Exploring the molecular basis of RNA recognition by the dimeric RNA-binding protein via molecular simulation methods

Structure based approach for understanding organism specific recognition of protein-RNA complexes

(2015) Raju Nagarajan et al.   Biology Direct

Understanding peptide competitive inhibition of botulinum neurotoxin a binding to SV2 protein via molecular dynamics simulations

(2015) Shan Chang et al.   BIOPOLYMERS

The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities

(2015) Samuel Genheden et al.   Expert Opinion on Drug Discovery

CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field

(2015) Jumin Lee et al.   Journal of Chemical Theory and Computation

Specificity and nonspecificity in RNA–protein interactions

(2015) Eckhard Jankowsky et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Structural basis underlying CAC RNA recognition by the RRM domain of dimeric RNA-binding protein RBPMS

(2015) Marianna Teplova et al.   QUARTERLY REVIEWS OF BIOPHYSICS

Evidence for cooperative tandem binding of hnRNP C RRMs in mRNA processing

(2015) Zuzana Cieniková et al.   RNA

The C-terminal RNA binding motif of HuR is a multi-functional domain leading to HuR oligomerization and binding to U-rich RNA targets

(2015) Rafael M Scheiba et al.   RNA Biology

g_mmpbsa—A GROMACS Tool for High-Throughput MM-PBSA Calculations

(2014) Rashmi Kumari et al.   Journal of Chemical Information and Modeling

Identification of the RNA recognition element of the RBPMS family of RNA-binding proteins and their transcriptome-wide mRNA targets

(2014) T. A. Farazi et al.   RNA

The Arginine-Rich RNA-Binding Motif of HIV-1 Rev Is Intrinsically Disordered and Folds upon RRE Binding

(2013) Fabio Casu et al.   BIOPHYSICAL JOURNAL

Engineering RNA-binding proteins for biology

(2013) Yu Chen et al.   FEBS Journal

Computational modeling of protein–RNA complex structures

(2013) Irina Tuszynska et al.   METHODS

The “Observer Effect” in Genome-wide Surveys of Protein-RNA Interactions

(2013) Kasandra J. Riley et al.   MOLECULAR CELL

Detection of peptide-binding sites on protein surfaces: The first step toward the modeling and targeting of peptide-mediated interactions

(2013) Assaf Lavi et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

RRM–RNA recognition: NMR or crystallography…and new findings

(2012) Gerrit M Daubner et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Network models reveal stability and structural rearrangement of signal recognition particle

(2012) Shan Chang et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Molecular dynamics simulations of wild type and mutants of human complement receptor 2 complexed with C3d

(2012) Hua Wan et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Computational biology of RNA interactions

(2012) Christoph Dieterich et al.   Wiley Interdisciplinary Reviews-RNA

Structural insight into RNA recognition motifs: versatile molecular Lego building blocks for biological systems

(2012) Yutaka Muto et al.   Wiley Interdisciplinary Reviews-RNA

Conformational Selection in the Recognition of Phosphorylated Substrates by the Catalytic Domain of Human Pin1

(2011) Hector A. Velazquez et al.   BIOCHEMISTRY

Computational methods for prediction of protein–RNA interactions

(2011) Tomasz Puton et al.   JOURNAL OF STRUCTURAL BIOLOGY

Peptoid conformational free energy landscapes from implicit-solvent molecular simulations in AMBER

(2010) Vincent A. Voelz et al.   BIOPOLYMERS

Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free Energy Calculations Based on Molecular Dynamics Simulations

(2010) Tingjun Hou et al.   Journal of Chemical Information and Modeling

Relation between Free Energy Landscapes of Proteins and Dynamics

(2010) Gia G. Maisuradze et al.   Journal of Chemical Theory and Computation

Use of the spliceosomal protein U1A to facilitate crystallization and structure determination of complex RNAs

(2010) Adrian R. Ferré-D’Amaré   METHODS

Substrate recognition and transport behavior analyses of amino acid antiporter with coarse-grained models

(2010) Shan Chang et al.   Molecular BioSystems

Binding of the Bacteriophage P22 N-Peptide to the boxB RNA Motif Studied by Molecular Dynamics Simulations

(2009) Ranjit P. Bahadur et al.   BIOPHYSICAL JOURNAL

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Free-energy landscape, principal component analysis, and structural clustering to identify representative conformations from molecular dynamics simulations: The myoglobin case

(2009) Elena Papaleo et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

RNA recognition motifs: boring? Not quite

(2008) Antoine Cléry et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

CHARMM-GUI: A web-based graphical user interface for CHARMM

(2008) Sunhwan Jo et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY