4.4 Review

Computational compound screening of biomolecules and soft materials by molecular simulations

Related references

Note: Only part of the references are listed.
Article Biochemical Research Methods

Atomistic and coarse-grained simulations of membrane proteins: A practical guide

Damien Jefferies et al.

Summary: Membrane proteins are amphipathic macromolecules with diverse chemical compositions and biological functions. Traditional experimental techniques and molecular modeling software, especially molecular dynamics algorithms, can provide comprehensive insights into the properties and dynamic behaviors of membrane proteins.

METHODS (2021)

Article Multidisciplinary Sciences

The unreasonable effectiveness of deep learning in artificial intelligence

Terrence J. Sejnowski

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

Article Chemistry, Physical

Inverse methods for design of soft materials

Zachary M. Sherman et al.

JOURNAL OF CHEMICAL PHYSICS (2020)

Article Chemistry, Physical

Ensemble learning of coarse-grained molecular dynamics force fields with a kernel approach

Jiang Wang et al.

JOURNAL OF CHEMICAL PHYSICS (2020)

Article Chemistry, Physical

Kernel-Based Machine Learning for Efficient Simulations of Molecular Liquids

Christoph Scherer et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2020)

Article Multidisciplinary Sciences

Molecular dynamics trajectories for 630 coarse-grained drug-membrane permeations

Christian Hoffmann et al.

SCIENTIFIC DATA (2020)

Article Chemistry, Physical

Discovery of Self-Assembling π-Conjugated Peptides by Active Learning-Directed Coarse-Grained Molecular Simulation

Kirill Shmilovich et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2020)

Article Materials Science, Multidisciplinary

Roadmap on multiscale materials modeling

Erik van der Giessen et al.

MODELLING AND SIMULATION IN MATERIALS SCIENCE AND ENGINEERING (2020)

Article Multidisciplinary Sciences

Al Feynman: A physics-inspired method for symbolic regression

Silviu-Marian Udrescu et al.

SCIENCE ADVANCES (2020)

Article Multidisciplinary Sciences

Designing exceptional gas-separation polymer membranes using machine learning

J. Wesley Barnett et al.

SCIENCE ADVANCES (2020)

Article Chemistry, Physical

Hydration free energies from kernel-based machine learning: Compound-database bias

Clemens Rauer et al.

JOURNAL OF CHEMICAL PHYSICS (2020)

Article Chemistry, Physical

Predicting molecular dipole moments by combining atomic partial charges and atomic dipoles

Max Veit et al.

JOURNAL OF CHEMICAL PHYSICS (2020)

Article Chemistry, Physical

Machine Learning Force Fields and Coarse-Grained Variables in Molecular Dynamics: Application to Materials and Biological Systems

Paraskevi Gkeka et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2020)

Article Multidisciplinary Sciences

Protein-ligand binding with the coarse-grained Martini model

Paulo C. T. Souza et al.

NATURE COMMUNICATIONS (2020)

Article Chemistry, Medicinal

Predicting Small Molecule Transfer Free Energies by Combining Molecular Dynamics Simulations and Deep Learning

W. F. Drew Bennett et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2020)

Article Multidisciplinary Sciences

Exploring the landscape of model representations

Thomas T. Foley et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

Editorial Material Multidisciplinary Sciences

Machine learning for chemical discovery

Alexandre Tkatchenko

NATURE COMMUNICATIONS (2020)

Article Chemistry, Physical

OPLS3e: Extending Force Field Coverage for Drug-Like Small Molecules

Katarina Roos et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2019)

Article Computer Science, Interdisciplinary Applications

Physics-informed neural networks: A deep learning framework for solving forward and inverse problems involving nonlinear partial differential equations

M. Raissi et al.

JOURNAL OF COMPUTATIONAL PHYSICS (2019)

Article Multidisciplinary Sciences

Accurate molecular polarizabilities with coupled cluster theory and machine learning

David M. Wilkins et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

Article Chemistry, Physical

Unsupervised machine learning in atomistic simulations, between predictions and understanding

Michele Ceriotti

JOURNAL OF CHEMICAL PHYSICS (2019)

Article Chemistry, Physical

Revisiting the Meyer-Overton rule for drug-membrane permeabilities

Roberto Menichetti et al.

MOLECULAR PHYSICS (2019)

Review Biotechnology & Applied Microbiology

Recent advances in machine learning towards multiscale soft materials design

Nicholas E. Jackson et al.

CURRENT OPINION IN CHEMICAL ENGINEERING (2019)

Article Chemistry, Multidisciplinary

Machine Learning of Coarse-Grained Molecular Dynamics Force Fields

Jiang Wang et al.

ACS CENTRAL SCIENCE (2019)

Article Materials Science, Multidisciplinary

Hoobas: A highly object-oriented builder for molecular dynamics

Martin Girard et al.

COMPUTATIONAL MATERIALS SCIENCE (2019)

Review Chemistry, Multidisciplinary

Data-Driven Materials Science: Status, Challenges, and Perspectives

Lauri Himanen et al.

ADVANCED SCIENCE (2019)

Editorial Material Chemistry, Multidisciplinary

Computational Discovery of the Origins of Life

Jan Meisner et al.

ACS CENTRAL SCIENCE (2019)

Article Chemistry, Physical

Incorporating long-range physics in atomic-scale machine learning

Andrea Grisafi et al.

JOURNAL OF CHEMICAL PHYSICS (2019)

Article Chemistry, Physical

Resolution limit of data-driven coarse-grained models spanning chemical space

Kiran H. Kanekal et al.

JOURNAL OF CHEMICAL PHYSICS (2019)

Article Chemistry, Physical

EncoderMap: Dimensionality Reduction and Generation of Molecule Conformations

Tobias Lemke et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2019)

Article Chemistry, Physical

Scalable Screening of Soft Matter: A Case Study of Mixtures of Ionic Liquids and Organic Solvents

Matthew W. Thompson et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2019)

Article Biochemistry & Molecular Biology

The MemProtMD database: a resource for membrane-embedded protein structures and their lipid interactions

Thomas D. Newport et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Chemistry, Multidisciplinary

Drug-Membrane Permeability across Chemical Space

Roberto Menichetti et al.

ACS CENTRAL SCIENCE (2019)

Review Mathematics, Interdisciplinary Applications

Recent Progress towards Chemically-Specific Coarse-Grained Simulation Models with Consistent Dynamical Properties

Joseph E. Rudzinski

COMPUTATION (2019)

Article Chemistry, Physical

BOCS: Bottom-up Open-source Coarse-graining Software

Nicholas J. H. Dunn et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2018)

Article Chemistry, Multidisciplinary

Quantum Machine Learning in Chemical Compound Space

O. Anatole von Lilienfeld

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2018)

Review Pharmacology & Pharmacy

Machine learning in chemoinformatics and drug discovery

Yu-Chen Lo et al.

DRUG DISCOVERY TODAY (2018)

Review Pharmacology & Pharmacy

The rise of deep learning in drug discovery

Hongming Chen et al.

DRUG DISCOVERY TODAY (2018)

Article Chemistry, Physical

Reweighted autoencoded variational Bayes for enhanced sampling (RAVE)

Joao Marcelo Lamim Ribeiro et al.

JOURNAL OF CHEMICAL PHYSICS (2018)

Article Chemistry, Physical

Alchemical and structural distribution based representation for universal quantum machine learning

Felix A. Faber et al.

JOURNAL OF CHEMICAL PHYSICS (2018)

Article Chemistry, Physical

Time-lagged autoencoders: Deep learning of slow collective variables for molecular kinetics

Christoph Wehmeyer et al.

JOURNAL OF CHEMICAL PHYSICS (2018)

Article Chemistry, Physical

Transferable Neural Networks for Enhanced Sampling of Protein Dynamics

Mohammad M. Sultan et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2018)

Article Chemistry, Physical

Link between Membrane Composition and Permeability to Drugs

Chi Hang Tse et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2018)

Review Chemistry, Multidisciplinary

Markov State Models: From an Art to a Science

Brooke E. Husic et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2018)

Article Chemistry, Physical

Machine learning and molecular design of self-assembling π-conjugated oligopeptides

Bryce A. Thurston et al.

MOLECULAR SIMULATION (2018)

Article Chemistry, Multidisciplinary

Lipid-Protein Interactions Are Unique Fingerprints for Membrane Proteins

Valentina Corradi et al.

ACS CENTRAL SCIENCE (2018)

Article Chemistry, Multidisciplinary

Automatic Chemical Design Using a Data-Driven Continuous Representation of Molecules

Rafael Gomez-Bombarelli et al.

ACS CENTRAL SCIENCE (2018)

Article Materials Science, Multidisciplinary

NOMAD: The FAIR concept for big data-driven materials science

Claudia Draxl et al.

MRS BULLETIN (2018)

Article Chemistry, Physical

Escaping Atom Types in Force Fields Using Direct Chemical Perception

David L. Mobley et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2018)

Review Physics, Multidisciplinary

Advanced simulation techniques for the thermodynamic and kinetic characterization of biological systems

Carlo Camilloni et al.

ADVANCES IN PHYSICS-X (2018)

Article Chemistry, Physical

Solvent Polarity Governs Ion Interactions and Transport in a Solvated Room-Temperature Ionic Liquid

Naresh C. Osti et al.

JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2017)

Article Chemistry, Physical

Machine Learning Force Field Parameters from Ab lnitio Data

Ying Li et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2017)

Article Chemistry, Physical

Prediction Errors of Molecular Machine Learning Models Lower than Hybrid DFT Error

Felix A. Faber et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2017)

Review Chemistry, Multidisciplinary

Deep learning for computational chemistry

Garrett B. Goh et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2017)

Article Chemistry, Physical

Predicting a Drug's Membrane Permeability: A Computational Model Validated With in Vitro Permeability Assay Data

Brian J. Bennion et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2017)

Article Chemistry, Physical

Building a More Predictive Protein Force Field: A Systematic and Reproducible Route to AMBER-FB15

Lee-Ping Wang et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2017)

Article Chemistry, Physical

Many-Body Coarse-Grained Interactions Using Gaussian Approximation Potentials

S. T. John et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2017)

Article Physics, Multidisciplinary

Uncovering structure-property relationships of materials by subgroup discovery

Bryan R. Goldsmith et al.

NEW JOURNAL OF PHYSICS (2017)

Article Multidisciplinary Sciences

Intrinsic map dynamics exploration for uncharted effective free-energy landscapes

Eliodoro Chiavazzo et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)

Article Polymer Science

Polymer Informatics: Opportunities and Challenges

Debra J. Audus et al.

ACS MACRO LETTERS (2017)

Article Multidisciplinary Sciences

Machine learning unifies the modeling of materials and molecules

Albert P. Bartok et al.

SCIENCE ADVANCES (2017)

Article Multidisciplinary Sciences

Machine learning of accurate energy-conserving molecular force fields

Stefan Chmiela et al.

SCIENCE ADVANCES (2017)

Review Chemistry, Physical

Machine learning in materials informatics: recent applications and prospects

Rampi Ramprasad et al.

NPJ COMPUTATIONAL MATERIALS (2017)

Review Chemistry, Multidisciplinary

Advancing Drug Discovery through Enhanced Free Energy Calculations

Robert Abel et al.

ACCOUNTS OF CHEMICAL RESEARCH (2017)

Article Chemistry, Physical

OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins

Edward Harder et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2016)

Article Multidisciplinary Sciences

Turning statistical physics models into materials design engines

Marc Z. Miskin et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)

Review Chemistry, Analytical

Microfluidics for cell-based high throughput screening platformsd-A review

Guansheng Du et al.

ANALYTICA CHIMICA ACTA (2016)

Review Chemistry, Physical

Enhancing Important Fluctuations: Rare Events and Metadynamics from a Conceptual Viewpoint

Omar Valsson et al.

ANNUAL REVIEW OF PHYSICAL CHEMISTRY, VOL 67 (2016)

Article Biochemistry & Molecular Biology

Molecular dynamics simulations of membrane proteins and their interactions: from nanoscale to mesoscale

Matthieu Chavent et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2016)

Article Materials Science, Multidisciplinary

The Materials Data Facility: Data Services to Advance Materials Science Research

B. Blaiszik et al.

Article Chemistry, Medicinal

Simulation-Based Approaches for Determining Membrane Permeability of Small Compounds

Christopher T. Lee et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2016)

Article Chemistry, Physical

Guiding ab initio calculations by alchemical derivatives

M. To Baben et al.

JOURNAL OF CHEMICAL PHYSICS (2016)

Article Chemistry, Physical

Perspective: Machine learning potentials for atomistic simulations

Joerg Behler

JOURNAL OF CHEMICAL PHYSICS (2016)

Article Chemistry, Physical

Using Dimensionality Reduction to Systematically Expand Conformational Sampling of Intrinsically Disordered Peptides

Oleksandra Kukharenko et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2016)

Article Chemistry, Physical

Beyond Born-Mayer: Improved Models for Short-Range Repulsion in ab Initio Force Fields

Mary J. Van Vleet et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2016)

Article Chemistry, Medicinal

Role of Molecular Dynamics and Related Methods in Drug Discovery

Marco De Vivo et al.

JOURNAL OF MEDICINAL CHEMISTRY (2016)

Article Multidisciplinary Sciences

Discovering governing equations from data by sparse identification of nonlinear dynamical systems

Steven L. Brunton et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)

Article Multidisciplinary Sciences

A polymer dataset for accelerated property prediction and design

Tran Doan Huan et al.

SCIENTIFIC DATA (2016)

Article Multidisciplinary Sciences

Comment: The FAIR Guiding Principles for scientific data management and stewardship

Mark D. Wilkinson et al.

SCIENTIFIC DATA (2016)

Review Nanoscience & Nanotechnology

Computational predictions of energy materials using density functional theory

Anubhav Jain et al.

NATURE REVIEWS MATERIALS (2016)

Article Nanoscience & Nanotechnology

Research Update: Computational materials discovery in soft matter

Tristan Bereau et al.

APL MATERIALS (2016)

Review Chemistry, Multidisciplinary

The Chemical Space Project

Jean-Louis Reymond

ACCOUNTS OF CHEMICAL RESEARCH (2015)

Article Chemistry, Multidisciplinary

Digital Alchemy for Materials Design: Colloids and Beyond

Greg van Anders et al.

ACS NANO (2015)

Review Materials Science, Multidisciplinary

What Is High-Throughput Virtual Screening? A Perspective from Organic Materials Discovery

Edward O. Pyzer-Knapp et al.

ANNUAL REVIEW OF MATERIALS RESEARCH, VOL 45 (2015)

Review Biochemistry & Molecular Biology

CHARMM additive and polarizable force fields for biophysics and computer-aided drug design

K. Vanommeslaeghe et al.

BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS (2015)

Review Biochemistry & Molecular Biology

Enhanced sampling techniques in molecular dynamics simulations of biological systems

Rafael C. Bernardi et al.

BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS (2015)

Review Chemistry, Physical

Gaussian approximation potentials: A brief tutorial introduction

Albert P. Bartok et al.

INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY (2015)

Article Chemistry, Physical

Folding and insertion thermodynamics of the transmembrane WALP peptide

Tristan Bereau et al.

JOURNAL OF CHEMICAL PHYSICS (2015)

Article Chemistry, Physical

High-Throughput Simulations of Dimer and Trimer Assembly of Membrane Proteins. The DAFT Approach

Tsjerk A. Wassenaar et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)

Article Chemistry, Physical

Automated Parametrization of the Coarse-Grained Martini Force Field for Small Organic Molecules

Tristan Bereau et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)

Article Chemistry, Physical

Computational Lipidomics with insane: A Versatile Tool for Generating Custom Membranes for Molecular Simulations

Tsjerk A. Wassenaar et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)

Article Chemistry, Physical

Transferable Atomic Multipole Machine Learning Models for Small Organic Molecules

Tristan Bereau et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)

Article Multidisciplinary Sciences

Accelerating molecular simulations of proteins using Bayesian inference on weak information

Alberto Perez et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)

Article Biochemistry & Molecular Biology

MemProtMD: Automated Insertion of Membrane Protein Structures into Explicit Lipid Membranes

Phillip J. Stansfeld et al.

STRUCTURE (2015)

Article Biochemistry & Molecular Biology

Enhanced Sampling of Coarse-Grained Transmembrane-Peptide Structure Formation from Hydrogen-Bond Replica Exchange

Tristan Bereau et al.

JOURNAL OF MEMBRANE BIOLOGY (2015)

Article Chemistry, Multidisciplinary

Exploring the sequence space for (tri-) peptide self-assembly to design and discover

Pim W. J. M. Frederix et al.

NATURE CHEMISTRY (2015)

Editorial Material Engineering, Chemical

Inverse Methods for Material Design

Avni Jain et al.

AICHE JOURNAL (2014)

Review Biochemistry & Molecular Biology

Membrane protein structure determination The next generation

Isabel Moraes et al.

BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES (2014)

Article Biochemistry & Molecular Biology

Markov state models of biomolecular conformational dynamics

John D. Chodera et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2014)

Article Biochemistry & Molecular Biology

Blind prediction of solvation free energies from the SAMPL4 challenge

David L. Mobley et al.

JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2014)

Article Chemistry, Multidisciplinary

Discovering chemistry with an ab initio nanoreactor

Lee-Ping Wang et al.

NATURE CHEMISTRY (2014)

Article Chemistry, Multidisciplinary

Molpher: a software framework for systematic chemical space exploration

David Hoksza et al.

JOURNAL OF CHEMINFORMATICS (2014)

Review Chemistry, Multidisciplinary

The power of coarse graining in biomolecular simulations

Helgi I. Ingolfsson et al.

WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2014)

Article Multidisciplinary Sciences

Quantum chemistry structures and properties of 134 kilo molecules

Raghunathan Ramakrishnan et al.

SCIENTIFIC DATA (2014)

Review Biochemistry & Molecular Biology

Back to the Future: Can Physical Models of Passive Membrane Permeability Help Reduce Drug Candidate Attrition and Move Us Beyond QSPR?

Robert V. Swift et al.

CHEMICAL BIOLOGY & DRUG DESIGN (2013)

Review Chemistry, Multidisciplinary

Perspective on the Martini model

Siewert J. Marrink et al.

CHEMICAL SOCIETY REVIEWS (2013)

Review Materials Science, Multidisciplinary

NSF cyberinfrastructures: A new paradigm for advancing materials simulation

Ellad B. Tadmor et al.

CURRENT OPINION IN SOLID STATE & MATERIALS SCIENCE (2013)

Article Biochemistry & Molecular Biology

To milliseconds and beyond: challenges in the simulation of protein folding

Thomas J. Lane et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2013)

Article Chemistry, Physical

Structural and dynamic properties of calcium aluminosilicate melts: A molecular dynamics study

M. Bouhadja et al.

JOURNAL OF CHEMICAL PHYSICS (2013)

Article Chemistry, Physical

Perspective: Coarse-grained models for biomolecular systems

W. G. Noid

JOURNAL OF CHEMICAL PHYSICS (2013)

Article Chemistry, Physical

Exploring Chemical Space with the Alchemical Derivatives

Robert Balawender et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)

Article Biochemistry & Molecular Biology

Lead optimization mapper: automating free energy calculations for lead optimization

Shuai Liu et al.

JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2013)

Article Chemistry, Multidisciplinary

Stochastic Voyages into Uncharted Chemical Space Produce a Representative Library of All Possible Drug-Like Compounds

Aaron M. Virshup et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2013)

Review Chemistry, Physical

The high-throughput highway to computational materials design

Stefano Curtarolo et al.

NATURE MATERIALS (2013)

Article Multidisciplinary Sciences

The Stuff of Dreams

Gerbrand Ceder et al.

SCIENTIFIC AMERICAN (2013)

Article Polymer Science

Inverse Design of Topographical Templates for Directed Self-Assembly of Block Copolymers

Adam F. Hannon et al.

ACS MACRO LETTERS (2013)

Article Nanoscience & Nanotechnology

Commentary: The Materials Project: A materials genome approach to accelerating materials innovation

Anubhav Jain et al.

APL MATERIALS (2013)

Review Chemistry, Multidisciplinary

Quantitative Structure-Property Relationship Modeling of Diverse Materials Properties

Tu Le et al.

CHEMICAL REVIEWS (2012)

Article Chemistry, Medicinal

Enumeration of 166 Billion Organic Small Molecules in the Chemical Universe Database GDB-17

Lars Ruddigkeit et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2012)

Article Chemistry, Physical

Perspective: Alchemical free energy calculations for drug discovery

David L. Mobley et al.

JOURNAL OF CHEMICAL PHYSICS (2012)

Article Chemistry, Physical

Improving the Prediction of Absolute Solvation Free Energies Using the Next Generation OPLS Force Field

Devleena Shivakumar et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)

Article Biochemistry & Molecular Biology

The future of molecular dynamics simulations in drug discovery

David W. Borhani et al.

JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2012)

Article Chemistry, Multidisciplinary

Synthesis and characterization of π-conjugated peptide-based supramolecular materials

Brian D. Wall et al.

PURE AND APPLIED CHEMISTRY (2012)

Review Multidisciplinary Sciences

The Protein-Folding Problem, 50 Years On

Ken A. Dill et al.

SCIENCE (2012)

Review Chemistry, Multidisciplinary

Combinatorial and High-Throughput Screening of Biomaterials

Carl G. Simon et al.

ADVANCED MATERIALS (2011)

Article Chemistry, Multidisciplinary

Towards Ultrastrong Glasses

Lothar Wondraczek et al.

ADVANCED MATERIALS (2011)

Review Electrochemistry

A review of high throughput and combinatorial electrochemistry

T. H. Muster et al.

ELECTROCHIMICA ACTA (2011)

Editorial Material Materials Science, Multidisciplinary

The potential of atomistic simulations and the knowledgebase of interatomic models

E. B. Tadmor et al.

Article Chemistry, Physical

Optimized Potential of Mean Force Calculations for Standard Binding Free Energies

Ignasi Buch et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2011)

Article Chemistry, Physical

An Automated Force Field Topology Builder (ATB) and Repository: Version 1.0

Alpeshkumar K. Malde et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2011)

Article Chemistry, Physical

Statistical Convergence of Equilibrium Properties in Simulations of Molecular Solutes Embedded in Lipid Bilayers

Chris Neale et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2011)

Article Chemistry, Multidisciplinary

PaDEL-Descriptor: An Open Source Software to Calculate Molecular Descriptors and Fingerprints

Chun Wei Yap

JOURNAL OF COMPUTATIONAL CHEMISTRY (2011)

Article Chemistry, Physical

Virtual Screening for Dipeptide Aggregation: Toward Predictive Tools for Peptide Self-Assembly

Pim W. J. M. Frederix et al.

JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2011)

Editorial Material Chemistry, Multidisciplinary

Open science is a research accelerator

Michael Woelfle et al.

NATURE CHEMISTRY (2011)

Article Biotechnology & Applied Microbiology

Impact of high-throughput screening in biomedical research

Ricardo Macarron et al.

NATURE REVIEWS DRUG DISCOVERY (2011)

Article Multidisciplinary Sciences

Simplifying the representation of complex free-energy landscapes using sketch-map

Michele Ceriotti et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

Article Multidisciplinary Sciences

Design principles for self-assembly with short-range interactions

Sahand Hormoz et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

Article Multidisciplinary Sciences

Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations

Ignasi Buch et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

Review Chemistry, Applied

Combinatorial and High-Throughput Screening of Materials Libraries: Review of State of the Art

Radislav Potyrailo et al.

ACS COMBINATORIAL SCIENCE (2011)

Review Chemistry, Multidisciplinary

Next-generation peptide nanomaterials: molecular networks, interfaces and supramolecular functionality

Mischa Zelzer et al.

CHEMICAL SOCIETY REVIEWS (2010)

Article Chemistry, Medicinal

High-Throughput All-Atom Molecular Dynamics Simulations Using Distributed Computing

I. Buch et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2010)

Article Chemistry, Physical

Prediction of Absolute Solvation Free Energies using Molecular Dynamics Free Energy Perturbation and the OPLS Force Field

Devleena Shivakumar et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2010)

Article Biochemistry & Molecular Biology

The SAMPL2 blind prediction challenge: introduction and overview

Matthew T. Geballe et al.

JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2010)

Article Biochemistry & Molecular Biology

Prediction of protein-ligand binding affinity by free energy simulations: assumptions, pitfalls and expectations

Julien Michel et al.

JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2010)

Review Biochemical Research Methods

Everything you wanted to know about Markov State Models but were afraid to ask

Vijay S. Pande et al.

METHODS (2010)

Article Biochemical Research Methods

Prediction of the human membrane proteome

Linn Fagerberg et al.

PROTEOMICS (2010)

Article Multidisciplinary Sciences

Atomic-Level Characterization of the Structural Dynamics of Proteins

David E. Shaw et al.

SCIENCE (2010)

Article Multidisciplinary Sciences

The Free-Energy Landscape of Clusters of Attractive Hard Spheres

Guangnan Meng et al.

SCIENCE (2010)

Review Chemistry, Multidisciplinary

Efficient Drug Lead Discovery and Optimization

William L. Jorgensen

ACCOUNTS OF CHEMICAL RESEARCH (2009)

Article Biochemical Research Methods

Properties and identification of human protein drug targets

Tala M. Bakheet et al.

BIOINFORMATICS (2009)

Article Pharmacology & Pharmacy

Novel trends in high-throughput screening

Lorenz M. Mayr et al.

CURRENT OPINION IN PHARMACOLOGY (2009)

Article Biochemistry & Molecular Biology

Systematic multiscale simulation of membrane protein systems

Gary S. Ayton et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2009)

Article Chemistry, Physical

Accurate ab initio energy gradients in chemical compound space

O. Anatole von Lilienfeld

JOURNAL OF CHEMICAL PHYSICS (2009)

Article Chemistry, Physical

Computations of Absolute Solvation Free Energies of Small Molecules Using Explicit and Implicit Solvent Model

Devleena Shivakumar et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2009)

Article Chemistry, Physical

Versatile Object-Oriented Toolkit for Coarse-Graining Applications

Victor Ruehle et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2009)

Article Chemistry, Physical

Small Molecule Hydration Free Energies in Explicit Solvent: An Extensive Test of Fixed-Charge Atomistic Simulations

David L. Mobley et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2009)

Article Chemistry, Multidisciplinary

PACKMOL: A Package for Building Initial Configurations for Molecular Dynamics Simulations

L. Martinez et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2009)

Editorial Material Chemistry, Physical

A Blind Challenge for Computational Solvation Free Energies: Introduction and Overview

J. Peter Guthrie

JOURNAL OF PHYSICAL CHEMISTRY B (2009)

Review Physics, Condensed Matter

Molecular simulation of ionic liquids: current status and future opportunities

E. J. Maginn

JOURNAL OF PHYSICS-CONDENSED MATTER (2009)

Article Biochemistry & Molecular Biology

The role of dynamic conformational ensembles in biomolecular recognition

David D. Boehr et al.

NATURE CHEMICAL BIOLOGY (2009)

Article Biochemistry & Molecular Biology

Quantifying biogenic bias in screening libraries

Jerome Hert et al.

NATURE CHEMICAL BIOLOGY (2009)

Review Chemistry, Physical

Ionic-liquid materials for the electrochemical challenges of the future

Michel Armand et al.

NATURE MATERIALS (2009)

Article Chemistry, Multidisciplinary

Fmoc-Diphenylalanine self assembles to a hydrogel via a novel architecture based on π-π interlocked β-sheets

Andrew M. Smith et al.

ADVANCED MATERIALS (2008)

Review Medicine, Research & Experimental

A review of high throughput technology for the screening of natural products

K. P. Mishra et al.

BIOMEDICINE & PHARMACOTHERAPY (2008)

Review Chemistry, Multidisciplinary

Modelling room temperature ionic liquids

B. L. Bhargava et al.

CHEMICAL COMMUNICATIONS (2008)

Article Chemistry, Physical

Probability distributions of molecular observables computed from Markov models

Frank Noe

JOURNAL OF CHEMICAL PHYSICS (2008)

Article Chemistry, Physical

The MARTINI coarse-grained force field: Extension to proteins

Luca Monticelli et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2008)

Article Chemistry, Multidisciplinary

Software news and updates - CHARNIM-GUI: A web-based grraphical user interface for CHARMM

Sunhwan Jo et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2008)

Review Chemistry, Multidisciplinary

Understanding ionic liquids through atomistic and coarse-grained molecular dynamics simulations

Yanting Wang et al.

ACCOUNTS OF CHEMICAL RESEARCH (2007)

Review Chemistry, Multidisciplinary

Simulations of ionic liquids, solutions, and surfaces

Ruth M. Lynden-Bell et al.

ACCOUNTS OF CHEMICAL RESEARCH (2007)

Article Chemistry, Physical

Comparison of charge models for fixed-charge force fields: Small-molecule hydration free energies in explicit solvent

David L. Mobley et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2007)

Review Biochemical Research Methods

Setting up and running molecular dynamics simulations of membrane proteins

Christian Kandt et al.

METHODS (2007)

Article Biochemical Research Methods

Automatic atom type and bond type perception in molecular mechanical calculations

Junmei Wang et al.

JOURNAL OF MOLECULAR GRAPHICS & MODELLING (2006)

Review Chemistry, Multidisciplinary

Protein folding thermodynamics and dynamics: Where physics, chemistry, and biology meet

Eugene Shakhnovich

CHEMICAL REVIEWS (2006)

Article Chemistry, Multidisciplinary

Designing molecules by optimizing potentials

ML Wang et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2006)

Article Multidisciplinary Sciences

Interfacial folding and membrane insertion of designed peptides studied by molecular dynamics simulations

W Im et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)

Article Chemistry, Physical

Solvation free energies of amino acid side chain analogs for common molecular mechanics water models

MR Shirts et al.

JOURNAL OF CHEMICAL PHYSICS (2005)

Review Multidisciplinary Sciences

The many roles of computation in drug discovery

WL Jorgensen

SCIENCE (2004)

Article Biochemistry & Molecular Biology

Exploring folding free energy landscapes using computational protein design

B Kuhlman et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2004)

Article Multidisciplinary Sciences

Chemical space and biology

CM Dobson

NATURE (2004)

Article Biochemistry & Molecular Biology

The progress of membrane protein structure determination

SH White

PROTEIN SCIENCE (2004)

Review Biotechnology & Applied Microbiology

Docking and scoring in virtual screening for drug discovery: Methods and applications

DB Kitchen et al.

NATURE REVIEWS DRUG DISCOVERY (2004)

Review Chemistry, Multidisciplinary

Empirical force fields for biological macromolecules: Overview and issues

AD Mackerell

JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)

Article Chemistry, Multidisciplinary

Active learning with support vector machines in the drug discovery process

MK Warmuth et al.

JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES (2003)

Article Multidisciplinary Sciences

Absolute comparison of simulated and experimental protein-folding dynamics

CD Snow et al.

NATURE (2002)

Review Biochemistry & Molecular Biology

Molecular dynamics simulations of biomolecules

M Karplus et al.

NATURE STRUCTURAL BIOLOGY (2002)

Article Chemistry, Multidisciplinary

Calculation of the free energy of solvation for neutral analogs of amino acid side chains

A Villa et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2002)

Article Chemistry, Physical

Free energy calculations. The long and winding gilded road

C Chipot et al.

MOLECULAR SIMULATION (2002)

Article Multidisciplinary Sciences

Self-assembly and mineralization of peptide-amphiphile nanofibers

JD Hartgerink et al.

SCIENCE (2001)

Article Chemistry, Physical

Scaling of hydrophobic solvation free energies

DM Huang et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2001)

Article Biochemistry & Molecular Biology

The Protein Data Bank

HM Berman et al.

NUCLEIC ACIDS RESEARCH (2000)