Changes in the free-energy landscape of p38α MAP kinase through its canonical activation and binding events as studied by enhanced molecular dynamics simulations

DNA-binding protects p53 from interactions with cofactors involved in transcription-independent functions

(2016) Matteo Lambrughi et al.   NUCLEIC ACIDS RESEARCH

The Effect of a Widespread Cancer-Causing Mutation on the Inactive to Active Dynamics of the B-Raf Kinase

(2015) Kristen A. Marino et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A dynamically coupled allosteric network underlies binding cooperativity in Src kinase

(2015) Zachariah H. Foda et al.   Nature Communications

Towards a Molecular Understanding of the Link between Imatinib Resistance and Kinase Conformational Dynamics

(2015) Silvia Lovera et al.   PLoS Computational Biology

Conformational Changes and Free Energies in a Proline Isomerase

(2014) Elena Papaleo et al.   Journal of Chemical Theory and Computation

Allosteric enhancement of MAP kinase p38α's activity and substrate selectivity by docking interactions

(2014) Yuji Tokunaga et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

X-ray refinement significantly underestimates the level of microscopic heterogeneity in biomolecular crystals

(2014) Antonija Kuzmanic et al.   Nature Communications

Activation pathway of Src kinase reveals intermediate states as targets for drug design

(2014) Diwakar Shukla et al.   Nature Communications

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

(2013) Sander Pronk et al.   BIOINFORMATICS

SnapShot: p38 MAPK Substrates

(2013) Natalia Trempolec et al.   CELL

PLUMED 2: New feathers for an old bird

(2013) Gareth A. Tribello et al.   COMPUTER PHYSICS COMMUNICATIONS

Peptide Crystal Simulations Reveal Hidden Dynamics

(2013) Pawel A. Janowski et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Vienna-PTM web server: a toolkit for MD simulations of protein post-translational modifications

(2013) Christian Margreitter et al.   NUCLEIC ACIDS RESEARCH

Effects of oncogenic mutations on the conformational free-energy landscape of EGFR kinase

(2013) L. Sutto et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transitions to catalytically inactive conformations in EGFR kinase

(2013) Y. Shan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

New Therapeutic Targets in Cardiology

(2012) Eva Denise Martin et al.   CIRCULATION

The Different Flexibility of c-Src and c-Abl Kinases Regulates the Accessibility of a Druggable Inactive Conformation

(2012) Silvia Lovera et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations

(2012) R. Anandakrishnan et al.   NUCLEIC ACIDS RESEARCH

New advances in metadynamics

(2012) Ludovico Sutto et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Mitogen-activated Protein Kinase (MAPK) Phosphatase 3-mediated Cross-talk between MAPKs ERK2 and p38α

(2011) Yuan-Yuan Zhang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A Distinct Interaction Mode Revealed by the Crystal Structure of the Kinase p38  with the MAPK Binding Domain of the Phosphatase MKP5

(2011) Y.-Y. Zhang et al.   Science Signaling

Mechanisms and functions of p38 MAPK signalling

(2010) Ana Cuadrado et al.   BIOCHEMICAL JOURNAL

Enhanced Sampling in the Well-Tempered Ensemble

(2010) M. Bonomi et al.   PHYSICAL REVIEW LETTERS

Protein kinases: evolution of dynamic regulatory proteins

(2010) Susan S. Taylor et al.   TRENDS IN BIOCHEMICAL SCIENCES

"Go upstream, young man": lessons learned from the p38 saga

(2009) D Hammaker et al.   ANNALS OF THE RHEUMATIC DISEASES

PLUMED: A portable plugin for free-energy calculations with molecular dynamics

(2009) Massimiliano Bonomi et al.   COMPUTER PHYSICS COMMUNICATIONS

The p38 MAPK inhibitors for the treatment of inflammatory diseases and cancer

(2009) Hae-Young Yong et al.   EXPERT OPINION ON INVESTIGATIONAL DRUGS

Hydrogen-Exchange Mass Spectrometry Reveals Activation-Induced Changes in the Conformational Mobility of p38α MAP Kinase

(2008) Kevin M. Sours et al.   JOURNAL OF MOLECULAR BIOLOGY

Protein Conformational Transitions: The Closure Mechanism of a Kinase Explored by Atomistic Simulations

(2008) Anna Berteotti et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A Novel Lipid Binding Site Formed by the MAP Kinase Insert in p38α

(2007) Ron Diskin et al.   JOURNAL OF MOLECULAR BIOLOGY