EnzyHTP: A High-Throughput Computational Platform for Enzyme Modeling

BFEE2: Automated, Streamlined, and Accurate Absolute Binding Free-Energy Calculations

(2021) Haohao Fu et al.   Journal of Chemical Information and Modeling

Local Electric Fields As a Natural Switch of Heme-Iron Protein Reactivity

(2021) Daniel Bím et al.   ACS Catalysis

Directed Evolution: Methodologies and Applications

(2021) Yajie Wang et al.   CHEMICAL REVIEWS

Comprehensive Understanding of Fluoroacetate Dehalogenase-Catalyzed Degradation of Fluorocarboxylic Acids: A QM/MM Approach

(2021) Yue Yue et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

PyAutoFEP: An Automated Free Energy Perturbation Workflow for GROMACS Integrating Enhanced Sampling Methods

(2021) Luan Carvalho Martins et al.   Journal of Chemical Theory and Computation

Rate-Perturbing Single Amino Acid Mutation for Hydrolases: A Statistical Profiling

(2021) Bailu Yan et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

Accurate prediction of protein structures and interactions using a three-track neural network

(2021) Minkyung Baek et al.   SCIENCE

Revealing enzyme functional architecture via high-throughput microfluidic enzyme kinetics

(2021) C. J. Markin et al.   SCIENCE

The Interplay of Electrostatics and Chemical Positioning in the Evolution of Antibiotic Resistance in TEM β-Lactamases

(2021) Samuel H. Schneider et al.   ACS Central Science

Fluoroacetate dehalogenase catalyzed dehalogenation of halogenated carboxylic acids: A QM/MM approach

(2020) Yue Yue et al.   CHEMOSPHERE

BRIDGE: An Open Platform for Reproducible High-Throughput Free Energy Simulations

(2020) Tharindu Senapathi et al.   Journal of Chemical Information and Modeling

Characterization and engineering of a two-enzyme system for plastics depolymerization

(2020) Brandon C. Knott et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

On the importance of statistics in molecular simulations for thermodynamics, kinetics and simulation box size

(2020) Vytautas Gapsys et al.   eLife

Design of novel enzyme biocatalysts for industrial bioprocess: Harnessing the power of protein engineering, high throughput screening and synthetic biology

(2020) Aravind Madhavan et al.   BIORESOURCE TECHNOLOGY

Quantum Mechanical Description of Electrostatics Provides a Unified Picture of Catalytic Action Across Methyltransferases

(2019) Zhongyue Yang et al.   Journal of Physical Chemistry Letters

Substrate-Based Allosteric Regulation of a Homodimeric Enzyme

(2019) Pedram Mehrabi et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Molecular annotation of food – Towards personalized diet and precision health

(2019) Junai Gan et al.   TRENDS IN FOOD SCIENCE & TECHNOLOGY

Fluctuations of Electric Fields in the Active Site of the Enzyme Ketosteroid Isomerase

(2019) Valerie Vaissier Welborn et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Time-resolved crystallography reveals allosteric communication aligned with molecular breathing

(2019) Pedram Mehrabi et al.   SCIENCE

Speeding up enzyme discovery and engineering with ultrahigh-throughput methods

(2018) Hans Adrian Bunzel et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Avoiding False Positive Conclusions in Molecular Simulation: The Importance of Replicas

(2018) Bernhard Knapp et al.   Journal of Chemical Theory and Computation

The hit-and-return system enables efficient time-resolved serial synchrotron crystallography

(2018) Eike C. Schulz et al.   NATURE METHODS

Enzymatic C H functionalizations for natural product synthesis

(2018) Fuzhuo Li et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

How Many Conformations Need To Be Sampled To Obtain Converged QM/MM Energies? The Curse of Exponential Averaging

(2017) Ulf Ryde   Journal of Chemical Theory and Computation

Systematic Quantum Mechanical Region Determination in QM/MM Simulation

(2017) Maria Karelina et al.   Journal of Chemical Theory and Computation

Investigating Substrate Scope and Enantioselectivity of a Defluorinase by a Stereochemical Probe

(2017) Jian-bo Wang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The Importance of the Scaffold for de Novo Enzymes: A Case Study with Kemp Eliminase

(2017) Asmit Bhowmick et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The role of dimer asymmetry and protomer dynamics in enzyme catalysis

(2017) Tae Hun Kim et al.   SCIENCE

Single-mutation fitness landscapes for an enzyme on multiple substrates reveal specificity is globally encoded

(2017) Emily E. Wrenbeck et al.   Nature Communications

Computational Optimization of Electric Fields for Improving Catalysis of a Designed Kemp Eliminase

(2017) Valerie Vaissier et al.   ACS Catalysis

CADEE: Computer-Aided Directed Evolution of Enzymes

(2017) Beat Anton Amrein et al.   IUCrJ

HTMD: High-Throughput Molecular Dynamics for Molecular Discovery

(2016) S. Doerr et al.   Journal of Chemical Theory and Computation

How Large Should the QM Region Be in QM/MM Calculations? The Case of Catechol O-Methyltransferase

(2016) Heather J. Kulik et al.   JOURNAL OF PHYSICAL CHEMISTRY B

The SWISS-MODEL Repository—new features and functionality

(2016) Stefan Bienert et al.   NUCLEIC ACIDS RESEARCH

Ensembler: Enabling High-Throughput Molecular Simulations at the Superfamily Scale

(2016) Daniel L. Parton et al.   PLoS Computational Biology

Measuring Electric Fields and Noncovalent Interactions Using the Vibrational Stark Effect

(2015) Stephen D. Fried et al.   ACCOUNTS OF CHEMICAL RESEARCH

XSEDE: Accelerating Scientific Discovery

(2014) John Towns et al.   COMPUTING IN SCIENCE & ENGINEERING

Computational Enzyme Design

(2013) Gert Kiss et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

De novo enzymes by computational design

(2013) Hajo Kries et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

(2013) Daniel R. Roe et al.   Journal of Chemical Theory and Computation

Engineering the third wave of biocatalysis

(2012) U. T. Bornscheuer et al.   NATURE

H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations

(2012) R. Anandakrishnan et al.   NUCLEIC ACIDS RESEARCH

PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKaPredictions

(2011) Mats H. M. Olsson et al.   Journal of Chemical Theory and Computation

Multiwfn: A multifunctional wavefunction analyzer

(2011) Tian Lu et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Open Babel: An open chemical toolbox

(2011) Noel M O'Boyle et al.   Journal of Cheminformatics

Modeling of loops in proteins: a multi-method approach

(2010) Michal Jamroz et al.   BMC STRUCTURAL BIOLOGY