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Dynamics and recognition within a protein-DNA complex: a molecular dynamics study of the SKN-1/DNA interaction

Nucleic acids research, 2016-02, Vol.44 (3), p.1440-1448

2016

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A molecular dynamics study of adenylyl cyclase: The impact of ATP and G-protein binding

PloS one, 2018-04, Vol.13 (4), p.e0196207-e0196207

2018

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Internal Normal Mode Analysis (iNMA) Applied to Protein Conformational Flexibility

Journal of chemical theory and computation, 2015-11, Vol.11 (11), p.5503-5512

2015

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Multiple protein-DNA interfaces unravelled by evolutionary information, physico-chemical and geometrical properties

PLoS computational biology, 2020-02, Vol.16 (2), p.e1007624-e1007624

2020

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Exploring polymorphisms in B-DNA helical conformations

Nucleic acids research, 2012-11, Vol.40 (21), p.10668-10678

2012

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Significance of Molecular Dynamics Simulations for Life Sciences

Israel journal of chemistry, 2014-08, Vol.54 (8-9), p.1042-1051

2014

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PaLaCe: A Coarse-Grain Protein Model for Studying Mechanical Properties

Journal of chemical theory and computation, 2013-01, Vol.9 (1), p.785-793

2013

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A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA

Nucleic acids research, 2010-01, Vol.38 (1), p.299-313

2010

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Towards a molecular view of transcriptional control

Current opinion in structural biology, 2012-04, Vol.22 (2), p.160-167

2012

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Kinking Occurs during Molecular Dynamics Simulations of Small DNA Minicircles

Structure (London), 2006-10, Vol.14 (10), p.1527-1534

2006

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Investigating the Local Flexibility of Functional Residues in Hemoproteins

Biophysical journal, 2006-04, Vol.90 (8), p.2706-2717

2006

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Cadherin Mechanics and Complexation: The Importance of Calcium Binding

Biophysical journal, 2005-12, Vol.89 (6), p.3895-3903

2005

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DNA minicircles clarify the specific role of DNA structure on retroviral integration

Nucleic acids research, 2016-09, Vol.44 (16), p.7830-7847

2016

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Internal Coordinate Normal Mode Analysis: A Strategy To Predict Protein Conformational Transitions

The journal of physical chemistry. B, 2019-02, Vol.123 (6), p.1294-1301

2019

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Structure and dynamics of DNA loops on nucleosomes studied with atomistic, microsecond-scale molecular dynamics

Nucleic acids research, 2016-06, Vol.44 (11), p.5450-5456

2016

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Identification of Protein Interaction Partners and Protein–Protein Interaction Sites

Journal of molecular biology, 2008-10, Vol.382 (5), p.1276-1289

2008

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Arbitrary protein-protein docking targets biologically relevant interfaces

BMC biophysics, 2012-05, Vol.5 (1), p.7-7, Article 7

2012

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Joint evolutionary trees: a large-scale method to predict protein interfaces based on sequence sampling

PLoS computational biology, 2009-01, Vol.5 (1), p.e1000267

2009

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DNA: An Extensible Molecule

Science (American Association for the Advancement of Science), 1996-02, Vol.271 (5250), p.792-794

1996

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Sequence-dependent response of DNA to torsional stress: a potential biological regulation mechanism

Nucleic acids research, 2018-02, Vol.46 (4), p.1684-1694

2018

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Probing the Flexibility of the Bacterial Reaction Center: The Wild-Type Protein Is More Rigid Than Two Site-Specific Mutants

Biochemistry (Easton), 2007-12, Vol.46 (51), p.14960-14968

2007

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Exciton States of Dynamic DNA Double Helices: Alternating dCdG Sequences

The journal of physical chemistry. B, 2005-08, Vol.109 (33), p.16109-16118

2005

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Analyzing ion distributions around DNA: sequence-dependence of potassium ion distributions from microsecond molecular dynamics

Nucleic acids research, 2015-02, Vol.43 (4), p.2412-2423

2015

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CURVES+ web server for analyzing and visualizing the helical, backbone and groove parameters of nucleic acid structures

Nucleic acids research, 2011-07, Vol.39 (Web Server issue), p.W68-W73

2011

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Protein-DNA interfaces: a molecular dynamics analysis of time-dependent recognition processes for three transcription factors

Nucleic acids research, 2016-11, Vol.44 (20), p.9990

2016

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Dynamics and recognition within a protein-DNA complex: a molecular dynamics study of the SKN-1/DNA interaction

A molecular dynamics study of adenylyl cyclase: The impact of ATP and G-protein binding

Internal Normal Mode Analysis (iNMA) Applied to Protein Conformational Flexibility

Multiple protein-DNA interfaces unravelled by evolutionary information, physico-chemical and geometrical properties

Exploring polymorphisms in B-DNA helical conformations

Significance of Molecular Dynamics Simulations for Life Sciences

PaLaCe: A Coarse-Grain Protein Model for Studying Mechanical Properties

A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA

Towards a molecular view of transcriptional control

Kinking Occurs during Molecular Dynamics Simulations of Small DNA Minicircles

Investigating the Local Flexibility of Functional Residues in Hemoproteins

Cadherin Mechanics and Complexation: The Importance of Calcium Binding

DNA minicircles clarify the specific role of DNA structure on retroviral integration

Internal Coordinate Normal Mode Analysis: A Strategy To Predict Protein Conformational Transitions

Structure and dynamics of DNA loops on nucleosomes studied with atomistic, microsecond-scale molecular dynamics

Identification of Protein Interaction Partners and Protein–Protein Interaction Sites

Arbitrary protein-protein docking targets biologically relevant interfaces

Joint evolutionary trees: a large-scale method to predict protein interfaces based on sequence sampling

DNA: An Extensible Molecule

Sequence-dependent response of DNA to torsional stress: a potential biological regulation mechanism

Probing the Flexibility of the Bacterial Reaction Center: The Wild-Type Protein Is More Rigid Than Two Site-Specific Mutants

Exciton States of Dynamic DNA Double Helices: Alternating dCdG Sequences

Analyzing ion distributions around DNA: sequence-dependence of potassium ion distributions from microsecond molecular dynamics

CURVES+ web server for analyzing and visualizing the helical, backbone and groove parameters of nucleic acid structures

Protein-DNA interfaces: a molecular dynamics analysis of time-dependent recognition processes for three transcription factors

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