007
    ....
  42. pmc Pentapeptide repeat proteins
    Matthew W Vetting
    Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, USA
    Biochemistry 45:1-10. 2006
    ..MfpA binds to DNA gyrase and inhibits its activity. The rod-shaped, dimeric protein exhibits remarkable similarity in size, shape, and electrostatics to DNA...
  43. pmc Pathogenic NAP57 mutations decrease ribonucleoprotein assembly in dyskeratosis congenita
    Petar N Grozdanov
    Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
    Hum Mol Genet 18:4546-51. 2009
    ..Pinpointing impaired interaction between NAP57 and SHQ1 as a potential molecular basis for X-linked DC has implications for therapeutic approaches, e.g. by targeting the NAP57-SHQ1 interface with small molecules...
  44. pmc Insights into the mechanism of microtubule stabilization by Taxol
    Hui Xiao
    Laboratory of Macromolecular Analysis and Proteomics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
    Proc Natl Acad Sci U S A 103:10166-73. 2006
    ..The present study also opens avenues for locating drug and protein binding sites and for deciphering the mechanisms by which their interactions alter the conformation of microtubules and tubulin dimers...
  45. pmc Toxoplasma gondii proteomics
    Louis M Weiss
    Division of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Forchheimer 504, 1300 Morris Park Avenue, Bronx, NY 10461, USA
    Expert Rev Proteomics 6:303-13. 2009
    ..Web-based resources, such as EPIC-DB and ToxoDB, provide proteomic data and support for studies on T. gondii. This review will summarize the current status of proteomic research on T. gondii...
  46. pmc The underlying molecular and network level mechanisms in the evolution of robustness in gene regulatory networks
    Mario Pujato
    Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, New York, United States of America
    PLoS Comput Biol 9:e1002865. 2013
    ..Meanwhile, in highly interconnected architectures (represented by long promoters), robustness evolves almost entirely via network level changes, deleting and creating binding sites that modify the network architecture...
  47. pmc Acetylsalicylic acid (aspirin) reduces damage to reconstituted human tissues infected with Candida species by inhibiting extracellular fungal lipases
    David Trofa
    Department of Medicine, Division of Infectious Diseases, Albert Einstein College of Medicine, 1300 Morris Park Avenue, NY 10461, USA
    Microbes Infect 11:1131-9. 2009
    ..parapsilosis in complex with ASA. The results suggest that development of inhibitors of fungal lipases could result in broad-spectrum therapeutics, especially since fungal lipases are not homologous to their human analogues...
  48. ncbi request reprint Structural basis of inducible costimulator ligand costimulatory function: determination of the cell surface oligomeric state and functional mapping of the receptor binding site of the protein
    Kausik Chattopadhyay
    Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
    J Immunol 177:3920-9. 2006
    ....
  49. pmc Evolutionary and biophysical relationships among the papillomavirus E2 proteins
    Dukagjin M Blakaj
    Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx NY 10461, USA
    Front Biosci (Landmark Ed) 14:900-17. 2009
    ..Rather, regions of high conservation are localized to small surface patches. Implications to cancer biology are discussed...