Mark A DePristo

Summary

Affiliation: Harvard University
Country: USA

Publications

  1. ncbi request reprint Crystallographic refinement by knowledge-based exploration of complex energy landscapes
    Mark A DePristo
    Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
    Structure 13:1311-9. 2005
  2. ncbi request reprint On the abundance, amino acid composition, and evolutionary dynamics of low-complexity regions in proteins
    Mark A DePristo
    Department of Organismic and Evolutionary Biology, Hartl Lab, 16 Divinity Street, Harvard University, Cambridge, MA 02138, USA
    Gene 378:19-30. 2006
  3. ncbi request reprint Missense meanderings in sequence space: a biophysical view of protein evolution
    Mark A DePristo
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Nat Rev Genet 6:678-87. 2005
  4. pmc Discrete restraint-based protein modeling and the Calpha-trace problem
    Mark A DePristo
    Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, England
    Protein Sci 12:2032-46. 2003
  5. ncbi request reprint Ab initio construction of polypeptide fragments: efficient generation of accurate, representative ensembles
    Mark A DePristo
    Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
    Proteins 51:41-55. 2003
  6. ncbi request reprint Advantages of fine-grained side chain conformer libraries
    Reshma P Shetty
    Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
    Protein Eng 16:963-9. 2003
  7. ncbi request reprint Mutational reversions during adaptive protein evolution
    Mark A DePristo
    Department of Organismic and Evolutionary Biology, Harvard University, MA, USA
    Mol Biol Evol 24:1608-10. 2007
  8. ncbi request reprint Darwinian evolution can follow only very few mutational paths to fitter proteins
    Daniel M Weinreich
    Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
    Science 312:111-4. 2006
  9. pmc Temporal constraints on the incorporation of regulatory mutants in evolutionary pathways
    Kyle M Brown
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
    Mol Biol Evol 26:2455-62. 2009
  10. pmc Low-complexity regions in Plasmodium falciparum: missing links in the evolution of an extreme genome
    Martine M Zilversmit
    Department of Organismic and Evolutionary Biology, Harvard University, Boston, MA, USA
    Mol Biol Evol 27:2198-209. 2010

Collaborators

Detail Information

Publications22

  1. ncbi request reprint Crystallographic refinement by knowledge-based exploration of complex energy landscapes
    Mark A DePristo
    Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
    Structure 13:1311-9. 2005
    ..Finally, we discuss the implications of this work on structure determination in particular and conformational sampling and energy minimization in general...
  2. ncbi request reprint On the abundance, amino acid composition, and evolutionary dynamics of low-complexity regions in proteins
    Mark A DePristo
    Department of Organismic and Evolutionary Biology, Hartl Lab, 16 Divinity Street, Harvard University, Cambridge, MA 02138, USA
    Gene 378:19-30. 2006
    ..We conclude with a mechanistic model for LCR evolution that links the pattern of LCRs within P. falciparum to its high genomic A+T content and recombination rate...
  3. ncbi request reprint Missense meanderings in sequence space: a biophysical view of protein evolution
    Mark A DePristo
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Nat Rev Genet 6:678-87. 2005
    ..We then advance a biophysical model of protein evolution that helps us to understand phenomena that range from the dynamics of molecular adaptation to the clock-like rate of protein evolution...
  4. pmc Discrete restraint-based protein modeling and the Calpha-trace problem
    Mark A DePristo
    Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, England
    Protein Sci 12:2032-46. 2003
    ..Issues relating to decoy set generation, experimental structure determination, efficiency of conformational sampling, and homology modeling are discussed...
  5. ncbi request reprint Ab initio construction of polypeptide fragments: efficient generation of accurate, representative ensembles
    Mark A DePristo
    Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
    Proteins 51:41-55. 2003
    ..In a subsequent study (de Bakker et al.: Proteins 2003;51:21-40), we demonstrate that the AMBER forcefield with the Generalized Born solvation model identifies near-native conformations significantly better than previous methods...
  6. ncbi request reprint Advantages of fine-grained side chain conformer libraries
    Reshma P Shetty
    Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
    Protein Eng 16:963-9. 2003
    ....
  7. ncbi request reprint Mutational reversions during adaptive protein evolution
    Mark A DePristo
    Department of Organismic and Evolutionary Biology, Harvard University, MA, USA
    Mol Biol Evol 24:1608-10. 2007
    ..Altogether, this discovery highlights the unusual and potentially circuitous routes natural selection can follow during adaptation...
  8. ncbi request reprint Darwinian evolution can follow only very few mutational paths to fitter proteins
    Daniel M Weinreich
    Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
    Science 312:111-4. 2006
    ..This implies that the protein tape of life may be largely reproducible and even predictable...
  9. pmc Temporal constraints on the incorporation of regulatory mutants in evolutionary pathways
    Kyle M Brown
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
    Mol Biol Evol 26:2455-62. 2009
    ..A mathematical model of beta-lactam resistance is examined in detail and shown to be consistent with the observed results...
  10. pmc Low-complexity regions in Plasmodium falciparum: missing links in the evolution of an extreme genome
    Martine M Zilversmit
    Department of Organismic and Evolutionary Biology, Harvard University, Boston, MA, USA
    Mol Biol Evol 27:2198-209. 2010
    ..We discuss how the discovery of these distinct species of PfLCRs helps to resolve previous contradictory studies on LCRs in malaria and contributes to our understanding of the evolution of the of the parasite's unusual genome...
  11. ncbi request reprint Knowledge-based real-space explorations for low-resolution structure determination
    Nicholas Furnham
    Sanger Building, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, United Kingdom
    Structure 14:1313-20. 2006
    ..This approach provides a means to extract quickly from experimental data useful information that would otherwise be discarded and to take into account the uncertainty in the interpretation--an overriding issue for low-resolution data...
  12. pmc Next-generation sequencing for HLA typing of class I loci
    Rachel L Erlich
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
    BMC Genomics 12:42. 2011
    ..We have coupled this process to a novel HLA calling algorithm to determine the most likely pair of alleles at each locus...
  13. ncbi request reprint Heterogeneity and inaccuracy in protein structures solved by X-ray crystallography
    Mark A DePristo
    Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
    Structure 12:831-8. 2004
    ..Further, it suggests that analyses that depend on small differences in the relative positions of atoms may be flawed...
  14. pmc Pacific biosciences sequencing technology for genotyping and variation discovery in human data
    Mauricio O Carneiro
    Broad Institute of MIT and Harvard, Medical and Population Genetics Program, Cambridge, MA 02141, USA
    BMC Genomics 13:375. 2012
    ..With these potential advantages in mind, we here evaluate the utility of the Pacific Biosciences RS platform for human medical amplicon resequencing projects...
  15. ncbi request reprint The RNA degradosome: life in the fast lane of adaptive molecular evolution
    Maria Jose Marcaida
    Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
    Trends Biochem Sci 31:359-65. 2006
    ....
  16. ncbi request reprint Ab initio construction of polypeptide fragments: Accuracy of loop decoy discrimination by an all-atom statistical potential and the AMBER force field with the Generalized Born solvation model
    Paul I W de Bakker
    Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
    Proteins 51:21-40. 2003
    ..3 A for 8-mers) when scoring with the AMBER/GBSA force field. This work provides the basis for a promising hybrid approach of ab initio and knowledge-based methods for loop modeling...
  17. pmc A framework for variation discovery and genotyping using next-generation DNA sequencing data
    Mark A DePristo
    Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
    Nat Genet 43:491-8. 2011
    ..We here discuss the application of these tools, instantiated in the Genome Analysis Toolkit, to deep whole-genome, whole-exome capture and multi-sample low-pass (∼4×) 1000 Genomes Project datasets...
  18. pmc The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data
    Aaron McKenna
    Program in Medical and Population Genetics, The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
    Genome Res 20:1297-303. 2010
    ....
  19. ncbi request reprint Conformer generation under restraints
    Paul I W de Bakker
    Department of Molecular Biology and Center for Human Genetic Research, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02114 2790, USA
    Curr Opin Struct Biol 16:160-5. 2006
    ..Computational approaches that combine dense, discrete sampling with all-atom energy evaluation and refinement may help to overcome the remaining barriers to solving these problems...
  20. pmc Relation between native ensembles and experimental structures of proteins
    Robert B Best
    Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, United Kingdom
    Proc Natl Acad Sci U S A 103:10901-6. 2006
    ....
  21. ncbi request reprint Is one solution good enough?
    Nicholas Furnham
    Nat Struct Mol Biol 13:184-5; discussion 185. 2006
  22. ncbi request reprint Simultaneous determination of protein structure and dynamics
    Kresten Lindorff-Larsen
    Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
    Nature 433:128-32. 2005
    ..The protocol is completely general and should lead to significant advances in our ability to understand and utilize the structures of native proteins...