Solving protein structures using short-distance cross-linking constraints as a guide for discrete molecular dynamics simulations

Applications of Discrete Molecular Dynamics in biology and medicine

(2016) Elizabeth A Proctor et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Demonstrating an Order-of-Magnitude Sampling Enhancement in Molecular Dynamics Simulations of Complex Protein Systems

(2016) Albert C. Pan et al.   Journal of Chemical Theory and Computation

Picosecond to Millisecond Structural Dynamics in Human Ubiquitin

(2016) Kresten Lindorff-Larsen et al.   JOURNAL OF PHYSICAL CHEMISTRY B

The novel isotopically coded short-range photo-reactive crosslinker 2,4,6-triazido-1,3,5-triazine (TATA) for studying protein structures

(2016) Nicholas I. Brodie et al.   Journal of Proteomics

A critical assessment of methods to recover information from averaged data

(2016) Enrico Ravera et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Blind protein structure prediction using accelerated free-energy simulations

(2016) A. Perez et al.   Science Advances

Structural Ensembles of Intrinsically Disordered Proteins Depend Strongly on Force Field: A Comparison to Experiment

(2015) Sarah Rauscher et al.   Journal of Chemical Theory and Computation

Molecular Dynamics Simulations of Intrinsically Disordered Proteins: Force Field Evaluation and Comparison with Experiment

(2015) João Henriques et al.   Journal of Chemical Theory and Computation

Isotopically-coded short-range hetero-bifunctional photo-reactive crosslinkers for studying protein structure

(2015) Nicholas I. Brodie et al.   Journal of Proteomics

HDX Match Software for the Data Analysis of Top-Down ECD-FTMS Hydrogen/Deuterium Exchange Experiments

(2015) Evgeniy V. Petrotchenko et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Serum Albumin Domain Structures in Human Blood Serum by Mass Spectrometry and Computational Biology

(2015) Adam Belsom et al.   MOLECULAR & CELLULAR PROTEOMICS

Determining protein structures by combining semireliable data with atomistic physical models by Bayesian inference

(2015) Justin L. MacCallum et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Accurate secondary structure prediction and fold recognition for circular dichroism spectroscopy

(2015) András Micsonai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nonnative SOD1 trimer is toxic to motor neurons in a model of amyotrophic lateral sclerosis

(2015) Elizabeth A. Proctor et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Accuracy of Current All-Atom Force-Fields in Modeling Protein Disordered States

(2014) Ferruccio Palazzesi et al.   Journal of Chemical Theory and Computation

The prolyl isomerase, FKBP25, interacts with RNA-engaged nucleolin and the pre-60S ribosomal subunit

(2014) G. Gudavicius et al.   RNA

Combining Experiments and Simulations Using the Maximum Entropy Principle

(2014) Wouter Boomsma et al.   PLoS Computational Biology

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

(2013) Sander Pronk et al.   BIOINFORMATICS

Discrete Molecular Dynamics: An Efficient And Versatile Simulation Method For Fine Protein Characterization

(2012) David Shirvanyants et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Using multiple structural proteomics approaches for the characterization of prion proteins

(2012) Jason J. Serpa et al.   Journal of Proteomics

The Protein-Folding Problem, 50 Years On

(2012) K. A. Dill et al.   SCIENCE

An Isotopically Coded CID-cleavable Biotinylated Cross-linker for Structural Proteomics

(2010) Evgeniy V. Petrotchenko et al.   MOLECULAR & CELLULAR PROTEOMICS

Atomic-Level Characterization of the Structural Dynamics of Proteins

(2010) D. E. Shaw et al.   SCIENCE

Protein structure prediction: when is it useful?

(2009) Yang Zhang   CURRENT OPINION IN STRUCTURAL BIOLOGY

Hydrogen/Deuterium Exchange Mass Spectrometry with Top-Down Electron Capture Dissociation for Characterizing Structural Transitions of a 17 kDa Protein

(2009) Jingxi Pan et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Protein structure prediction on the Web: a case study using the Phyre server

(2009) Lawrence A Kelley et al.   Nature Protocols

MedusaScore: An Accurate Force Field-Based Scoring Function for Virtual Drug Screening

(2008) Shuangye Yin et al.   Journal of Chemical Information and Modeling

The Jpred 3 secondary structure prediction server

(2008) C. Cole et al.   NUCLEIC ACIDS RESEARCH

Ab Initio Folding of Proteins with All-Atom Discrete Molecular Dynamics

(2008) Feng Ding et al.   STRUCTURE