Structural dynamics and allostery of Rab proteins: strategies for drug discovery and design

Allostery in Its Many Disguises: From Theory to Applications

(2019) Shoshana J. Wodak et al.   STRUCTURE

Discovering Putative Protein Targets of Small Molecules: A Study of the p53 Activator Nutlin

(2019) Minh N. Nguyen et al.   Journal of Chemical Information and Modeling

Applications of machine learning in drug discovery and development

(2019) Jessica Vamathevan et al.   NATURE REVIEWS DRUG DISCOVERY

Protein–ligand interfaces are polarized: discovery of a strong trend for intermolecular hydrogen bonds to favor donors on the protein side with implications for predicting and designing ligand complexes

(2018) Sebastian Raschka et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Allosteric binding sites in Rab11 for potential drug candidates

(2018) Ammu Prasanna Kumar et al.   PLoS One

AlloMAPS: allosteric mutation analysis and polymorphism of signaling database

(2018) Zhen Wah Tan et al.   NUCLEIC ACIDS RESEARCH

Identification of Protein–Ligand Binding Sites by Sequence Information and Ensemble Classifier

(2017) Yijie Ding et al.   Journal of Chemical Information and Modeling

Improved Method for the Identification and Validation of Allosteric Sites

(2017) Kun Song et al.   Journal of Chemical Information and Modeling

CRISPR-Cas9 conformational activation as elucidated from enhanced molecular simulations

(2017) Giulia Palermo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Visualizing correlated motion with HDBSCAN clustering

(2017) Ryan L. Melvin et al.   PROTEIN SCIENCE

AnchorQuery: Rapid online virtual screening for small-molecule protein-protein interaction inhibitors

(2017) David R. Koes et al.   PROTEIN SCIENCE

Discovery of Rab1 binding sites using an ensemble of clustering methods

(2017) Suryani Lukman et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Predicting Protein Dynamics and Allostery Using Multi-Protein Atomic Distance Constraints

(2017) Joe G. Greener et al.   STRUCTURE

Protein conformational flexibility modulates kinetics and thermodynamics of drug binding

(2017) M. Amaral et al.   Nature Communications

Machine Learning and Network Analysis of Molecular Dynamics Trajectories Reveal Two Chains of Red/Ox-specific Residue Interactions in Human Protein Disulfide Isomerase

(2017) Razieh Karamzadeh et al.   Scientific Reports

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

(2017) Shashank Jariwala et al.   Jove-Journal of Visualized Experiments

Protein Binding Pocket Dynamics

(2016) Antonia Stank et al.   ACCOUNTS OF CHEMICAL RESEARCH

Ras Conformational Ensembles, Allostery, and Signaling

(2016) Shaoyong Lu et al.   CHEMICAL REVIEWS

Protein thermal denaturation is modulated by central residues in the protein structure network

(2016) Valquiria P. Souza et al.   FEBS Journal

CryptoSite: Expanding the Druggable Proteome by Characterization and Prediction of Cryptic Binding Sites

(2016) Peter Cimermancic et al.   JOURNAL OF MOLECULAR BIOLOGY

Rapid Characterization of Allosteric Networks with Ensemble Normal Mode Analysis

(2016) Xin-Qiu Yao et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Benzene Probes in Molecular Dynamics Simulations Reveal Novel Binding Sites for Ligand Design

(2016) Yaw Sing Tan et al.   Journal of Physical Chemistry Letters

A Random Forest Model for Predicting Allosteric and Functional Sites on Proteins

(2016) Ava S.-Y. Chen et al.   Molecular Informatics

NAPS: Network Analysis of Protein Structures

(2016) Broto Chakrabarty et al.   NUCLEIC ACIDS RESEARCH

ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules

(2016) Haim Ashkenazy et al.   NUCLEIC ACIDS RESEARCH

The RING 2.0 web server for high quality residue interaction networks

(2016) Damiano Piovesan et al.   NUCLEIC ACIDS RESEARCH

Accelerated structure-based design of chemically diverse allosteric modulators of a muscarinic G protein-coupled receptor

(2016) Yinglong Miao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure-Based Statistical Mechanical Model Accounts for the Causality and Energetics of Allosteric Communication

(2016) Enrico Guarnera et al.   PLoS Computational Biology

Vinardo: A Scoring Function Based on Autodock Vina Improves Scoring, Docking, and Virtual Screening

(2016) Rodrigo Quiroga et al.   PLoS One

ASBench: benchmarking sets for allosteric discovery: Fig. 1.

(2015) Wenkang Huang et al.   BIOINFORMATICS

AlloPred: prediction of allosteric pockets on proteins using normal mode perturbation analysis

(2015) Joe G Greener et al.   BMC BIOINFORMATICS

MST2-RASSF protein–protein interactions through SARAH domains

(2015) Goar Sánchez-Sanz et al.   BRIEFINGS IN BIOINFORMATICS

A survey of current trends in computational drug repositioning

(2015) Jiao Li et al.   BRIEFINGS IN BIOINFORMATICS

Discovery of multiple hidden allosteric sites by combining Markov state models and experiments

(2015) Gregory R. Bowman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hierarchical Density Estimates for Data Clustering, Visualization, and Outlier Detection

(2015) Ricardo J. G. B. Campello et al.   ACM Transactions on Knowledge Discovery from Data

PARS: a web server for the prediction of Protein Allosteric and Regulatory Sites

(2014) Alejandro Panjkovich et al.   BIOINFORMATICS

ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers

(2014) B. G. Pierce et al.   BIOINFORMATICS

Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation

(2014) Yinglong Miao et al.   Journal of Chemical Theory and Computation

Efficient Characterization of Protein Cavities within Molecular Simulation Trajectories: trj_cavity

(2014) Teresa Paramo et al.   Journal of Chemical Theory and Computation

Molecular Simulations with Solvent Competition Quantify Water Displaceability and Provide Accurate Interaction Maps of Protein Binding Sites

(2014) Daniel Alvarez-Garcia et al.   JOURNAL OF MEDICINAL CHEMISTRY

Ligand-Based Pharmacophore Modeling and Virtual Screening for the Discovery of Novel 17β-Hydroxysteroid Dehydrogenase 2 Inhibitors

(2014) Anna Vuorinen et al.   JOURNAL OF MEDICINAL CHEMISTRY

The ensemble nature of allostery

(2014) Hesam N. Motlagh et al.   NATURE

Capping protein regulators fine-tune actin assembly dynamics

(2014) Marc Edwards et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Computational Design of a pH Stable Enzyme: Understanding Molecular Mechanism of Penicillin Acylase's Adaptation to Alkaline Conditions

(2014) Dmitry Suplatov et al.   PLoS One

Allosite: a method for predicting allosteric sites

(2013) Wenkang Huang et al.   BIOINFORMATICS

Lessons Learned in Empirical Scoring with smina from the CSAR 2011 Benchmarking Exercise

(2013) David Ryan Koes et al.   Journal of Chemical Information and Modeling

The Role of Balanced Training and Testing Data Sets for Binary Classifiers in Bioinformatics

(2013) Qiong Wei et al.   PLoS One

Computational identification of a transiently open L1/S3 pocket for reactivation of mutant p53

(2013) Christopher D. Wassman et al.   Nature Communications

STRUCTURE-BASED METHODS FOR COMPUTATIONAL PROTEIN FUNCTIONAL SITE PREDICTION

(2013) B KC Dukka   Computational and Structural Biotechnology Journal

Using Ligand-Mapping Simulations to Design a Ligand Selectively Targeting a Cryptic Surface Pocket of Polo-Like Kinase 1

(2012) Yaw Sing Tan et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Exploiting protein flexibility to predict the location of allosteric sites

(2012) Alejandro Panjkovich et al.   BMC BIOINFORMATICS

Multiscale modeling of macromolecular biosystems

(2012) S. C. Flores et al.   BRIEFINGS IN BIOINFORMATICS

Centroid-Based Actionable 3D Subspace Clustering

(2012) Kelvin Sim et al.   IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING

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

FTMAP: extended protein mapping with user-selected probe molecules

(2012) C. H. Ngan et al.   NUCLEIC ACIDS RESEARCH

Enabling Large-Scale Design, Synthesis and Validation of Small Molecule Protein-Protein Antagonists

(2012) David Koes et al.   PLoS One

The Interaction Properties of the Human Rab GTPase Family – A Comparative Analysis Reveals Determinants of Molecular Binding Selectivity

(2012) Matthias Stein et al.   PLoS One

Identification of Potential Small Molecule Binding Pockets on Rho Family GTPases

(2012) Juan Manuel Ortiz-Sanchez et al.   PLoS One

Catalytic mechanism of a mammalian Rab{middle dot}RabGAP complex in atomic detail

(2012) K. Gavriljuk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Softening the Rule of Five—where to draw the line?

(2011) Joachim Petit et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Structure-based druggability assessment—identifying suitable targets for small molecule therapeutics

(2011) Eric B Fauman et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Slow dynamics in protein fluctuations revealed by time-structure based independent component analysis: The case of domain motions

(2011) Yusuke Naritomi et al.   JOURNAL OF CHEMICAL PHYSICS

Mutant K-Ras Activation of the Proapoptotic MST2 Pathway Is Antagonized by Wild-Type K-Ras

(2011) David Matallanas et al.   MOLECULAR CELL

CLICK—topology-independent comparison of biomolecular 3D structures

(2011) M. N. Nguyen et al.   NUCLEIC ACIDS RESEARCH

Studying functional dynamics in bio-molecules using accelerated molecular dynamics

(2011) Phineus R. L. Markwick et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Novel Allosteric Sites on Ras for Lead Generation

(2011) Barry J. Grant et al.   PLoS One

Conformational dynamics of capping protein and interaction partners: Simulation studies

(2011) Suryani Lukman et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Unraveling evolutionary constraints: A heterogeneous conservation in dynamics of the titin Ig domains

(2010) Suryani Lukman et al.   FEBS LETTERS

AMINONET– a tool to construct and visualize amino acid networks, and to calculate topological parameters

(2010) Md. Aftabuddin et al.   JOURNAL OF APPLIED CRYSTALLOGRAPHY

Correlating allostery with rigidity

(2010) A. J. Rader et al.   Molecular BioSystems

ASD: a comprehensive database of allosteric proteins and modulators

(2010) Z. Huang et al.   NUCLEIC ACIDS RESEARCH

3V: cavity, channel and cleft volume calculator and extractor

(2010) N. R. Voss et al.   NUCLEIC ACIDS RESEARCH

All-atom normal-mode analysis reveals an RNA-induced allostery in a bacteriophage coat protein

(2010) Eric C. Dykeman et al.   PHYSICAL REVIEW E

Allosteric modulation of Ras positions Q61 for a direct role in catalysis

(2010) G. Buhrman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Two Distinct Mechanisms for Actin Capping Protein Regulation—Steric and Allosteric Inhibition

(2010) Shuichi Takeda et al.   PLOS BIOLOGY

The Distinct Conformational Dynamics of K-Ras and H-Ras A59G

(2010) Suryani Lukman et al.   PLoS Computational Biology

Fpocket: An open source platform for ligand pocket detection

(2009) Vincent Le Guilloux et al.   BMC BIOINFORMATICS

Normal Mode Analysis of Biomolecular Structures: Functional Mechanisms of Membrane Proteins

(2009) Ivet Bahar et al.   CHEMICAL REVIEWS

Combining Machine Learning and Pharmacophore-Based Interaction Fingerprint for in Silico Screening

(2009) Tomohiro Sato et al.   Journal of Chemical Information and Modeling

Binding Site Detection and Druggability Index from First Principles

(2009) Jesus Seco et al.   JOURNAL OF MEDICINAL CHEMISTRY

MetaPocket: A Meta Approach to Improve Protein Ligand Binding Site Prediction

(2009) Bingding Huang   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

A network of dynamically conserved residues deciphers the motions of maltose transporter

(2009) Suryani Lukman et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Detection of multiscale pockets on protein surfaces using mathematical morphology

(2009) Takeshi Kawabata   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Computation of Conformational Coupling in Allosteric Proteins

(2009) Brian A. Kidd et al.   PLoS Computational Biology

Computational Fragment-Based Binding Site Identification by Ligand Competitive Saturation

(2009) Olgun Guvench et al.   PLoS Computational Biology

Ras Conformational Switching: Simulating Nucleotide-Dependent Conformational Transitions with Accelerated Molecular Dynamics

(2009) Barry J. Grant et al.   PLoS Computational Biology

Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure

(2009) John A. Capra et al.   PLoS Computational Biology

Large nucleotide-dependent conformational change in Rab28

(2008) Sung Haeng Lee et al.   FEBS LETTERS

Perspective on Free-Energy Perturbation Calculations for Chemical Equilibria

(2008) William L. Jorgensen et al.   Journal of Chemical Theory and Computation

Allostery: Absence of a Change in Shape Does Not Imply that Allostery Is Not at Play

(2008) Chung-Jung Tsai et al.   JOURNAL OF MOLECULAR BIOLOGY

Normal mode analysis for proteins

(2008) Lars Skjaerven et al.   JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM

The CATH classification revisited--architectures reviewed and new ways to characterize structural divergence in superfamilies

(2008) A. L. Cuff et al.   NUCLEIC ACIDS RESEARCH

Allosteric effects in the marginally stable von Hippel-Lindau tumor suppressor protein and allostery-based rescue mutant design

(2008) J. Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

HOLLOW: Generating Accurate Representations of Channel and Interior Surfaces in Molecular Structures

(2008) Bosco K Ho et al.   BMC STRUCTURAL BIOLOGY