Accelerating molecular discovery through data and physical sciences: Applications to peptide-membrane interactions

Activity of Antimicrobial Peptide Aggregates Decreases with Increased Cell Membrane Embedding Free Energy Cost

(2018) Rongfeng Zou et al.   BIOCHEMISTRY

In silico screening of drug-membrane thermodynamics reveals linear relations between bulk partitioning and the potential of mean force

(2017) Roberto Menichetti et al.   JOURNAL OF CHEMICAL PHYSICS

Science and data science

(2017) David M. Blei et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Engineering monolayer poration for rapid exfoliation of microbial membranes

(2017) Alice Pyne et al.   Chemical Science

Robust Inference of Genetic Exchange Communities from Microbial Genomes Using TF-IDF

(2017) Yingnan Cong et al.   Frontiers in Microbiology

Rational Design: A High-Throughput Computational Screening and Experimental Validation Methodology for Lead-Free and Emergent Hybrid Perovskites

(2017) Sudip Chakraborty et al.   ACS Energy Letters

Duality and quantum state engineering in cavity arrays

(2017) Nilakantha Meher et al.   Scientific Reports

Efficient preparation and analysis of membrane and membrane protein systems

(2016) Matti Javanainen et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Informedkmer selection forde novotranscriptome assembly

(2016) Dilip A. Durai et al.   BIOINFORMATICS

Antimicrobial peptide exposure selects forStaphylococcus aureusresistance to human defence peptides

(2016) Jessica Z. Kubicek-Sutherland et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Antimicrobial Peptide Simulations and the Influence of Force Field on the Free Energy for Pore Formation in Lipid Bilayers

(2016) W. F. Drew Bennett et al.   Journal of Chemical Theory and Computation

UniProt: the universal protein knowledgebase

(2016)   NUCLEIC ACIDS RESEARCH

DRAMP: a comprehensive data repository of antimicrobial peptides

(2016) Linlin Fan et al.   Scientific Reports

A novel alignment-free method for detection of lateral genetic transfer based on TF-IDF

(2016) Yingnan Cong et al.   Scientific Reports

Exploring lateral genetic transfer among microbial genomes using TF-IDF

(2016) Yingnan Cong et al.   Scientific Reports

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

(2015) Edward O. Pyzer-Knapp et al.   Annual Review of Materials Research

Designing Cell-Targeted Therapeutic Proteins Reveals the Interplay between Domain Connectivity and Cell Binding

(2014) Avi Robinson-Mosher et al.   BIOPHYSICAL JOURNAL

A metal-free organic–inorganic aqueous flow battery

(2014) Brian Huskinson et al.   NATURE

Clinical development success rates for investigational drugs

(2014) Michael Hay et al.   NATURE BIOTECHNOLOGY

Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features

(2014) Mahmoud Ghandi et al.   PLoS Computational Biology

Perspective on the Martini model

(2013) Siewert J. Marrink et al.   CHEMICAL SOCIETY REVIEWS

Engineering Antimicrobial Peptides with Improved Antimicrobial and Hemolytic Activities

(2013) Jun Zhao et al.   Journal of Chemical Information and Modeling

kmer-SVM: a web server for identifying predictive regulatory sequence features in genomic data sets

(2013) Christopher Fletez-Brant et al.   NUCLEIC ACIDS RESEARCH

On representing chemical environments

(2013) Albert P. Bartók et al.   PHYSICAL REVIEW B

Nanoscale imaging reveals laterally expanding antimicrobial pores in lipid bilayers

(2013) P. D. Rakowska et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2013) Anubhav Jain et al.   APL Materials

Therapeutic antimicrobial peptides may compromise natural immunity

(2012) M. G. J. L. Habets et al.   Biology Letters

Modeling and Simulation of Ion Channels

(2012) Christopher Maffeo et al.   CHEMICAL REVIEWS

ClassAMP: A Prediction Tool for Classification of Antimicrobial Peptides

(2012) Shaini Joseph et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Ab Initio Design of Potent Anti-MRSA Peptides Based on Database Filtering Technology

(2012) Biswajit Mishra et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

AVPpred: collection and prediction of highly effective antiviral peptides

(2012) Nishant Thakur et al.   NUCLEIC ACIDS RESEARCH

Identification, Characterization, and Recombinant Expression of Epidermicin NI01, a Novel Unmodified Bacteriocin Produced by Staphylococcus epidermidis That Displays Potent Activity against Staphylococci

(2011) Stephanie Sandiford et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

The future of molecular dynamics simulations in drug discovery

(2011) David W. Borhani et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

The Harvard Clean Energy Project: Large-Scale Computational Screening and Design of Organic Photovoltaics on the World Community Grid

(2011) Johannes Hachmann et al.   Journal of Physical Chemistry Letters

Ribosomal synthesis and in situ isolation of peptide molecules in a cell-free translation system

(2010) Kyung-Ho Lee et al.   PROTEIN EXPRESSION AND PURIFICATION

The Roles of Antimicrobial Peptides in Innate Host Defense

(2009) Gill Diamond et al.   CURRENT PHARMACEUTICAL DESIGN

De novogeneration of antimicrobial LK peptides with a single tryptophan at the critical amphipathic interface

(2009) Su-Jin Kang et al.   JOURNAL OF PEPTIDE SCIENCE

CAMP: a useful resource for research on antimicrobial peptides

(2009) Shaini Thomas et al.   NUCLEIC ACIDS RESEARCH

Coarse-grained simulation: a high-throughput computational approach to membrane proteins

(2008) Mark S.P. Sansom et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

CHARMM-GUI: A web-based graphical user interface for CHARMM

(2008) Sunhwan Jo et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Agar and broth dilution methods to determine the minimal inhibitory concentration (MIC) of antimicrobial substances

(2008) Irith Wiegand et al.   Nature Protocols

UniPROBE: an online database of protein binding microarray data on protein-DNA interactions

(2008) D. E. Newburger et al.   NUCLEIC ACIDS RESEARCH