MMB-GUI: a fast morphing method demonstrates a possible ribosomal tRNA translocation trajectory

YASARA View—molecular graphics for all devices—from smartphones to workstations

(2014) Elmar Krieger et al.   BIOINFORMATICS

iMODS: internal coordinates normal mode analysis server

(2014) José Ramón López-Blanco et al.   NUCLEIC ACIDS RESEARCH

A multiscale approach to predicting affinity changes in protein-protein interfaces

(2014) Daniel F. A. R. Dourado et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Energy barriers and driving forces in tRNA translocation through the ribosome

(2013) Lars V Bock et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Fast fitting to low resolution density maps: elucidating large-scale motions of the ribosome

(2013) Samuel Coulbourn Flores   NUCLEIC ACIDS RESEARCH

Editorial: NAR Surveys the Past, Present and Future of Restriction Endonucleases

(2013) W. Dynan et al.   NUCLEIC ACIDS RESEARCH

Visualization of two transfer RNAs trapped in transit during elongation factor G-mediated translocation

(2013) D. J. F. Ramrath et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure of the ribosome with elongation factor G trapped in the pretranslocation state

(2013) A. F. Brilot et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Connecting the Kinetics and Energy Landscape of tRNA Translocation on the Ribosome

(2013) Paul C. Whitford et al.   PLoS Computational Biology

KOSMOS: a universal morph server for nucleic acids, proteins and their complexes

(2012) S. Seo et al.   NUCLEIC ACIDS RESEARCH

Modeling and design by hierarchical natural moves

(2012) A. Y. L. Sim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rotation of the head of the 30S ribosomal subunit during mRNA translocation

(2012) Z. Guo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Maximum likelihood models and algorithms for gene tree evolution with duplications and losses

(2011) Pawel Górecki et al.   BMC BIOINFORMATICS

Messenger RNA interactions in the decoding center control the rate of translocation

(2011) Prashant K Khade et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

mRNA translocation occurs during the second step of ribosomal intersubunit rotation

(2011) Dmitri N Ermolenko et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

ModeRNA: a tool for comparative modeling of RNA 3D structure

(2011) Magdalena Rother et al.   NUCLEIC ACIDS RESEARCH

Umbrella sampling

(2011) Johannes Kästner   Wiley Interdisciplinary Reviews-Computational Molecular Science

Fast Flexible Modeling of RNA Structure Using Internal Coordinates

(2010) S. C. Flores et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Quantitative analysis of cryo-EM density map segmentation by watershed and scale-space filtering, and fitting of structures by alignment to regions

(2010) Grigore D. Pintilie et al.   JOURNAL OF STRUCTURAL BIOLOGY

Head swivel on the ribosome facilitates translocation by means of intra-subunit tRNA hybrid sites

(2010) Andreas H. Ratje et al.   NATURE

Turning limited experimental information into 3D models of RNA

(2010) S. C. Flores et al.   RNA

Accommodation of aminoacyl-tRNA into the ribosome involves reversible excursions along multiple pathways

(2010) P. C. Whitford et al.   RNA

Insights into substrate stabilization from snapshots of the peptidyl transferase center of the intact 70S ribosome

(2009) Rebecca M Voorhees et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Allosteric collaboration between elongation factor G and the ribosomal L1 stalk directs tRNA movements during translation

(2009) J. Fei et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Following movement of the L1 stalk between three functional states in single ribosomes

(2009) Peter V. Cornish et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Structure of the Ribosome with Elongation Factor G Trapped in the Posttranslocational State

(2009) Y.-G. Gao et al.   SCIENCE

Can Morphing Methods Predict Intermediate Structures?

(2008) Dahlia R. Weiss et al.   JOURNAL OF MOLECULAR BIOLOGY

Spontaneous Intersubunit Rotation in Single Ribosomes

(2008) Peter V. Cornish et al.   MOLECULAR CELL

HingeMaster: Normal mode hinge prediction approach and integration of complementary predictors

(2008) Samuel C. Flores et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

A role for the 30S subunit E site in maintenance of the translational reading frame

(2008) A. Devaraj et al.   RNA

Flexible Fitting of Atomic Structures into Electron Microscopy Maps Using Molecular Dynamics

(2008) Leonardo G. Trabuco et al.   STRUCTURE