A unified coarse-grained model of biological macromolecules based on mean-field multipole–multipole interactions

The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems

(2014) Fabio Sterpone et al.   CHEMICAL SOCIETY REVIEWS

Kinks, loops, and protein folding, with protein A as an example

(2014) Andrey Krokhotin et al.   JOURNAL OF CHEMICAL PHYSICS

Evaluation of coarse-grained mapping schemes for polysaccharide chains in cellulose

(2013) Sergiy Markutsya et al.   JOURNAL OF CHEMICAL PHYSICS

Importance of the Ion-Pair Interactions in the OPEP Coarse-Grained Force Field: Parametrization and Validation

(2013) Fabio Sterpone et al.   Journal of Chemical Theory and Computation

Improvement of the Treatment of Loop Structures in the UNRES Force Field by Inclusion of Coupling between Backbone- and Side-Chain-Local Conformational States

(2013) Paweł Krupa et al.   Journal of Chemical Theory and Computation

Coarse-Grained Simulations of RNA and DNA Duplexes

(2013) Tristan Cragnolini et al.   JOURNAL OF PHYSICAL CHEMISTRY B

RNA 3D Structure Prediction by Using a Coarse-Grained Model and Experimental Data

(2013) Zhen Xia et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Coarse graining: a tool for large-scale simulations or more?

(2013) Adam Liwo   PHYSICA SCRIPTA

Mean-Field Interactions between Nucleic-Acid-Base Dipoles can Drive the Formation of a Double Helix

(2013) Yi He et al.   PHYSICAL REVIEW LETTERS

Lessons from application of the UNRES force field to predictions of structures of CASP10 targets

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

Combining coarse-grained nonbonded and atomistic bonded interactions for protein modeling

(2013) Martin Zacharias   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

PolySac3DB: an annotated data base of 3 dimensional structures of polysaccharides

(2012) Anita Sarkar et al.   BMC BIOINFORMATICS

Coexistence of Phases in a Protein Heterodimer

(2012) Andrey Krokhotin et al.   JOURNAL OF CHEMICAL PHYSICS

Hidden Protein Folding Pathways in Free-Energy Landscapes Uncovered by Network Analysis

(2012) Yanping Yin et al.   Journal of Chemical Theory and Computation

Simulation of the Opening and Closing of Hsp70 Chaperones by Coarse-Grained Molecular Dynamics

(2012) Ewa Gołaś et al.   Journal of Chemical Theory and Computation

Determination of Effective Potentials for the Stretching of Cα···Cα Virtual Bonds in Polypeptide Chains for Coarse-Grained Simulations of Proteins from ab Initio Energy Surfaces of N-Methylacetamide and N-Acetylpyrrolidine

(2012) Adam K. Sieradzan et al.   Journal of Chemical Theory and Computation

Effects of Mutation, Truncation, and Temperature on the Folding Kinetics of a WW Domain

(2012) Gia G. Maisuradze et al.   JOURNAL OF MOLECULAR BIOLOGY

The Coarse-Grained OPEP Force Field for Non-Amyloid and Amyloid Proteins

(2012) Yassmine Chebaro et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Structure and Dynamics of the ATP-Bound Open Conformation of Hsp70 Chaperones

(2012) Roman Kityk et al.   MOLECULAR CELL

Correcting for Heat Capacity and 5′-TA Type Terminal Nearest Neighbors Improves Prediction of DNA Melting Temperatures Using Nearest-Neighbor Thermodynamic Models

(2011) Curtis B. Hughesman et al.   BIOCHEMISTRY

Role of the Heat Capacity Change in Understanding and Modeling Melting Thermodynamics of Complementary Duplexes Containing Standard and Nucleobase-Modified LNA

(2011) Curtis B. Hughesman et al.   BIOCHEMISTRY

Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model

(2011) Thomas E. Ouldridge et al.   JOURNAL OF CHEMICAL PHYSICS

Simple Physics-Based Analytical Formulas for the Potentials of Mean Force of the Interaction of Amino-Acid Side Chains in Water. V. Like-Charged Side Chains

(2011) Mariusz Makowski et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A Study of the α-Helical Intermediate Preceding the Aggregation of the Amino-Terminal Fragment of the β Amyloid Peptide (Aβ1–28)

(2011) Ana V. Rojas et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Exploration of Transferability in Multiscale Coarse-Grained Peptide Models

(2011) Ian F. Thorpe et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Simple Physics-Based Analytical Formulas for the Potentials of Mean Force of the Interaction of Amino-Acid Side Chains in Water. VI. Oppositely Charged Side Chains

(2011) Mariusz Makowski et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Coarse-grained force field: general folding theory

(2011) Adam Liwo et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Fully differentiable coarse-grained and all-atom knowledge-based potentials for RNA structure evaluation

(2011) J. Bernauer et al.   RNA

Implementation of Molecular Dynamics and Its Extensions with the Coarse-Grained UNRES Force Field on Massively Parallel Systems: Toward Millisecond-Scale Simulations of Protein Structure, Dynamics, and Thermodynamics

(2010) Adam Liwo et al.   Journal of Chemical Theory and Computation

Mechanism of Fiber Assembly: Treatment of Aβ Peptide Aggregation with a Coarse-Grained United-Residue Force Field

(2010) Ana Rojas et al.   JOURNAL OF MOLECULAR BIOLOGY

PDZ Binding to the BAR Domain of PICK1 is Elucidated by Coarse-grained Molecular Dynamics

(2010) Yi He et al.   JOURNAL OF MOLECULAR BIOLOGY

Investigation of Protein Folding by Coarse-Grained Molecular Dynamics with the UNRES Force Field

(2010) Gia G. Maisuradze et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Coarse-Grained Model for Simulation of RNA Three-Dimensional Structures

(2010) Zhen Xia et al.   JOURNAL OF PHYSICAL CHEMISTRY B

HiRE-RNA: A High Resolution Coarse-Grained Energy Model for RNA

(2010) Samuela Pasquali et al.   JOURNAL OF PHYSICAL CHEMISTRY B

DNA Nanotweezers Studied with a Coarse-Grained Model of DNA

(2010) Thomas E. Ouldridge et al.   PHYSICAL REVIEW LETTERS

Atomic-Level Characterization of the Structural Dynamics of Proteins

(2010) D. E. Shaw et al.   SCIENCE

Martini Coarse-Grained Force Field: Extension to Carbohydrates

(2009) Cesar A. López et al.   Journal of Chemical Theory and Computation

Application of Multiplexed Replica Exchange Molecular Dynamics to the UNRES Force Field: Tests with α and α+β Proteins

(2009) Cezary Czaplewski et al.   Journal of Chemical Theory and Computation

Exploring the parameter space of the coarse-grained UNRES force field by random search: Selecting a transferable medium-resolution force field

(2009) Yi He et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Accelerating molecular dynamic simulation on graphics processing units

(2009) Mark S. Friedrichs et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

How Adequate are One- and Two-Dimensional Free Energy Landscapes for Protein Folding Dynamics?

(2009) Gia G. Maisuradze et al.   PHYSICAL REVIEW LETTERS

Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters

(2009) M. A. Jonikas et al.   RNA

Anton, a special-purpose machine for molecular dynamics simulation

(2008) David E. Shaw et al.   COMMUNICATIONS OF THE ACM

The MARTINI Coarse-Grained Force Field: Extension to Proteins

(2008) Luca Monticelli et al.   Journal of Chemical Theory and Computation

Coarse-grained force field for the nucleosome from self-consistent multiscaling

(2008) Karine Voltz et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Simple Physics-Based Analytical Formulas for the Potentials of Mean Force for the Interaction of Amino Acid Side Chains in Water. IV. Pairs of Different Hydrophobic Side Chains

(2008) Mariusz Makowski et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Peptide Folding Using Multiscale Coarse-Grained Models

(2008) Ian F. Thorpe et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Self-Assembly of the β2-Microglobulin NHVTLSQ Peptide Using a Coarse-Grained Protein Model Reveals a β-Barrel Species

(2008) Wei Song et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Thermodynamics and dynamics of amyloid peptide oligomerization are sequence dependent

(2008) Yan Lu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Ab initio RNA folding by discrete molecular dynamics: From structure prediction to folding mechanisms

(2008) F. Ding et al.   RNA

Coarse-grained models of protein folding: toy models or predictive tools?

(2007) Cecilia Clementi   CURRENT OPINION IN STRUCTURAL BIOLOGY

Coarse-grained Models for Simulations of Multiprotein Complexes: Application to Ubiquitin Binding

(2007) Young C. Kim et al.   JOURNAL OF MOLECULAR BIOLOGY