Rigidity theory for biomolecules: concepts, software, and applications

Rigidity Theory-Based Approximation of Vibrational Entropy Changes upon Binding to Biomolecules

(2017) Holger Gohlke et al.   Journal of Chemical Theory and Computation

Structural intermediates and directionality of the swiveling motion of Pyruvate Phosphate Dikinase

(2017) Alexander Minges et al.   Scientific Reports

Mutations in Antibody Fragments Modulate Allosteric Response Via Hydrogen-Bond Network Fluctuations

(2016) Amit Srivastava et al.   BIOPHYSICAL JOURNAL

Quantitative FRET studies and integrative modeling unravel the structure and dynamics of biomolecular systems

(2016) Mykola Dimura et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Coupled Motions in β2AR:Gαs Conformational Ensembles

(2016) Dimitar V. Pachov et al.   Journal of Chemical Theory and Computation

Role of Enzyme Flexibility in Ligand Access and Egress to Active Site: Bias-Exchange Metadynamics Study of 1,3,7-Trimethyluric Acid in Cytochrome P450 3A4

(2016) Markéta Paloncýová et al.   Journal of Chemical Theory and Computation

Probing RNA Native Conformational Ensembles with Structural Constraints

(2016) Rasmus Fonseca et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Detecting the native ligand orientation by interfacial rigidity: SiteInterlock

(2016) Sebastian Raschka et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Application of Rigidity Theory to the Thermostabilization of Lipase A from Bacillus subtilis

(2016) Prakash Chandra Rathi et al.   PLoS Computational Biology

Large scale rigidity-based flexibility analysis of biomolecules

(2016) Ileana Streinu   Structural Dynamics

Trading off stability against activity in extremophilic aldolases

(2016) Markus Dick et al.   Scientific Reports

VisualCNA: a GUI for interactive constraint network analysis and protein engineering for improving thermostability: Fig. 1.

(2015) Prakash Chandra Rathi et al.   BIOINFORMATICS

X-ray, spectroscopic and normal-mode dynamics of calexcitin: structure–function studies of a neuronal calcium-signalling protein

(2015) P. T. Erskine et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Flexibility Correlation between Active Site Regions Is Conserved across Four AmpC β-Lactamase Enzymes

(2015) Jenna R. Brown et al.   PLoS One

Structural Rigidity and Protein Thermostability in Variants of Lipase A from Bacillus subtilis

(2015) Prakash Chandra Rathi et al.   PLoS One

Identification and X-ray Co-crystal Structure of a Small-Molecule Activator of LFA-1-ICAM-1 Binding

(2014) Martin Hintersteiner et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

The role of protein dynamics in GPCR function: insights from the β2AR and rhodopsin

(2014) Aashish Manglik et al.   CURRENT OPINION IN CELL BIOLOGY

A Large-Scale Test of Free-Energy Simulation Estimates of Protein–Ligand Binding Affinities

(2014) Paulius Mikulskis et al.   Journal of Chemical Information and Modeling

Constrained geometric simulation of the nicotinic acetylcholine receptor

(2014) William J. Belfield et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Characterizing RNA ensembles from NMR data with kinematic models

(2014) Rasmus Fonseca et al.   NUCLEIC ACIDS RESEARCH

Constrained geometric dynamics of the Fenna–Matthews–Olson complex: the role of correlated motion in reducing uncertainty in excitation energy transfer

(2014) Alexander S. Fokas et al.   PHOTOSYNTHESIS RESEARCH

Thermodynamic Stability and Flexibility Characteristics of Antibody Fragment Complexes

(2014) Tong Li et al.   PROTEIN AND PEPTIDE LETTERS

Structures of mesophilic and extremophilic citrate synthases reveal rigidity and flexibility for function

(2014) Stephen A. Wells et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Solving nucleic acid structures by molecular replacement: examples from group II intron studies

(2013) Marco Marcia et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

The Underappreciated Role of Allostery in the Cellular Network

(2013) Ruth Nussinov et al.   Annual Review of Biophysics

Towards accurate modeling of noncovalent interactions for protein rigidity analysis

(2013) Naomi Fox et al.   BMC BIOINFORMATICS

Impact of intracellular domain flexibility upon properties of activated human 5-HT3receptors

(2013) J L Kozuska et al.   BRITISH JOURNAL OF PHARMACOLOGY

Constraint Network Analysis (CNA): A Python Software Package for Efficiently Linking Biomacromolecular Structure, Flexibility, (Thermo-)Stability, and Function

(2013) Christopher Pfleger et al.   Journal of Chemical Information and Modeling

CNA web server: rigidity theory-based thermal unfolding simulations of proteins for linking structure, (thermo-)stability, and function

(2013) Dennis M. Krüger et al.   NUCLEIC ACIDS RESEARCH

Probing protein ensemble rigidity and hydrogen–deuterium exchange

(2013) Adnan Sljoka et al.   PHYSICAL BIOLOGY

Efficient and Robust Analysis of Biomacromolecular Flexibility Using Ensembles of Network Topologies Based on Fuzzy Noncovalent Constraints

(2013) Christopher Pfleger et al.   STRUCTURE

Variations within Class-A β-Lactamase Physiochemical Properties Reflect Evolutionary and Environmental Patterns, but not Antibiotic Specificity

(2013) Deeptak Verma et al.   PLoS Computational Biology

High-resolution NMR studies of structure and dynamics of human ERp27 indicate extensive interdomain flexibility

(2012) Nader T. Amin et al.   BIOCHEMICAL JOURNAL

Exploring the Energy Landscapes of Protein Folding Simulations with Bayesian Computation

(2012) Nikolas S. Burkoff et al.   BIOPHYSICAL JOURNAL

Thermostabilizing mutations preferentially occur at structural weak spots with a high mutation ratio

(2012) Prakash C. Rathi et al.   JOURNAL OF BIOTECHNOLOGY

Global and local indices for characterizing biomolecular flexibility and rigidity

(2012) Christopher Pfleger et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

NMSim Web Server: integrated approach for normal mode-based geometric simulations of biologically relevant conformational transitions in proteins

(2012) D. M. Kruger et al.   NUCLEIC ACIDS RESEARCH

Rapid simulation of protein motion: merging flexibility, rigidity and normal mode analyses

(2012) J E Jimenez-Roldan et al.   PHYSICAL BIOLOGY

Calculating Ensemble Averaged Descriptions of Protein Rigidity without Sampling

(2012) Luis C. González et al.   PLoS One

Changes in Lysozyme Flexibility upon Mutation Are Frequent, Large and Long-Ranged

(2012) Deeptak Verma et al.   PLoS Computational Biology

Predicting the Melting Point of Human C-Type Lysozyme Mutants

(2011) Deeptak Verma et al.   CURRENT PROTEIN & PEPTIDE SCIENCE

A Proof of the Molecular Conjecture

(2011) Naoki Katoh et al.   DISCRETE & COMPUTATIONAL GEOMETRY

Allosteric Communication in Cysteinyl tRNA Synthetase

(2011) Amit Ghosh et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A Normal Mode-Based Geometric Simulation Approach for Exploring Biologically Relevant Conformational Transitions in Proteins

(2011) Aqeel Ahmed et al.   Journal of Chemical Information and Modeling

Hot Spots and Transient Pockets: Predicting the Determinants of Small-Molecule Binding to a Protein–Protein Interface

(2011) Alexander Metz et al.   Journal of Chemical Information and Modeling

A Force Field with Discrete Displaceable Waters and Desolvation Entropy for Hydrated Ligand Docking

(2011) Stefano Forli et al.   JOURNAL OF MEDICINAL CHEMISTRY

In Vitro Evolved Non-Aggregating and Thermostable Lipase: Structural and Thermodynamic Investigation

(2011) Md. Zahid Kamal et al.   JOURNAL OF MOLECULAR BIOLOGY

KINARI-Web: a server for protein rigidity analysis

(2011) N. Fox et al.   NUCLEIC ACIDS RESEARCH

Sampling-based exploration of folded state of a protein under kinematic and geometric constraints

(2011) Peggy Yao et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Union of Geometric Constraint-Based Simulations with Molecular Dynamics for Protein Structure Prediction

(2010) Tyler J. Glembo et al.   BIOPHYSICAL JOURNAL

Allosteric Response Is both Conserved and Variable across Three CheY Orthologs

(2010) James M. Mottonen et al.   BIOPHYSICAL JOURNAL

The key function of a conserved and modified rRNA residue in the ribosomal response to the nascent peptide

(2010) Nora Vázquez-Laslop et al.   EMBO JOURNAL

HIV-1 TAR RNA Spontaneously Undergoes Relevant Apo-to-Holo Conformational Transitions in Molecular Dynamics and Constrained Geometrical Simulations

(2010) Simone Fulle et al.   Journal of Chemical Information and Modeling

On the entropy of protein folding

(2010) George I. Makhatadze et al.   PROTEIN SCIENCE

Large-scale comparison of protein essential dynamics from molecular dynamics simulations and coarse-grained normal mode analyses

(2010) Aqeel Ahmed et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Generating stereochemically acceptable protein pathways

(2010) Daniel W. Farrell et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein rigidity and thermophilic adaptation

(2010) Sebastian Radestock et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Free State Conformational Sampling of the SAM-I Riboswitch Aptamer Domain

(2010) Colby D. Stoddard et al.   STRUCTURE

Intra and Inter-Molecular Communications Through Protein Structure Network

(2009) Saraswathi Vishveshwara et al.   CURRENT PROTEIN & PEPTIDE SCIENCE

Statics of the Ribosomal Exit Tunnel: Implications for Cotranslational Peptide Folding, Elongation Regulation, and Antibiotics Binding

(2009) Simone Fulle et al.   JOURNAL OF MOLECULAR BIOLOGY

A graph theoretical approach for assessing bio-macromolecular complex structural stability

(2009) Carlos Adriel Del Carpio et al.   JOURNAL OF MOLECULAR MODELING

Constraint counting on RNA structures: Linking flexibility and function

(2009) Simone Fulle et al.   METHODS

Dynamic activation of an allosteric regulatory protein

(2009) Shiou-Ru Tzeng et al.   NATURE

Dynamical networks in tRNA:protein complexes

(2009) A. Sethi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Thermally denatured state determines refolding in lipase: Mutational analysis

(2009) Shoeb Ahmad et al.   PROTEIN SCIENCE

Structural Insight into Nascent Polypeptide Chain-Mediated Translational Stalling

(2009) B. Seidelt et al.   SCIENCE

Allosteric Communication Occurs via Networks of Tertiary and Quaternary Motions in Proteins

(2009) Michael D. Daily et al.   PLoS Computational Biology

Design and synthesis of a series of meta aniline-based LFA-1 ICAM inhibitors

(2008) Kevin M. Guckian et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Four-Scale Description of Membrane Sculpting by BAR Domains

(2008) Anton Arkhipov et al.   BIOPHYSICAL JOURNAL

Analyzing the Flexibility of RNA Structures by Constraint Counting

(2008) Simone Fulle et al.   BIOPHYSICAL JOURNAL

Hydrogen bond networks determine emergent mechanical and thermodynamic properties across a protein family

(2008) Dennis R Livesay et al.   Chemistry Central Journal

Proteins As Networks: Usefulness of Graph Theory in Protein Science

(2008) Alessandro Giuliani et al.   CURRENT PROTEIN & PEPTIDE SCIENCE

Exploiting the Link between Protein Rigidity and Thermostability for Data-Driven Protein Engineering

(2008) S. Radestock et al.   ENGINEERING IN LIFE SCIENCES

Target Flexibility: An Emerging Consideration in Drug Discovery and Design†

(2008) Pietro Cozzini et al.   JOURNAL OF MEDICINAL CHEMISTRY

Thermostable Bacillus subtilis Lipases: In Vitro Evolution and Structural Insight

(2008) Shoeb Ahmad et al.   JOURNAL OF MOLECULAR BIOLOGY

Characterization of the pre-force-generation state in the actomyosin cross-bridge cycle

(2008) M. Sun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Unifying mechanical and thermodynamic descriptions across the thioredoxin protein family

(2008) James M. Mottonen et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Identification of putative, stable binding regions through flexibility analysis of HIV-1 gp120

(2008) Hepan Tan et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Fitting Low-Resolution Cryo-EM Maps of Proteins Using Constrained Geometric Simulations

(2007) Craig C. Jolley et al.   BIOPHYSICAL JOURNAL

Pebble game algorithms and sparse graphs

(2007) Audrey Lee et al.   DISCRETE MATHEMATICS