Home » Knapp Lab
Numata, Jorge
Freie Universität Berlin
Degree   MSc.
Organisation   DFG
Status   PhD-student
Telephone   +49-30-838-53484
Contact   numata(at)
Funding SFB765 Multivalency as chemical organization and action principle: New architectures, functions and applications. Support is gratefully acknowledged.
Current work Techniques:
  • Molecular dynamics simulation and statistical mechanical modeling
  • Information theoretical approaches for biomolecular motion
  • Development of a new method to calculate conformational entropy (for a copy of the program, contact me)
  • Thermodynamics of protein folding and receptor-ligand binding
  • Conformational entropy of beta-amyloid aggregation
  • Dynamic modulation of photosynthetic pigment transition energies

Michael Wan, Aspuru-Guzik Research group at Harvard University

Academic Degrees
1998 BSc. in Chemical Engineering - Tecnolgico de Monterrey (ITESM) Mexico
Specialization in chemical process simulation
2005 MSc. in Bioinformatics - Freie Universität Berlin - Germany
Specialization in biological and biophysical modeling
1999-2001 Bayer de Mexico - MaterialScience
Production leader for Polyurethanes: Production planning, chemical plant trouble-shooting, corporate culture correspondence with Bayer USA
Selected talks given
14.08.2008 MedILS Split, Croatia, Entropy in Biomolecular systems, "Conformational entropy from biomolecular simulation using information theory"
26.09.2007 Institut Franais du Petrol, Thermodynamics 2007, "Entropy in biomolecular simulation: Better methods through information theory"
01.08.2007 University of Tokyo, International Workshop on Bioinformatics and Systems Biology, "Protein thermodynamics from MD Simulation: Beyond the quasi-harmonic approximation"
20.07.2006 Harvard University, Chemistry and Chemical Biology, "Entropic contributions in macromolecules: the case of protein aggregation"

Conformational entropy image


Influence of Spacer-Receptor Interactions on the Stability of Bivalent Ligand-Receptor Complexes
J. Phys. Chem. B, 116 (8), pp 2595 to 2604, 2012
Numata - Juneja - Diestler - Knapp

Balanced and bias-corrected computation of conformational entropy differences for molecular trajectories
J. Chem. Theory Comput.,, 2012
Numata - Knapp

Merging Implicit with Explicit Solvent Simulations: Polyethylene Glycol
J. Chem. Theory Comput., 6 (6), pp 1871-1883, 2010
Juneja - Numata - Nilsson - Knapp

Position dependent effects of fluorinated amino acids on hydrophobic core formation of a coiled coil heterodimer
Chem. Eur. J., 2009
Salwiczek - Samsonov - Vagt - Baldauf - Nyakatura - Fleige - Numata - Clfen - Pisabarro - Koksch

Entropy and thermodynamics in biomolecular simulation
Handbook of Res. on Sys. Biol. Applications in Medicine, 2008

Measuring correlations in metabolomic networks with mutual information
Genome Informatics Volume 20, 2008
Numata - Ebenhoeh - Knapp

Conformational entropy of biomolecules: Beyond the quasi-harmonic approximation
Genome Informatics Volume 18, 192-205, 2007
Numata - Wan - Knapp

The Application of Comparative Genomics and Structure Prediction in Dental Research
Handbook of Research on Informatics in Healthcare and Biomedicine, 2006



Fabeckstr. 36a, D-14195, Germany, Berlin-Dahlem
+49 30 838 54387
+49 30 838 56921 (Fax)

Protein Electrostatics 2016

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Selected publications

Journal Cover
Aysam Guerler, Connie Wang and E. W. Knapp

Journal Cover
Alok Juneja, Henning Riedesel, Milan Hodoscek and E. W. Knapp

Journal Cover
Gegham Galstyan and E. W. Knapp

Journal Cover
Ilkay Sakalli and E. W. Knapp

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