Sandor Vajda

Summary

Affiliation: Boston University
Country: USA

Publications

  1. ncbi request reprint Characterization of protein-ligand interaction sites using experimental and computational methods
    Sandor Vajda
    Department of Biomedical Engineering, Boston University and SolMap Pharmaceuticals, 44 Cummington Street, Boston, MA 02215, USA
    Curr Opin Drug Discov Devel 9:354-62. 2006
  2. pmc PRECISE: a Database of Predicted and Consensus Interaction Sites in Enzymes
    Shu Hsien Sheu
    Department of Biomedical Engineering and Program in Bioinformatics, Boston University, CA, USA
    Nucleic Acids Res 33:D206-11. 2005
  3. pmc Convergence and combination of methods in protein-protein docking
    Sandor Vajda
    BioMolecular Engineering Research Center, Department of Biomedical Engineering, Boston University, 44 Cummington Street, Boston, MA 02215, USA
    Curr Opin Struct Biol 19:164-70. 2009
  4. pmc Achieving reliability and high accuracy in automated protein docking: ClusPro, PIPER, SDU, and stability analysis in CAPRI rounds 13-19
    Dima Kozakov
    BioMolecular Engineering Research Center, Boston University, Boston, Massachusetts 02215, USA
    Proteins 78:3124-30. 2010
  5. ncbi request reprint Classification of protein complexes based on docking difficulty
    Sandor Vajda
    Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA
    Proteins 60:176-80. 2005
  6. ncbi request reprint Protein-protein docking: is the glass half-full or half-empty?
    Sandor Vajda
    Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
    Trends Biotechnol 22:110-6. 2004
  7. ncbi request reprint Docking with PIPER and refinement with SDU in rounds 6-11 of CAPRI
    Yang Shen
    BioMolecular Engineering Research Center, Boston University, Boston, Massachusetts 02215, USA
    Proteins 69:734-42. 2007
  8. ncbi request reprint ClusPro: performance in CAPRI rounds 6-11 and the new server
    Stephen R Comeau
    Dyax Corp, Cambridge, Massachusetts, USA
    Proteins 69:781-5. 2007
  9. ncbi request reprint Identification of substrate binding sites in enzymes by computational solvent mapping
    Michael Silberstein
    Program in Bioinformatics, Boston University, Boston, MA 02215, USA
    J Mol Biol 332:1095-113. 2003
  10. ncbi request reprint Performance of the first protein docking server ClusPro in CAPRI rounds 3-5
    Stephen R Comeau
    Bioinformatics Graduate Program, Boston University, Boston, Massachusetts, USA
    Proteins 60:239-44. 2005

Research Grants

Collaborators

Detail Information

Publications67

  1. ncbi request reprint Characterization of protein-ligand interaction sites using experimental and computational methods
    Sandor Vajda
    Department of Biomedical Engineering, Boston University and SolMap Pharmaceuticals, 44 Cummington Street, Boston, MA 02215, USA
    Curr Opin Drug Discov Devel 9:354-62. 2006
    ..Both methods can be used to reliably identify druggable sites on proteins and to facilitate the design of novel, low-nanomolar-affinity ligands...
  2. pmc PRECISE: a Database of Predicted and Consensus Interaction Sites in Enzymes
    Shu Hsien Sheu
    Department of Biomedical Engineering and Program in Bioinformatics, Boston University, CA, USA
    Nucleic Acids Res 33:D206-11. 2005
    ..The binding site information is essential for understanding and altering substrate specificity and for the design of enzyme inhibitors...
  3. pmc Convergence and combination of methods in protein-protein docking
    Sandor Vajda
    BioMolecular Engineering Research Center, Department of Biomedical Engineering, Boston University, 44 Cummington Street, Boston, MA 02215, USA
    Curr Opin Struct Biol 19:164-70. 2009
    ..Although each method is optimal for a specific class of docking problems, combining computational steps from different methods can improve the reliability and accuracy of results...
  4. pmc Achieving reliability and high accuracy in automated protein docking: ClusPro, PIPER, SDU, and stability analysis in CAPRI rounds 13-19
    Dima Kozakov
    BioMolecular Engineering Research Center, Boston University, Boston, Massachusetts 02215, USA
    Proteins 78:3124-30. 2010
    ..Third, despite occasional successes, homology modeling requires further improvement to achieve reliable docking results...
  5. ncbi request reprint Classification of protein complexes based on docking difficulty
    Sandor Vajda
    Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA
    Proteins 60:176-80. 2005
    ..The analysis indicates that CAPRI and other relatively large-scale docking studies represent very important steps toward understanding the capabilities and limitations of current protein-protein docking methods...
  6. ncbi request reprint Protein-protein docking: is the glass half-full or half-empty?
    Sandor Vajda
    Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
    Trends Biotechnol 22:110-6. 2004
    ..Transient complexes with large interface areas undergo substantial conformational change and are beyond the reach of current docking methods. The docking of such complexes might therefore require fundamentally new approaches...
  7. ncbi request reprint Docking with PIPER and refinement with SDU in rounds 6-11 of CAPRI
    Yang Shen
    BioMolecular Engineering Research Center, Boston University, Boston, Massachusetts 02215, USA
    Proteins 69:734-42. 2007
    ....
  8. ncbi request reprint ClusPro: performance in CAPRI rounds 6-11 and the new server
    Stephen R Comeau
    Dyax Corp, Cambridge, Massachusetts, USA
    Proteins 69:781-5. 2007
    ..PIPER is based on the fast Fourier transform correlation approach, but the method is extended to use pairwise interaction potentials, thereby increasing the number of near-native docked structures...
  9. ncbi request reprint Identification of substrate binding sites in enzymes by computational solvent mapping
    Michael Silberstein
    Program in Bioinformatics, Boston University, Boston, MA 02215, USA
    J Mol Biol 332:1095-113. 2003
    ..Calculations on ligand-bound and apo structures of enzymes show that the mapping results are not very sensitive to moderate variations in the protein coordinates...
  10. ncbi request reprint Performance of the first protein docking server ClusPro in CAPRI rounds 3-5
    Stephen R Comeau
    Bioinformatics Graduate Program, Boston University, Boston, Massachusetts, USA
    Proteins 60:239-44. 2005
    ..Not including targets that had a significant structural rearrangement upon binding, the success rate of ClusPro was found to be around 71%...
  11. pmc How good is automated protein docking?
    Dima Kozakov
    Department of Biomedical Engineering, Boston University, Boston, Massachusetts, 02215
    Proteins 81:2159-66. 2013
    ....
  12. ncbi request reprint Improved mapping of protein binding sites
    Tamas Kortvelyesi
    Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA
    J Comput Aided Mol Des 17:173-86. 2003
    ..Results show that most of the rotational states are separated by low free energy barriers at the experimental temperature, and hence the entropy of binding in the active site is expected to be high...
  13. pmc Protein-protein docking with reduced potentials by exploiting multi-dimensional energy funnels
    Ioannis Ch Paschalidis
    Center for Information and Systems Eng, and Dept of Manufacturing Eng, Boston University, Blookline, MA 2446, USA
    Conf Proc IEEE Eng Med Biol Soc 1:5330-3. 2006
    ..To achieve the same level of performance (produce a near-native < or =3 A RMSD complex) our approach reduces energy evaluations by more than a factor of two, on average...
  14. pmc Protein docking by the underestimation of free energy funnels in the space of encounter complexes
    Yang Shen
    Department of Biomedical Engineering, BioMolecular Engineering Research Center, Boston University, Boston, Massachusetts, United States of America
    PLoS Comput Biol 4:e1000191. 2008
    ....
  15. pmc Structural conservation of druggable hot spots in protein-protein interfaces
    Dima Kozakov
    Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
    Proc Natl Acad Sci U S A 108:13528-33. 2011
    ....
  16. pmc FTMAP: extended protein mapping with user-selected probe molecules
    Chi Ho Ngan
    Department of Biomedical Engineering, Boston University, 44 Cummington Street, Boston, MA 02215, USA
    Nucleic Acids Res 40:W271-5. 2012
    ..This approach helps to predict bound poses of the user-selected molecules, detects if a compound is not likely to bind in the hot spot region, and provides input for the design of larger ligands...
  17. pmc FTFlex: accounting for binding site flexibility to improve fragment-based identification of druggable hot spots
    Laurie E Grove
    Department of Sciences, Wentworth Institute of Technology, Boston, MA 01746, USA
    Bioinformatics 29:1218-9. 2013
    ..In cases where the mapping results of the apo and bound structures were in good agreement, no new structure was predicted...
  18. pmc Application of asymmetric statistical potentials to antibody-protein docking
    Ryan Brenke
    Department of Biomedical Engineering, Boston University, Boston, MA, USA
    Bioinformatics 28:2608-14. 2012
    ..Specifically, phenylalanine, tryptophan and tyrosine residues highly populate the paratope of the antibody but not the epitope of the antigen...
  19. pmc The structural basis of pregnane X receptor binding promiscuity
    Chi Ho Ngan
    Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA
    Biochemistry 48:11572-81. 2009
    ..Results also suggest a unique signal transduction mechanism between the PXR homodimerization interface and its coactivator binding site...
  20. ncbi request reprint ClusPro: an automated docking and discrimination method for the prediction of protein complexes
    Stephen R Comeau
    Bioinformatics Graduate Program and Department, Boston University, 44 Cummington St, Boston, MA 02215, USA
    Bioinformatics 20:45-50. 2004
    ..e. structures with good surface complementarity but far from the native...
  21. pmc Optimal clustering for detecting near-native conformations in protein docking
    Dima Kozakov
    Department of Biomedical Engineering, Boston University, Massachusetts, USA
    Biophys J 89:867-75. 2005
    ..We show that using this optimal radius further improves the discrimination of near-native complex structures...
  22. ncbi request reprint Algorithms for computational solvent mapping of proteins
    Tamas Kortvelyesi
    Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA
    Proteins 51:340-51. 2003
    ..We conclude that good sampling is the most important requirement for successful mapping, but accounting for desolvation and clustering of ligand positions also help to reduce the number of false positives...
  23. pmc Fragment-based identification of druggable 'hot spots' of proteins using Fourier domain correlation techniques
    Ryan Brenke
    Program in Bioinformatics, Boston University, Boston, MA, USA
    Bioinformatics 25:621-7. 2009
    ..Our goal is to determine the 'hot spots' computationally rather than experimentally...
  24. pmc Computational mapping reveals dramatic effect of Hoogsteen breathing on duplex DNA reactivity with formaldehyde
    Tanggis Bohnuud
    Graduate Program in Bioinformatics, Boston University, Boston, MA 02215, USA
    Nucleic Acids Res 40:7644-52. 2012
    ..The extensive literature on DNA interaction with formaldehyde is analyzed in light of the new findings. The obtained data emphasize the significance of DNA HG breathing...
  25. pmc Hot spot analysis for driving the development of hits into leads in fragment-based drug discovery
    David R Hall
    Department of Biomedical Engineering, Boston University, 44 Cummington Street, Boston, Massachusetts 02215, USA
    J Chem Inf Model 52:199-209. 2012
    ....
  26. pmc Analysis of protein binding sites by computational solvent mapping
    David R Hall
    Department of Biomedical Engineering, BioMolecular Engineering Research Center, Boston University, Boston, MA, USA
    Methods Mol Biol 819:13-27. 2012
    ..Due to its sensitivity to conformational changes, the method can also be used for comparing the binding sites in different structures of a protein...
  27. pmc Binding hot spots and amantadine orientation in the influenza a virus M2 proton channel
    Gwo Yu Chuang
    Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
    Biophys J 97:2846-53. 2009
    ....
  28. ncbi request reprint Identification of hot spots within druggable binding regions by computational solvent mapping of proteins
    Melissa R Landon
    Bioinformatics Graduate Program, Boston University, 24 Cummington Street, Boston, Massachusetts, USA
    J Med Chem 50:1231-40. 2007
    ..Based on our analyses, we conclude that the information provided by CS-Map can contribute substantially to the identification of hot spots, a necessary predecessor of fragment-based drug discovery efforts...
  29. ncbi request reprint Computational methods for functional site identification suggest a substrate access channel in transaldolase
    Michael Silberstein
    Graduate Program in Bioinformatics, Boston University, Boston, Massachusetts 02215, USA
    Genome Inform 17:13-22. 2006
    ..Further experimental procedures will be necessary to examine the biological feasibility of this proposed ligand shuttling path...
  30. pmc Relationship between hot spot residues and ligand binding hot spots in protein-protein interfaces
    Brandon S Zerbe
    Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA
    J Chem Inf Model 52:2236-44. 2012
    ..Hence, only a minority of hot spots identified by alanine scanning represent sites that are potentially useful for small inhibitor binding, and it is this subset that is identified by experimental or computational fragment screening...
  31. pmc FTSite: high accuracy detection of ligand binding sites on unbound protein structures
    Chi Ho Ngan
    Department of Biomedical Engineering, Boston University, Boston, MA 02115, USA
    Bioinformatics 28:286-7. 2012
    ....
  32. ncbi request reprint Exploring the binding site structure of the PPAR gamma ligand-binding domain by computational solvent mapping
    Shu Hsien Sheu
    Department of Biomedical Engineering, Boston University, 44 Cummington Street, Boston, Massachusetts 02215, USA
    Biochemistry 44:1193-209. 2005
    ..The number of probe clusters retained by these sites depends on the properties of the bound agonist, providing information on the origin of correlations between ligand and coactivator binding...
  33. ncbi request reprint Clustering of domains of functionally related enzymes in the interaction database PRECISE by the generation of primary sequence patterns
    Melissa R Landon
    Graduate Program in Bioinformatics and Systems Biology, Boston University, Boston, MA 02215, USA
    J Mol Graph Model 24:426-33. 2006
    ....
  34. ncbi request reprint PIPER: an FFT-based protein docking program with pairwise potentials
    Dima Kozakov
    Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA
    Proteins 65:392-406. 2006
    ..Although the potential is far from optimal for antibody-antigen pairs, the results are still slightly better than those given by an earlier FFT method. The docking program PIPER is freely available for noncommercial applications...
  35. pmc Encounter complexes and dimensionality reduction in protein-protein association
    Dima Kozakov
    Department of Biomedical Engineering, Boston University, Boston, United States
    elife 3:e01370. 2014
    ..Thus, proteins tend to associate along preferred pathways, similar to sliding of a protein along DNA in the process of protein-DNA recognition. DOI: http://dx.doi.org/10.7554/eLife.01370.001. ..
  36. pmc ClusPro: a fully automated algorithm for protein-protein docking
    Stephen R Comeau
    Bioinformatics Graduate Program, Boston University, 44 Cummington Street, Boston, MA 02215, USA
    Nucleic Acids Res 32:W96-9. 2004
    ..The program output is a short list of putative complexes ranked according to their clustering properties, which is automatically sent back to the user via email...
  37. pmc Comprehensive experimental and computational analysis of binding energy hot spots at the NF-κB essential modulator/IKKβ protein-protein interface
    Mary S Golden
    Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, USA
    J Am Chem Soc 135:6242-56. 2013
    ....
  38. pmc Robust identification of binding hot spots using continuum electrostatics: application to hen egg-white lysozyme
    David H Hall
    Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA
    J Am Chem Soc 133:20668-71. 2011
    ....
  39. pmc DARS (Decoys As the Reference State) potentials for protein-protein docking
    Gwo Yu Chuang
    Department of Biomedical Engineering, and Program in Bioinformatics, Boston University, Boston, Massachusetts, USA
    Biophys J 95:4217-27. 2008
    ..Similar asymmetry does occur in the few other complexes with poor DARS docking results...
  40. pmc Anchor residues in protein-protein interactions
    Deepa Rajamani
    Departments of Biology and Biomedical Engineering and Bioinformatics Program, Boston University, Boston, MA 02215, USA
    Proc Natl Acad Sci U S A 101:11287-92. 2004
    ..Implications for protein docking are also discussed...
  41. pmc Structural insights into recognition of beta2-glycoprotein I by the lipoprotein receptors
    Dmitri Beglov
    Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA
    Proteins 77:940-9. 2009
    ..Our model, which is in the agreement with the NMR data, suggests that the binding interface of B2GPI for the lipoprotein receptors is centered at three lysine residues of B2GPI-DV, Lys 308, Lys 282, and Lys317...
  42. ncbi request reprint Computational screening of phthalate monoesters for binding to PPARgamma
    Taner Kaya
    Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
    Chem Res Toxicol 19:999-1009. 2006
    ..These findings support the use of computational methods to identify environmental chemicals that warrant further experimental evaluation for PPAR binding and trans-activation potential in cell-based models...
  43. pmc Where does amantadine bind to the influenza virus M2 proton channel?
    Dima Kozakov
    Department of Biomedical Engineering, Boston University, 44 Cummington Street, Boston, MA 02215, USA
    Trends Biochem Sci 35:471-5. 2010
    ..By considering all available models, we propose the primary drug binding site is inside the pore, but that exterior binding occurs under appropriate conditions...
  44. doi request reprint The FTMap family of web servers for determining and characterizing ligand-binding hot spots of proteins
    Dima Kozakov
    Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
    Nat Protoc 10:733-55. 2015
    ..As FTFlex performs mapping for all low-energy conformers of side chains in the binding site, its completion time is proportionately longer. ..
  45. pmc Sampling and scoring: a marriage made in heaven
    Sandor Vajda
    Department of Biomedical Engineering, Boston University, Boston, Massachusetts, 02215
    Proteins 81:1874-84. 2013
    ..Although we focus on protein-protein docking, our observations most likely also apply to other conformational search problems, including protein structure prediction and the docking of small molecules to proteins...
  46. pmc Discrimination of near-native structures in protein-protein docking by testing the stability of local minima
    Dima Kozakov
    Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
    Proteins 72:993-1004. 2008
    ....
  47. pmc Domain motion and interdomain hot spots in a multidomain enzyme
    Gwo Yu Chuang
    Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA
    Protein Sci 19:1662-72. 2010
    ....
  48. ncbi request reprint Computational solvent mapping reveals the importance of local conformational changes for broad substrate specificity in mammalian cytochromes P450
    Karl H Clodfelter
    Bioinformatics Program, Boston University, 44 Cummington Street, Boston, Massachusetts 02215, USA
    Biochemistry 45:9393-407. 2006
    ..In addition, the binding of S-warfarin to P450 2C9 creates a high-affinity site for a second ligand, which may help to explain the prevalence of drug-drug interactions involving this and other mammalian P450s...
  49. ncbi request reprint Ensemble modeling of substrate binding to cytochromes P450: analysis of catalytic differences between CYP1A orthologs
    Jahnavi C Prasad
    Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA
    Biochemistry 46:2640-54. 2007
    ..The results demonstrate the utility of this ensemble modeling method, which can account for uncertainty inherent in homology modeling and docking by producing statistical distributions of ligand positions...
  50. pmc Novel druggable hot spots in avian influenza neuraminidase H5N1 revealed by computational solvent mapping of a reduced and representative receptor ensemble
    Melissa R Landon
    Bioinformatics Graduate Program, Boston University, Boston, MA 02215, USA
    Chem Biol Drug Des 71:106-16. 2008
    ..Our hot spot analysis provides further support for the feasibility of developing high-affinity inhibitors capable of binding these regions, which appear to be unique to the N1 strain...
  51. ncbi request reprint Combination of scoring functions improves discrimination in protein-protein docking
    John Murphy
    Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA
    Proteins 53:840-54. 2003
    ....
  52. pmc Consensus alignment server for reliable comparative modeling with distant templates
    Jahnavi C Prasad
    Bioinformatics Graduate Program, Boston University, Boston, MA 02215, USA
    Nucleic Acids Res 32:W50-4. 2004
    ..The Consensus server should prove useful for modelers for whom the structural reliability of the model is critical in their applications. It is currently available at http://structure.bu.edu/cgi-bin/consensus/consensus.cgi...
  53. ncbi request reprint Exploring the binding sites of the haloalkane dehalogenase DhlA from Xanthobacter autotrophicus GJ10
    Michael Silberstein
    Bioinformatics Program, Boston University, 44 Cummington Street, Boston, Massachusetts 02215, USA
    Biochemistry 46:9239-49. 2007
    ....
  54. ncbi request reprint Engineering a novel, stable dimeric streptavidin with lower isoelectric point
    Filiz M Aslan
    Center for Advanced Biotechnology, Boston University, Boston, MA 02215, USA
    J Biotechnol 128:213-25. 2007
    ....
  55. pmc Minimal ensembles of side chain conformers for modeling protein-protein interactions
    Dmitri Beglov
    BioMolecular Engineering Research Center, Boston University, Boston, Massachusetts Department of Biomedical Engineering, Boston University, Boston, Massachusetts
    Proteins 80:591-601. 2012
    ..Side-chain search with the reduced search space will also be incorporated into protein docking algorithms...
  56. pmc How proteins bind macrocycles
    Elizabeth A Villar
    Department of Chemistry, Boston University, Boston, Massachusetts, USA
    Nat Chem Biol 10:723-31. 2014
    ....
  57. pmc Docking server for the identification of heparin binding sites on proteins
    Scott E Mottarella
    Program in Bioinformatics and Department of Biomedical Engineering, Boston University, 44 Cummington Street, Boston, Massachusetts 02215, United States
    J Chem Inf Model 54:2068-78. 2014
    ..The heparin docking method is available as an advanced option of the ClusPro server at http://cluspro.bu.edu/ . ..
  58. pmc Computational mapping identifies the binding sites of organic solvents on proteins
    Sheldon Dennis
    Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
    Proc Natl Acad Sci U S A 99:4290-5. 2002
    ..Specific substrates and/or inhibitors of hen egg-white lysozyme and thermolysin interact with the same side chains identified by the mapping, but form several hydrogen bonds and bind in unique orientations...
  59. ncbi request reprint Modeling of protein interactions in genomes
    Sandor Vajda
    Biomedical Engineering, Boston University, Boston, Massachusetts, USA
    Proteins 47:444-6. 2002
  60. ncbi request reprint Protein-protein association kinetics and protein docking
    Carlos J Camacho
    Department of Biomedical Engineering, Boston University, 44 Commonwealth Avenue, Boston, MA 02215, USA
    Curr Opin Struct Biol 12:36-40. 2002
    ..An alternative approach emulates the process of protein-protein association, that is, first finding the region in which binding is likely to occur and then refining the complex while allowing for flexibility...
  61. doi request reprint The impact of side-chain packing on protein docking refinement
    Mohammad Moghadasi
    Division of Systems Engineering, Center for Information and Systems Engineering, Department of Biomedical Engineering, Department of Mechanical Engineering, and Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts 02215, United States
    J Chem Inf Model 55:872-81. 2015
    ..Furthermore, we establish that the inclusion of unbound side-chain conformers in the side-chain positioning problem is critical in these performance improvements. The code is available to the community under open source license. ..
  62. pmc A first-generation multi-functional cytokine for simultaneous optical tracking and tumor therapy
    Shawn Hingtgen
    Molecular Neurotherapy and Imaging Laboratory, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
    PLoS ONE 7:e40234. 2012
    ..Collectively, these studies define a promising new approach to treating highly aggressive cancers, including GBM, using the optimized therapeutic molecule SM7L...
  63. pmc Evidence of conformational selection driving the formation of ligand binding sites in protein-protein interfaces
    Tanggis Bohnuud
    Program in Bioinformatics, Boston University, Boston, Massachusetts, United States of America
    PLoS Comput Biol 10:e1003872. 2014
    ..Thus, forming the sites in protein-protein interfaces that bind peptides and can be targeted by small ligands always includes conformational selection, although other recognition mechanisms may also be involved. ..
  64. pmc Ligand binding and activation of PPARγ by Firemaster® 550: effects on adipogenesis and osteogenesis in vitro
    Hari K Pillai
    Department of Environmental Health, Boston University, Boston, Massachusetts, USA
    Environ Health Perspect 122:1225-32. 2014
    ..One alternative, Firemaster® 550 (FM550), induces obesity in rats. Triphenyl phosphate (TPP), a component of FM550, has a structure similar to that of organotins, which are obesogenic in rodents...
  65. ncbi request reprint CAPRI: a Critical Assessment of PRedicted Interactions
    Joel Janin
    Laboratoire d Enzymologie et Biochimie Structurales, CNRS, Gif sur Yvette, France
    Proteins 52:2-9. 2003
    ....
  66. pmc Accelerating and focusing protein-protein docking correlations using multi-dimensional rotational FFT generating functions
    David W Ritchie
    Department of Computing Science, University of Aberdeen, Aberdeen, Scotland, UK
    Bioinformatics 24:1865-73. 2008
    ..Hence there is a need to develop more powerful and more versatile FFT docking techniques...
  67. pmc Deletion of Ser-171 causes inactivation, proteasome-mediated degradation and complete deficiency of human transaldolase
    Craig E Grossman
    Department of Medicine, State University of New York UMU, College of Medicine, 750 East Adams Street, Syracuse, NY 13210, USA
    Biochem J 382:725-31. 2004
    ..Since TAL-H is a regulator of apoptosis signal processing, complete deficiency of TAL-H may be relevant for the pathogenesis of liver cirrhosis...

Research Grants3

  1. Improved Protein Mapping for Fragment-Based Drug Design
    Sandor Vajda; Fiscal Year: 2005
    ..Preliminary results suggest that mapping with fragments from well designed libraries will provide very useful information for drug design. ..
  2. Conference Modeling of Protein Interactions in Genomes
    Sandor Vajda; Fiscal Year: 2005
    ..This will primarily achieved by contacting faculty members working in the areas of Biophysics and Biochemistry in minority-serving institutions. ..
  3. Modeling of Protein Interactions 2007
    Sandor Vajda; Fiscal Year: 2007
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