David Pearlman
Lexington, Massachusetts, United States
1K followers
500 connections
About
Summary experience:
Pioneering computational chemist who has repeatedly taken…
Activity
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Top7 - the first de novo protein design - was designed with Rosetta in 2003. It's amazing how far the field has come in 20 years, and just as amazing…
Top7 - the first de novo protein design - was designed with Rosetta in 2003. It's amazing how far the field has come in 20 years, and just as amazing…
Liked by David Pearlman
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I am insanely thrilled to be associated the David Baker and the amazing Rosetta community that generated the tools that lead to a Nobel Prize. I am…
I am insanely thrilled to be associated the David Baker and the amazing Rosetta community that generated the tools that lead to a Nobel Prize. I am…
Liked by David Pearlman
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Why quantum for drug lead optimization? Our QUELO customer says: "...the ability to incorporate quantum mechanics into dynamics-based relative free…
Why quantum for drug lead optimization? Our QUELO customer says: "...the ability to incorporate quantum mechanics into dynamics-based relative free…
Liked by David Pearlman
Experience
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Education
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Stanford University
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Activities and Societies: Primary pop-rock music review for the Stanford Daily. Manager of the record department for the Stanford Bookstore.
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Ph.D. Physical Chemistry with Professor Sung-Hou Kim. Focus on computational chemistry. This was the first Ph.D. degree ever awarded by UC Berkeley in the field of modern computational chemistry/molecular modeling.
Studies of effects of photodamage on DNA, the conformational dynamics of nucleic acids, the first experimental determination of partial charges for nucleic acds. -
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Worked with Peter Kollman. Computational chemistry: Methodology development and application
– First author / primary developer of the AMBER software package, versions 4-5
– Numerous early, defining, methodology papers on free energy calculations (FEP, TI)
– Determination of NMR structures from NOE data, including time-averaged restraints
For a full description of AMBER (the world's most widely used molecular modeling package) see:
D.A. Pearlman, D.A. Case, J.W. Caldwell…Worked with Peter Kollman. Computational chemistry: Methodology development and application
– First author / primary developer of the AMBER software package, versions 4-5
– Numerous early, defining, methodology papers on free energy calculations (FEP, TI)
– Determination of NMR structures from NOE data, including time-averaged restraints
For a full description of AMBER (the world's most widely used molecular modeling package) see:
D.A. Pearlman, D.A. Case, J.W. Caldwell, W.S. Ross, T.E. Cheatham, III, S. DeBolt, D. Ferguson, G. Seibel, and P. Kollman. Comp. Phys. Commun. 91, 1-41 (1995). -
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Publications
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Predicting mutations deleterious to function in beta-lacatamase TEM1 using MM-GBSA
PLoS ONE
Missense mutations can have disastrous effects on the function of a protein. And as a result, they have been implicated in numerous diseases. However, the majority of missense variants only have a nominal impact on protein function. Thus, the ability to distinguish these two classes of missense mutations would greatly aid drug discovery efforts in target identification and validation as well as medical diagnosis. Monitoring the co-occurrence of a given missense mutation and a disease phenotype…
Missense mutations can have disastrous effects on the function of a protein. And as a result, they have been implicated in numerous diseases. However, the majority of missense variants only have a nominal impact on protein function. Thus, the ability to distinguish these two classes of missense mutations would greatly aid drug discovery efforts in target identification and validation as well as medical diagnosis. Monitoring the co-occurrence of a given missense mutation and a disease phenotype provides a pathway for classifying functionally disrupting missense mutations. But, the occurrence of a specific missense variant is often extremely rare making statistical links challenging to infer. In this study, we benchmark a physics-based approach for predicting changes in stability, MM-GBSA, and apply it to classifying mutations as functionally disrupting. A large and diverse dataset of 990 residue mutations in beta-lactamase TEM1 is used to assess performance as it is rich in both functionally disrupting mutations and functionally neutral/beneficial mutations. On this dataset, we compare the performance of MM-GBSA to alternative strategies for predicting functionally disrupting mutations. We observe that the MM-GBSA method obtains an area under the curve (AUC) of 0.75 on the entire dataset, outperforming all other predictors tested. More importantly, MM-GBSA’s performance is robust to various divisions of the dataset, speaking to the generality of the approach. Though there is one notable exception: Mutations on the surface of the protein are the mutations that are the most difficult to classify as functionally disrupting for all methods tested. This is likely due to the many mechanisms available to surface mutations to disrupt function, and thus provides a direction of focus for future studies.
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Predicting the Effect of Amino Acid Single-Point Mutations on Protein Stability—Large-Scale Validation of MD-Based Relative Free Energy Calculations
Thomas Steinbrecher, Chongkai Zhu, Lingle Wang, Robert Abel, Christopher Negron, David Pearlman, Eric Feyfant, Jianxin Duan, Woody Sherman (2016) `` Predicting the Effect of Amino Acid Single Point Mutations on Protein Stability–Large Scale Validation of MD-based Relative Free Energy Calculations’’ Journal of Molecular Biology 429, 948-963.
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Antibody structure determination using a combination of homology modeling, energy‐based refinement, and loop prediction
K Zhu, T Day, D Warshaviak, C Murrett, R Friesner, D Pearlman
Proteins: Structure, Function, and Bioinformatics 82 (8), 1646-1655Other authors -
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Physics‐based enzyme design: Predicting binding affinity and catalytic activity
S Sirin, DA Pearlman, W Sherman
Proteins: Structure, Function, and Bioinformatics 82 (12), 3397-3409Other authors -
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Structure-based approach to the prediction of disulfide bonds in proteins
NK Salam*, M Adzhigirey, W Sherman, DA Pearlman*
Protein Engineering, Design & Selection 27 (10), 365-374Other authors -
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Applying physics-based scoring to calculate free energies of binding for single amino acid mutations in protein-protein complexes
H Beard, A Cholleti, D Pearlman, W Sherman, KA Loving
PloS one 8 (12), e82849Other authors -
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AAK1 identified as an inhibitor of neuregulin-1/ErbB4-dependent neurotrophic factor signaling using integrative chemical genomics and proteomics
Letian Kuai, Shao-En Ong, Jon M Madison, Xiang Wang, Jeremy R Duvall, Timothy A Lewis, Catherine J Luce, Sean D Conner, David A Pearlman, John L Wood, Stuart L Schreiber, Steven A Carr, Edward M Scolnick and Stephen J Haggarty (2011) ``AAK1 Identified as an Inhibitor of Neuregulin-1/ErbB4-Dependent Neurotrophic Factor Signaling Using Integrative Chemical Genomics and Proteomics’’ Chemistry & Biology 18, 891-906.
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FURSMASA: A new approach to rapid scoring functions that uses a MD‐averaged potential energy grid and a solvent‐accessible surface area term with parameters GA fit to experimental data
DA Pearlman, BG Rao, P Charifson
Proteins: Structure, Function, and Bioinformatics 71 (3), 1519-1538Other authors -
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Evaluating the molecular mechanics Poisson− Boltzmann surface area free energy method using a congeneric series of ligands to p38 MAP kinase
See publicationDA Pearlman
Journal of medicinal chemistry 48 (24), 7796-7807 -
AMBER: a program for simulation of biological and organic molecules
Kollman P, Caldwell JW, Ross WS, Pearlman DA, Case DA, DeBolt S, Cheatham TE III, Ferguson D, Seibel G (1988) AMBER: A program for simulation of biological and organic molecules. In: von Rague Schleyer P (ed) Encyclopedia of Computational Chemistry, Vol 1. Wiley, Chichester, pp 11-13
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Are free energy calculations useful in practice? A comparison with rapid scoring functions for the p38 MAP kinase protein system
DA Pearlman, PS Charifson
Journal of medicinal chemistry 44 (21), 3417-3423Other authors -
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Free energy calculations: methods for estimating ligand binding affinities
See publicationDavid A. Pearlman (2001) ``Free Energy Calculations: Methods for Estimating Ligand Binding Affinities'' In: Free Energy Calculations in Rational Drug Design (M. Rami Reddy and Mark D. Erion eds.) Kluwer Academic/Plenum Publishers, 2001, pp. 9-35.
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Improved scoring of ligand− protein interactions using OWFEG free energy grids
DA Pearlman, PS Charifson
Journal of medicinal chemistry 44 (4), 502-511Other authors -
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Automated detection of problem restraints in NMR data sets using the FINGAR genetic algorithm method
See publicationDA Pearlman
Journal of Biomolecular NMR 13 (4), 325-335 -
Free energy grids: a practical qualitative application of free energy perturbation to ligand design using the OWFEG method
See publicationDA Pearlman
Journal of medicinal chemistry 42 (21), 4313-4324 -
Free energy calculations: methods and applications
David A. Pearlman and B. Govinda Rao (1998) ``Free Energy Calculations: Methods and Applications'' In: The Encyclopedia of Computational Chemistry (P von Rague Schleyer, N L Allinger, T Clark J Gasteiger, P A Kollman, H F Schaefer III and R P Schreiner eds.), John Wiley & Sons, NY, pp. 1036-1061
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Ionic charging free energies: Spherical versus periodic boundary conditions
T Darden, D Pearlman, LG Pedersen
The Journal of chemical physics 109 (24), 10921-10935Other authors -
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Applications of Free Energy Calculations to Drug Design
David A. Pearlman (1997) ``Applications of Free Energy Calculations to Drug Design.'' In: Thermodynamics and Structure-Based Drug Design (J. Ladbury, P.R. Connelly, eds.), pp. 1-17, R.G. Landes Co., London.
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Protein solution structure calculations in solution: Solvated molecular dynamics refinement of calbindin D 9k
J Kördel, DA Pearlman, WJ Chazin
Journal of biomolecular NMR 10 (3), 231-243Other authors -
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Benzene dimer: A good model for π− π interactions in proteins? A comparison between the benzene and the toluene dimers in the gas phase and in an aqueous solution
C Chipot, R Jaffe, B Maigret, DA Pearlman, PA Kollman
Journal of the American Chemical Society 118 (45), 11217-11224Other authors -
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CONCERTS: dynamic connection of fragments as an approach to de novo ligand design
DA Pearlman, MA Murcko
Journal of medicinal chemistry 39 (8), 1651-1663Other authors -
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Fingar: A new genetic algorithm-based method for fitting NMR data
See publicationDA Pearlman
Journal of Biomolecular NMR 8 (1), 49-66 -
Molecular Dynamics Potential of Mean Force Calculations: A Study of the Toluene− Ammonium π-Cation Interactions
C Chipot, B Maigret, DA Pearlman, PA Kollman
Journal of the American Chemical Society 118 (12), 2998-3005Other authors -
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Practical applications of time-averaged restrained molecular dynamics to ligand-receptor systems: FK506 bound to the Q50R, A95H, K98I triple mutant of FKBP-13
CA Lepre, DA Pearlman, O Futer, DJ Livingston, JM Moore
Journal of biomolecular NMR 8 (1), 67-76Other authors -
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Alternative approaches to potential of mean force calculations: Free energy perturbation versus thermodynamic integration. The case study of hydrophobic interactions
C Chipot, B Maigret, DA Pearlman
AIP Conference Proceedings 330 (1), 287-294Other authors -
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AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules
David A Pearlman, David A Case, James W Caldwell, William S Ross, Thomas C Cheatham, Stephen E DeBolt, David M Ferguson, George L Seibel and Peter A Kollman (1995) ``AMBER, a Package of Computer Programs for Applying Molecular Mechanics, Molecular Dynamics and Free Energy Calculations to Simulate the Structural and Energetic Properties of Molecules'' Computer Physics Communications 91, 1-41.
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Conformation of FK506 in X-ray structures of its complexes with human recombinant FKBP12 mutants
S Itoh, MT DeCenzo, DJ Livingston, DA Pearlman, MA Navia
Bioorganic & Medicinal Chemistry Letters 5 (17), 1983-1988Other authors -
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A comparison of alternative approaches to free energy calculations
See publicationDA Pearlman
The Journal of Physical Chemistry 98 (5), 1487-1493 -
Free energy derivatives: A new method for probing the convergence problem in free energy calculations
See publicationDA Pearlman
Journal of computational chemistry 15 (1), 105-123 -
Free energy perturbation calculations on parallel computers: Demonstrations of scalable linear speedup
SE Debolt, DA Pearlman, PA Kollman
Journal of computational chemistry 15 (3), 351-373Other authors -
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How is an NMR structure best defined? An analysis of molecular dynamics distance-based approaches
See publicationDA Pearlman
Journal of biomolecular NMR 4 (1), 1-16 -
How well do time-averaged J-coupling restraints work?
See publicationDA Pearlman
Journal of biomolecular NMR 4 (2), 279-299 -
Solution structure of FK506 bound to the R42K, H87V double mutant of FKBP-12
CA Lepre, DA Pearlman, JW Cheng, MT DeCenzo, JM Moore, DJ Livingston
Biochemistry 33 (46), 13571-13580Other authors -
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Walking on the free energy hypersurface of the 18‐crown‐6 ion system using free energy derivatives
P Cieplak, DA Pearlman, PA Kollman
The Journal of chemical physics 101 (1), 627-633Other authors -
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Calculations of the relative free energies of aqueous solvation of several fluorocarbons: A test of the bond potential of mean force correction
CA Gough, DA Pearlman, P Kollman
The Journal of chemical physics 99 (11), 9103-9110Other authors -
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CONCEPTS: New dynamic algorithm for de novo drug suggestion
DA Pearlman, MA Murcko
Journal of computational chemistry 14 (10), 1184-1193Other authors -
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Determining the contributions of constraints in free energy calculations: Development, characterization, and recommendations
See publicationDA Pearlman
The Journal of chemical physics 98 (11), 8946-8957 -
Free energy component analysis: application to the “Z-Phobicity” of A· T base pairs
SB Singh, DA Pearlman, PA Kollman
Journal of Biomolecular Structure and Dynamics 11 (2), 303-311Other authors -
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Comparison of solution structures of mutant bovine pancreatic trypsin inhibitor proteins using two‐dimensional nuclear magnetic resonance
MR Hurle, CD Eads, DA Pearlman, GL Seibel, J Thomason, PA Kosen, ...
Protein Science 1 (1), 91-106Other authors -
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Free energy perturbation calculations involving potential function changes
DM Ferguson, DA Pearlman, WC Swope, PA Kollman
Journal of computational chemistry 13 (3), 362-370Other authors -
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Simulation of the solvation free energies for methane, ethane, and propane and corresponding amino acid dipeptides: a critical test of the bond-PMF correction, a new set of hydrocarbon parameters, and the gas phase-water hydrophobicity scale
Y Sun, D Spellmeyer, DA Pearlman, P Kollman
Journal of the American Chemical Society 114 (17), 6798-6801Other authors -
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Evaluating the assumptions underlying force field development and application using free energy conformational maps for nucleosides
DA Pearlman, PA Kollman
Journal of the American Chemical Society 113 (19), 7167-7177Other authors -
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Free energy perturbation calculations on binding and catalysis after mutating threonine 220 in subtilisin.
N Mizushima, D Spellmeyer, S Hirono, D Pearlman, P Kollman
Journal of Biological Chemistry 266 (18), 11801-11809Other authors -
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Refinement of three-dimensional protein and DNA structures in solution from NMR data
Thomas L. James, Miriam Gochin, Deborah J. Kerwood, David A. Pearlman, Uli Schmitz and Paul D. Thomas (1991) ``Refinement of Three-Dimensional Protein and DNA Structures from NMR Data.'' In: Computational Aspects of the Study of Biological Macromolecules by Nuclear Magnetic Resonance Spectrsocopy (J.C. Hoch, F.M. Poulsen and C. Redfield, eds.), pp. 331-347, Plenum Press, New York
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Solution structure of [d (GTATATAC)] 2 via restrained molecular dynamics simulations with nuclear magnetic resonance constraints derived from relaxation matrix analysis of two-dimensional nuclear Overhauser effect experiments
U Schmitz, DA Pearlman, TL James
Journal of molecular biology 221 (1), 271-292Other authors -
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The overlooked bond‐stretching contribution in free energy perturbation calculations
DA Pearlman, PA Kollman
The Journal of chemical physics 94 (6), 4532-4545Other authors -
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Are Free Energy Calculations Necessary? A Comparison of DNA Modeling Studies
Theoretical Chemistry and Molecular Biophysics , Adenine Press, New York
David A. Pearlman and Peter A. Kollman (1990) ``Are Free Energy Calculations Necessary? A Comparison of DNA Modeling Studies.'' In: Theoretical Chemistry and Molecular Biophysics (D.L. Beveridge and R.L. Lavery, eds.), pp. 139-152, Adenine Press, New York
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Atomic Partial Charges For Nucleic Acids From X-Ray Diffraction Data
Theoretical Chemistry and Molecular Biophysics , Adenine Press, New York
David A. Pearlman and Sung-Hou Kim (1990) ``Atomic Partial Charges For Nucleic Acids From X-Ray Diffraction Data.'' In: Theoretical Chemistry and Molecular Biophysics (D.L. Beveridge and R.L. Lavery, eds.), pp. 259-270, Adenine Press, New York.
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Why do AT base pairs inhibit Z-DNA formation?
LX Dang, DA Pearlman, PA Kollman
Proceedings of the National Academy of Sciences 87 (12), 4630-4634Other authors -
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A new method for carrying out free energy perturbation calculations: dynamically modified windows
DA Pearlman, PA Kollman
The Journal of Chemical Physics 90 (4), 2460-2470Other authors -
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Effects of nucleotide bromination on the stabilities of Z‐RNA and Z‐DNA: A molecular mechanics/thermodynamic perturbation study
WS Ross, CC Hardin, I Tinoco, SN Rao, DA Pearlman, PA Kollman
Biopolymers 28 (11), 1939-1957Other authors -
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Free energy perturbation calculations: Problems and pitfalls along the gilded road
David A. Pearlman and Peter A. Kollman (1989) ``Free Energy Perturbation Calculations: Problems and Pitfalls Along the Gilded Road.'' In: Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications (W. van Gunsteren and P.K. Weiner, eds.), pp. 101-119, Escom Science Publishers, Netherlands.
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The lag between the Hamiltonian and the system configuration in free energy perturbation calculations
See publicationDA Pearlman, PA Kollman
The Journal of chemical physics 91 (12), 7831-7839 -
Molecular models of photodamaged DNA
See publicationSR Holbrook, DA Pearlman, SH Kim
Research on Chemical Intermediates 10 (1), 71-100 -
Structure of DNA damaged by UV and psoralen
SH Kim, MT Tomic, DE Wemmer, D Pearlman, S Holbrook
Biochemical pharmacology 37 (9), 1791Other authors -
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Conformational studies of nucleic acids: III. Empirical multiple correlation functions for nucleic acid torsion angles
DA Pearlman, SH Kim
Journal of Biomolecular Structure and Dynamics 4 (1), 49-67Other authors -
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Conformational studies of nucleic acids: IV. The conformational energetics of oligonucleotides: d (ApApApA) and ApApApA
See publicationDA Pearlman, SH Kim
Journal of Biomolecular Structure and Dynamics 4 (1), 69-98 -
Conformational Studies of Nucleic Acids I. A Rapid and Direct Method for Generating Furanose Coordinates from the Pseudorotation Angle
DA Pearlman, SH Kim
Journal of Biomolecular Structure and Dynamics 3 (1), 85-98Other authors -
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Conformational studies of nucleic acids II. The conformational energetics of commonly occurring nucleosides
DA Pearlman, SH Kim
Journal of Biomolecular Structure and Dynamics 3 (1), 99-125Other authors -
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Structures of DNA containing psoralen crosslink and thymine dimer
See publicationSung-Hou Kim, David A. Pearlman, Stephen R. Holbrook and David H. Pirkle (1985) ``Structures of DNA Containing Psoralen Crosslink and Thymine Dimer.'' In: Molecular Basis of Cancer (R. Rein, ed.), pp. 143-152, Alan R. Liss, Inc., New York.
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The Conformational Effects of UV Induced Damage on DNA
DA Pearlman, SR Holbrook & SH Kim (1985) In: Interrelationship Among Aging, Cancer and Differentiation: Proceedings of the Eighteenth Jerusalem Symposium on Quantum Chemistry and Biochemistry, B Pullman, Paul OP Ts'O, EL Schneider eds, Reiden: Boston, pp 163-171.
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The conformations and energetics of photodamaged DNA
See publicationDA Pearlman, SH Kim
Journal of Biosciences 8 (3), 579-592
Patents
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Inhibitors of IMPDH enzyme
Issued US 7989498
The present invention relates to compounds which inhibit IMPDH. This invention also relates to pharmaceutical compositions comprising these compounds. The compounds and pharmaceutical compositions of this invention are particularly well suited for inhibiting IMPDH enzyme activity and consequently, may be advantageously used as therapeutic agents for IMPDH mediated processes. This invention also relates to methods for inhibiting the activity of IMPDH using the compounds of this invention and…
The present invention relates to compounds which inhibit IMPDH. This invention also relates to pharmaceutical compositions comprising these compounds. The compounds and pharmaceutical compositions of this invention are particularly well suited for inhibiting IMPDH enzyme activity and consequently, may be advantageously used as therapeutic agents for IMPDH mediated processes. This invention also relates to methods for inhibiting the activity of IMPDH using the compounds of this invention and related compounds.
Other inventors -
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Inhibitors of IMPDH enzyme technical field of the invention
Issued US 6653309
See patentThe present invention relates to compounds which inhibit IMPDH. This invention also relates to pharmaceutical compositions comprising these compounds. The compounds and pharmaceutical compositions of this invention are particularly well-suited for inhibiting IMPDH enzyme activity and consequently, may be advantageously used as therapeutic agents for IMPDH mediated processes. This invention also relates to methods for inhibiting the activity of IMPDH using the compounds of this invention and…
The present invention relates to compounds which inhibit IMPDH. This invention also relates to pharmaceutical compositions comprising these compounds. The compounds and pharmaceutical compositions of this invention are particularly well-suited for inhibiting IMPDH enzyme activity and consequently, may be advantageously used as therapeutic agents for IMPDH mediated processes. This invention also relates to methods for inhibiting the activity of IMPDH using the compounds of this invention and related compounds.
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Inhibitors of IMPDH enzyme
Issued US 6518291
See patentThe present invention relates to a novel class of compounds which are IMPDH inhibitors. This invention also relates to pharmaceutical compositions comprising these compounds. The compounds and pharmaceutical compositions of this invention are particularly well suited for inhibiting IMPDH enzyme activity and consequently, may be advantageously used as therapeutic agents for IMPDH mediated processes. This invention also relates to methods for inhibiting the activity of IMPDH using the compounds…
The present invention relates to a novel class of compounds which are IMPDH inhibitors. This invention also relates to pharmaceutical compositions comprising these compounds. The compounds and pharmaceutical compositions of this invention are particularly well suited for inhibiting IMPDH enzyme activity and consequently, may be advantageously used as therapeutic agents for IMPDH mediated processes. This invention also relates to methods for inhibiting the activity of IMPDH using the compounds of this invention and related compounds.
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Inhibitors of IMPDH enzyme
Issued US 5932600
See patentThe present invention relates to a novel class of compounds which are IMPDH inhibitors. This invention also relates to pharmaceutical compositions comprising these compounds. The compounds and pharmaceutical compositions of this invention are particularly well suited for inhibiting IMPDH enzyme activity and consequently, may be advantageously used as therapeutic agents for IMPDH mediated processes. This invention also relates to methods for inhibiting the activity of IMPDH using the compounds…
The present invention relates to a novel class of compounds which are IMPDH inhibitors. This invention also relates to pharmaceutical compositions comprising these compounds. The compounds and pharmaceutical compositions of this invention are particularly well suited for inhibiting IMPDH enzyme activity and consequently, may be advantageously used as therapeutic agents for IMPDH mediated processes. This invention also relates to methods for inhibiting the activity of IMPDH using the compounds of this invention and related compounds.
Projects
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First bridge to commercial music promotion on the Internet
- Present
See projectI created the first avenue for commercial promotion of music on the Internet in 1994, via the newsgroup Rec.Music.Promotional. Prior to this, commercial promotion on the then dominant Usenet groups that defined most of the informational disseminated on the Internet was disallowed by consensus.
I created Rec.Music.Promotional to offer an olive branch to commercial entities to promote their music. This required justification and a vote among the Internet population. Opposition to such…I created the first avenue for commercial promotion of music on the Internet in 1994, via the newsgroup Rec.Music.Promotional. Prior to this, commercial promotion on the then dominant Usenet groups that defined most of the informational disseminated on the Internet was disallowed by consensus.
I created Rec.Music.Promotional to offer an olive branch to commercial entities to promote their music. This required justification and a vote among the Internet population. Opposition to such things had generally been vehement, and required finesse.
Within a few years, graphic browsers and the advent of the World Wide Web would obviate the significance of Rec.Music.Promotional. But this was an important signpost.
The URL provides a link to an announcement of the group in Billboard Magazine (the bible of the music industry).
Honors & Awards
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Grant awarded: Deterrmination of atomic partial charges for commonly occurring amino acids
SBIR
Sole PI on SBIR grant:
https://www.sbir.gov/sbirsearch/detail/110628
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For the past 25 years, my students and I have been developing techniques to detect all forms of digital manipulation. For almost as long, I've been…
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Today I will give a Keynote address at American Association of Pharmaceutical Scientists (AAPS) | @aapscomms #AAPSPharmSci360 titled "Drug Discovery…
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Reality check on "In the Pipeline" on AI drug discovery companies. I think a lot of the hype would go away if AI were regarded as one of many tools…
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After months of assembling the brightest minds in chemistry, engineering, AI, and beyond, bringing the CuspAI team together for the first time at our…
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Avoiding manufacturing liabilities in biologics is critical to successful manufacturing. However, manufacturing liability analysis is often…
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🧬 Make short work of long reads... with LongPlex! 🧬 I could not be more proud of the work our great team at seqWell has done to bring the workflow…
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Thank you Argonautic Ventures there is so much amazing work coming out of the Baker lab, this Nobel is very well deserved but it is just the very…
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Honored to have been part of Cyrus Biotechnology, co-founded by David Baker, winner of 2024 Nobel Prize in Chemistry.
Honored to have been part of Cyrus Biotechnology, co-founded by David Baker, winner of 2024 Nobel Prize in Chemistry.
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🔍 Are your lab resources underutilized? It's time to change that! Maximizing lab utilization isn't just about squeezing more hours out of your equipment—it's about **strategic resource management** that drives results. Here are some crucial tips to optimize your lab's overall efficiency. 💡 **1. Analyze Your Lab’s Workflow** Take a closer look at your current processes. Are there bottlenecks in scheduling or equipment usage? Utilize techniques like value stream mapping to identify inefficiencies. Remember, every minute counts! 📊 **2. Implement Scheduling Software** Manual scheduling can lead to chaos. Invest in software that centralizes booking and resource allocation. It minimizes conflicts and maximizes usage. Think of it as your lab’s personal assistant! 👥 **3. Foster Cross-Department Collaboration** Breaking down silos between teams can lead to more resourceful utilization. Encourage departments to share equipment or conduct joint experiments. Synergy can create greater impact! 📈 **4. Regularly Train Your Team** A well-trained team can operate equipment more efficiently and troubleshoot issues on the spot. Hold quarterly training sessions to keep everyone informed on the latest technologies and best practices. 💬 **5. Solicit Feedback and Adapt** Constant improvement is key! Regularly seek input from your team about the lab’s processes. What’s working? What isn’t? Adapting based on firsthand experiences ensures your lab stays agile. 🚀 **Conclusion: Taking Your Lab to New Heights** In the fast-paced world of research and innovation, **maximizing resource utilization is vital** for success. Are your lab’s efficiencies on par with the challenges ahead? 👉 Let's discuss! Share your thoughts or questions below. How do you ensure your lab operates at its best? #LabManagement #ResourceOptimization #Efficiency #ContinuousImprovement #Collaboration
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Rui Teixeira
As the U.S. tech giants are exploring the reactivation of older nuclear plants, investing massively, it's crucial to consider both the potential and the risks. These plants were designed decades ago, meaning they may not meet today's advanced safety standards without significant upgrades. As a reminder, while the U.S. Nuclear Regulatory Commission (NRC) mandates ongoing reviews for life extension, critics argue that gaps remain between older designs and modern requirements as U.S. Nuclear regulatory is far behind EU regulatory, specially in safety. Private companies managing these plants are facing financial pressures (the pursuit of AI and it's voracius demand for energy), and this could potentially lead to deferred safety upgrades. In Europe, stricter safety reviews ensure nuclear plants comply with modern standards on a more regular basis, providing a proactive layer of security not always seen in the U.S. system. Investments in updating aging infrastructure and rigorous oversight are essential to ensuring safety while exploring nuclear energy’s role in future power needs. Any thoughts? #NuclearEnergy #EnergyPolicy #SafetyStandards
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Naresh Waran Gnanasegaran
Labour Day, also known as International Workers' Day or May Day, is celebrated on May 1st each year. ✨ Historical Origins: - The roots of Labour Day trace back to the Haymarket Affair in 1886. In Chicago, American laborers were advocating for an 8-hour workday, which they believed was fair. However, peaceful protests escalated into violence, resulting in deaths and injuries. - Despite the turmoil, socialist parties across Europe convened in 1889 and designated May 1 as International Labour Day. This day symbolizes hope and resilience for workers worldwide, even in challenging circumstances. ✨ Significance: ✅ Honoring Workers: Labour Day recognizes the vital role played by workers and the working class in shaping our societies. It reminds us that their commitment and loyalty cannot be quantified by mere monetary compensation. ✅ Advocacy for Rights: Beyond a public holiday, Labour Day serves as a platform to acknowledge the contributions of individuals to societal development without bias. It emphasizes the importance of workers' rights and welfare. ✅ Global Celebration: Countries around the world join hands on May 1 to celebrate the hard work and dedication of workers, regardless of their roles. It's a day to express gratitude and appreciation for their tireless efforts. Happy Labour Day dear friends 💐
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Antonio Montano 🪄
💥💥💥 Orthrus: Towards Evolutionary and Functional RNA Foundation Models Abstract In the face of rapidly accumulating genomic data, our understanding of the RNA regulatory code remains incomplete. Pre-trained genomic foundation models offer an avenue to adapt learned RNA representations to biological prediction tasks. However, existing genomic foundation models are trained using strategies borrowed from textual or visual domains, such as masked language modelling or next token prediction, that do not leverage biological domain knowledge. Here, we introduce Orthrus, a Mamba based RNA foundation model pre-trained using a novel self-supervised contrastive learning objective with biological augmentations. Orthrus is trained by maximizing embedding similarity between curated pairs of RNA transcripts, where pairs are formed from splice isoforms of 10 model organisms and transcripts from orthologous genes in 400 mammalian species from the Zoonomia Project. This training objective results in a latent representation that clusters RNA sequences with functional and evolutionary similarities. We find that the generalized mature RNA isoform representations learned by Orthrus significantly outperform existing genomic foundation models on five mRNA property prediction tasks, and requires only a fraction of fine-tuning data. 👉 https://lnkd.in/dJCTHWcA #machinelearning
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Doris-Maria Heilmann
Potential health effects that continuous exposure to environmental micro/nano-PLASTICS (MNPLs) may cause on humans. Due to their persistent nature, MNPLs may accumulate in different organs & tissues & may induce in the long term the development of cancer https://lnkd.in/d_T2ic8G
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Andrew Wyatt
If you're into biomaterials or chemistry research, you won't want to miss Sapio Sciences' latest blog post. They dive deep into the world of specialized Electronic Lab Notebooks (#ELN) and how they're transforming data management in the lab. Perfect for anyone looking to level up their #LabInformatics game!
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