D. Jacobs

发表

An Algorithm for Two-Dimensional Rigidity Percolation

B. Hendrickson, D. Jacobs, 1997 .

Regular ArticleAn Algorithm for Two-Dimensional Rigidity Percolation: The Pebble Game

B. Hendrickson, D. Jacobs, 1997 .

Protein flexibility predictions using graph theory

D. Jacobs, A. Rader, L. Kuhn, 2001, Proteins.

Network rigidity at finite temperature: relationships between thermodynamic stability, the nonadditivity of entropy, and cooperativity in molecular systems.

G. G. Wood, D. Jacobs, S. Dallakyan, 2003, Physical review. E, Statistical, nonlinear, and soft matter physics.

Protein flexibility and dynamics using constraint theory.

D. Jacobs, A. Rader, L. Kuhn, 2001, Journal of molecular graphics & modelling.

Hydrogen bond networks determine emergent mechanical and thermodynamic properties across a protein family

D. Jacobs, D. Livesay, S. Dallakyan, 2008, Chemistry Central journal.

Decomposing Dynamical Couplings in Mutated scFv Antibody Fragments into Stabilizing and Destabilizing Effects.

D. Jacobs, Azhagiya Singam Ettayapuram Ramaprasad, S. Uddin, 2017, Journal of the American Chemical Society.

Unifying mechanical and thermodynamic descriptions across the thioredoxin protein family

Dennis R Livesay, Minli Xu, Donald J Jacobs, 2009, Proteins.

Mutations in Antibody Fragments Modulate Allosteric Response Via Hydrogen-Bond Network Fluctuations.

D. Jacobs, D. Livesay, Amit Srivastava, 2016, Biophysical journal.

4 An Interfacial Thermodynamics Model for Protein Stability

D. Jacobs, 2018 .

An Interfacial Thermodynamics Model for Protein Stability

Donald J. Jacobs, D. Jacobs, 2012 .

Conserved quantitative stability/flexibility relationships (QSFR) in an orthologous RNase H pair

Dennis R Livesay, Donald J Jacobs, D. Jacobs, 2005, Proteins.

Elucidating protein thermodynamics from the three-dimensional structure of the native state using network rigidity.

Donald J Jacobs, D. Jacobs, S. Dallakyan, 2005, Biophysical journal.

Self-organization in network glasses

Donald J. Jacobs, Michael Thorpe, J. C. Phillips, 2000 .

New insight into long‐range nonadditivity within protein double‐mutant cycles

Dennis R Livesay, M Michael Gromiha, Donald J Jacobs, 2008, Proteins.

High throughput nonparametric probability density estimation

D. Jacobs, Jenny Farmer, 2018, PloS one.

Allosteric response is both conserved and variable across three CheY orthologs.

Dennis R Livesay, Donald J Jacobs, D. Jacobs, 2010, Biophysical journal.

Ensemble properties of network rigidity reveal allosteric mechanisms.

Dennis R Livesay, Deeptak Verma, Donald J Jacobs, 2012, Methods in molecular biology.

Floppy modes and the free energy: Rigidity and connectivity percolation on Bethe lattices

M. F. Thorpe, P. M. Duxbury, Cristian F. Moukarzel, 1999 .

An image-based reaction field method for electrostatic interactions in molecular dynamics simulations of aqueous solutions.

Donald J. Jacobs, Shaozhong Deng, Andrij Baumketner, 2009, The Journal of chemical physics.

On the role of structural class of a protein with two‐state folding kinetics in determining correlations between its size, topology, and folding rate

Dennis R Livesay, Donald J Jacobs, D. Jacobs, 2007, Protein science : a publication of the Protein Society.

Ionic solvation studied by image-charge reaction field method.

D. Jacobs, W. Cai, Yuchun Lin, 2011, The Journal of chemical physics.

Generic rigidity in three-dimensional bond-bending networks

Donald J. Jacobs, D. Jacobs, 1998 .

Rigidity and flexibility characteristics of DD[E/D]‐transposases Mos1 and Sleeping Beauty

D. Jacobs, I. Nesmelova, Christopher M. Singer, 2019, Proteins.

Constraint Theory applied to Proteins

D. Jacobs, A. Rader, L. Kuhn, 2004 .

Novel Ricin Subunit Antigens With Enhanced Capacity to Elicit Toxin-Neutralizing Antibody Responses in Mice.

J. Karanicolas, D. Jacobs, S. Joshi, 2016, Journal of pharmaceutical sciences.

Effect of the Reaction Field on Molecular Forces and Torques Revealed by an Image-Charge Solvation Model.

D. Jacobs, Yuchun Lin, A. Baumketner, 2013, Communications in computational physics.

Preferential binding effects on protein structure and dynamics revealed by coarse-grained Monte Carlo simulation.

D. Jacobs, R. Pandey, B. Farmer, 2017, The Journal of chemical physics.

GAI MoRFs Regulate Cleft and Channel Binding Pathways for Gibberellin in GID1A

D. Jacobs, E. Rikkerink, Marion Wood, 2020, bioRxiv.

Protein Function Analysis through Machine Learning

D. Jacobs, John Patterson, Chris S. Avery, 2022, Biomolecules.

Non-Randomness in Network Glasses and Rigidity

J. C. Phillips, D. Jacobs, M. Thorpe, 2001 .

Nonparametric Maximum Entropy Probability Density Estimation

D. Jacobs, Jenny Farmer, 2016, 1606.08861.

Quasar Identification Using Multivariate Probability Density Estimated from Nonparametric Conditional Probabilities

D. Jacobs, Jenny Farmer, Eve Allen, 2022, Mathematics.

Predicting flexibility in proteins using constraint theory

Ming Lei, Leslie A. Kuhn, Donald J. Jacobs, 2000 .

Functional Dynamics of Substrate Recognition in TEM Beta-Lactamase

D. Jacobs, Chris S. Avery, L. Baker, 2022, Entropy.

Kinetics and thermodynamics of the rate-limiting conformational change in the actomyosin V mechanochemical cycle.

Charles C. David, D. Jacobs, C. Yengo, 2011, Journal of molecular biology.

Molecular dynamic simulation of polyhedral oligomeric silsesquioxane porphyrin molecules: Self-assembly and influence on morphology

Juan L. Vivero-Escoto, D. Jacobs, Paula Loman-Cortes, 2021, Materials Today Communications.

Statistical Measures to Quantify Similarity between Molecular Dynamics Simulation Trajectories

Donald J. Jacobs, Matthew C. B. Tsilimigras, Jenny Farmer, 2017, Entropy.

Principal component analysis: a method for determining the essential dynamics of proteins.

Charles C. David, Donald J Jacobs, Charles C David, 2014, Methods in molecular biology.

A flexible approach for understanding protein stability

G. G. Wood, D. Jacobs, D. Livesay, 2004, FEBS letters.

Variations within Class-A β-Lactamase Physiochemical Properties Reflect Evolutionary and Environmental Patterns, but not Antibiotic Specificity

Donald J. Jacobs, Dennis R. Livesay, Deeptak Verma, 2013, PLoS Comput. Biol..

Rigidity Emerges during Antibody Evolution in Three Distinct Antibody Systems: Evidence from QSFR Analysis of Fab Fragments

Tong Li, Malgorzata B. Tracka, Shahid Uddin, 2015, PLoS Comput. Biol..

Conformational Entropy of an Ideal Cross-Linking Polymer Chain

Donald J. Jacobs, Dennis R. Livesay, Oleg K. Vorov, 2008, Entropy.

Dynamics and thermodynamic properties of CXCL7 chemokine

Donald J Jacobs, Charles A Herring, D. Jacobs, 2015, Proteins.

Molecular Dynamics Study of the Structure, Flexibility and Dynamics of Thermostable L1 Lipase at High Temperatures

D. Jacobs, M. Basri, A. Salleh, 2009, The protein journal.

Investigations on the alpha-helix to coil transition in HP heterogeneous polypeptides using network rigidity

G. G. Wood, D. Jacobs, M. S. Lee, 2004 .

Understanding the α‐helix to coil transition in polypeptides using network rigidity: Predicting heat and cold denaturation in mixed solvent conditions

G. G. Wood, D. Jacobs, 2004, Biopolymers.

Changes in Lysozyme Flexibility upon Mutation Are Frequent, Large and Long-Ranged

Donald J. Jacobs, Dennis R. Livesay, Deeptak Verma, 2012, PLoS Comput. Biol..

A case study comparing quantitative stability-flexibility relationships across five metallo-β-lactamases highlighting differences within NDM-1.

Dennis R Livesay, Deeptak Verma, Donald J Jacobs, 2014, Methods in molecular biology.

Part II. Chalcogenide and organic semiconductors Section 16. Growth and structural properties Self-organization in network glasses

J. C. Phillips, D. Jacobs, M. Thorpe, 2000 .

Extending the fast multipole method to charges inside or outside a dielectric sphere

Wei Cai, Shaozhong Deng, Donald Jacobs, 2007, J. Comput. Phys..

GENERIC RIGIDITY OF NETWORK GLASSES

Donald J. Jacobs, Michael Thorpe, A. J. Rader, 2002 .

The Structure and Mechanical Properties of Networks

D. Jacobs, M. Thorpe, B. Djordjević, 1997 .

Biased Hypothesis Formation From Projection Pursuit pdf

Donald J. Jacobs, John Patterson, Chris Avery, 2022, Adv. Artif. Intell. Mach. Learn..

Multivariate visual explanation for high dimensional datasets

Yujie Liu, Scott Barlowe, Tianyi Zhang, 2008, 2008 IEEE Symposium on Visual Analytics Science and Technology.

Kinetic and thermodynamic characterization of dihydrotestosterone-induced conformational perturbations in androgen receptor ligand-binding domain.

D. Jacobs, D. Livesay, C. Yengo, 2009, Molecular endocrinology.

Victory Tax: A Holistic Income Tax System

D. Jacobs, 2021, Entropy.

The Structure and Rigidity of Network Glasses

D. Jacobs, M. Thorpe, B. Djordjević, 2000 .

Molecular clustering and percolation characteristics near the glass transition in aqueous trehalose and choline dihydrogen phosphate solutions.

D. Jacobs, G. Elliott, E. R. Azhagiya Singam, 2018, Physical chemistry chemical physics : PCCP.

ICSM: An order N method for calculating electrostatic interactions added to TINKER

Wei Cai, Katherine Baker, Shaozhong Deng, 2013, Comput. Phys. Commun..

A virtual pebble game to ensemble average graph rigidity

D. Jacobs, D. Livesay, Luis C. González, 2015, Algorithms for Molecular Biology.

Redistribution of Flexibility in Stabilizing Antibody Fragment Mutants Follows Le Châtelier’s Principle

Malgorzata B. Tracka, Shahid Uddin, Donald J. Jacobs, 2014, PloS one.

Thermodynamic stability and flexibility characteristics of antibody fragment complexes.

Dennis R Livesay, Deeptak Verma, Donald J Jacobs, 2013, Protein and peptide letters.

Calculating Ensemble Averaged Descriptions of Protein Rigidity without Sampling

Donald J. Jacobs, Dennis R. Livesay, D. Jacobs, 2012, PloS one.

Nonadditivity in conformational entropy upon molecular rigidification reveals a universal mechanism affecting folding cooperativity.

Donald J. Jacobs, Dennis R. Livesay, D. Jacobs, 2011, Biophysical journal.

Predicting the melting point of human C-type lysozyme mutants.

Dennis R Livesay, Deeptak Verma, Donald J Jacobs, 2010, Current protein & peptide science.

Helix/coil nucleation: a local response to global demands.

Dennis R Livesay, Donald J Jacobs, D. Jacobs, 2009, Biophysical journal.

Structural rigidity in the capsid assembly of cowpea chlorotic mottle virus

D. Jacobs, M. Thorpe, B. Hespenheide, 2004 .

Constraint Theory applied to Proteins

D. Jacobs, A. Rader, L. Kuhn, 2004 .

Flexible and Rigid Regions in Proteins

Leslie A. Kuhn, Donald J. Jacobs, Michael Thorpe, 2002 .

Non-Randomness in Network Glasses and Rigidity 1

J. C. Phillips, D. Jacobs, M. Thorpe, 2022 .

Improving protein flexibility predictions by combining statistical sampling with a mean-field virtual Pebble Game

Donald J. Jacobs, Dennis R. Livesay, Luis C. González, 2011, BCB '11.

Comment on “infinite-cluster geometry in central-force networks”

D. Jacobs, M. Thorpe, 1998 .

Characterization of the pre-force-generation state in the actomyosin cross-bridge cycle

D. Jacobs, C. Yengo, Mingxuan Sun, 2008, Proceedings of the National Academy of Sciences.

PROCEEDINGS OF THE INTERNATIONAL CONFERENCE "THERMODYNAMICS AND CHEMICAL STRUCTURE OF MELTS AND GLASSES"

J. C. Phillips, D. Jacobs, M. Thorpe, 2001 .

Molecular insights into water vapor absorption by aqueous lithium bromide and lithium bromide/sodium formate solutions

D. Jacobs, G. Elliott, Lindong Weng, 2016 .

Universal Sample Size Invariant Measures for Uncertainty Quantification in Density Estimation

Donald J. Jacobs, Alexander Gray, Jenny Farmer, 2019, Entropy.

Characterizing protein motions from structure.

Charles C. David, Donald J Jacobs, Charles C David, 2011, Journal of molecular graphics & modelling.

Elucidating the Conformational Dependence of Calculated pKa Values.

Patrick D. Kidd, D. Jacobs, D. Livesay, 2006, Journal of chemical theory and computation.

Best Probability Density Function for Random Sampled Data

Donald J. Jacobs, D. Jacobs, 2009, Entropy.

MATLAB tool for probability density assessment and nonparametric estimation

D. Jacobs, Jenny Farmer, 2022, SoftwareX.

Generic rigidity percolation: The pebble game.

Jacobs, Thorpe, D. Jacobs, 1995, Physical review letters.

Floppy modes and the free energy: Rigidity and connectivity percolation on Bethe lattices

D. Jacobs, M. Thorpe, C. Moukarzel, 1998, cond-mat/9807073.

Generic rigidity percolation in two dimensions.

Jacobs, Thorpe, D. Jacobs, 1996, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.

JED: a Java Essential Dynamics Program for comparative analysis of protein trajectories

Donald J. Jacobs, Charles C. David, Ettayapuram Ramaprasad Azhagiya Singam, 2017, BMC Bioinformatics.

Image Charge Methods for a Three-Dielectric-Layer Hybrid Solvation Model of Biomolecules.

Donald J. Jacobs, Peihua Qin, Zhenli Xu, 2009, Communications in computational physics.

An image-based reaction field method for electrostatic interactions in molecular dynamics simulations of aqueous solutions.

D. Jacobs, Yuchun Lin, A. Baumketner, 2009, The Journal of chemical physics.

Characterizing protein motions from structure.

Charles C. David, D. Jacobs, 2011, Journal of molecular graphics & modelling.

Probability Density Estimation through Nonparametric Adaptive Partitioning and Stitching

D. Jacobs, Jenny Farmer, Zach D. Merino, 2023, Algorithms.

Generalized image charge solvation model for electrostatic interactions in molecular dynamics simulations of aqueous solutions

Wei Cai, Shaozhong Deng, Donald Jacobs, 2013, J. Comput. Phys..

A comparable study of image approximations to the reaction field

Wei Cai, Shaozhong Deng, Donald Jacobs, 2007, Comput. Phys. Commun..

Elucidating quantitative stability/flexibility relationships within thioredoxin and its fragments using a distance constraint model.

Dennis R Livesay, M. L. Tasayco, Donald J Jacobs, 2006, Journal of molecular biology.

Kinetics and thermodynamics of the rate-limiting conformational change in the actomyosin V mechanochemical cycle.

Charles C. David, Donald J Jacobs, D. Jacobs, 2011, Journal of molecular biology.

Switch II mutants reveal coupling between the nucleotide- and actin-binding regions in myosin V.

Charles C. David, Donald J Jacobs, D. Jacobs, 2012, Biophysical journal.

JED: a Java Essential Dynamics Program for comparative analysis of protein trajectories

Charles C. David, D. Jacobs, E. R. A. Singam, 2017, BMC Bioinformatics.