Relaxation Estimation of RMSD in Molecular Dynamics Immunosimulations

The triplex vaccine effects in mammary carcinoma: A nonlinear model in tune with SimTriplex

(2012) Carlo Bianca et al.   NONLINEAR ANALYSIS-REAL WORLD APPLICATIONS

Is an Intuitive Convergence Definition of Molecular Dynamics Simulations Solely Based on the Root Mean Square Deviation Possible?

(2011) B. Knapp et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Automated Sampling Assessment for Molecular Simulations Using the Effective Sample Size

(2010) Xin Zhang et al.   Journal of Chemical Theory and Computation

MULTIPRED2: A computational system for large-scale identification of peptides predicted to bind to HLA supertypes and alleles

(2010) Guang Lan Zhang et al.   JOURNAL OF IMMUNOLOGICAL METHODS

A statistical mechanics approach to autopoietic immune networks

(2010) Adriano Barra et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

MATHEMATICAL MODELING FOR KELOID FORMATION TRIGGERED BY VIRUS: MALIGNANT EFFECTS AND IMMUNE SYSTEM COMPETITION

(2010) CARLO BIANCA   MATHEMATICAL MODELS & METHODS IN APPLIED SCIENCES

Stochastic dynamics for idiotypic immune networks

(2010) Adriano Barra et al.   PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS

A Comparative Approach Linking Molecular Dynamics of Altered Peptide Ligands and MHC with In Vivo Immune Responses

(2010) Bernhard Knapp et al.   PLoS One

ImmunoGrid, an integrative environment for large-scale simulation of the immune system for vaccine discovery, design and optimization

(2009) F. Pappalardo et al.   BRIEFINGS IN BIOINFORMATICS

The Cellular Context of T Cell Signaling

(2009) Michael L. Dustin   IMMUNITY

A critical cross-validation of high throughput structural binding prediction methods for pMHC

(2009) Bernhard Knapp et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

3-Layer-based analysis of peptide–MHC interaction: In silico prediction, peptide binding affinity and T cell activation in a relevant allergen-specific model

(2009) Bernhard Knapp et al.   MOLECULAR IMMUNOLOGY

Different Thermodynamic Binding Mechanisms and Peptide Fine Specificities Associated with a Panel of Structurally Similar High-Affinity T Cell Receptors†‡

(2008) Lindsay L. Jones et al.   BIOCHEMISTRY

Optimal vaccination schedules using simulated annealing

(2008) M. Pennisi et al.   BIOINFORMATICS

Evaluation of MHC class I peptide binding prediction servers: Applications for vaccine research

(2008) Hong Lin et al.   BMC IMMUNOLOGY

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation

Analysis of key parameters for molecular dynamics of pMHC molecules

(2008) Ulrich Omasits et al.   MOLECULAR SIMULATION

Side chain substitution benchmark for peptide/MHC interaction

(2008) Bernhard Knapp et al.   PROTEIN SCIENCE