Quantum chemical modeling of rhodopsin mutants displaying switchable colors

An inward proton transport using anabaena sensory rhodopsin

(2011) Akira Kawanabe et al.   JOURNAL OF MICROBIOLOGY

The Ultrafast Photoisomerizations of Rhodopsin and Bathorhodopsin Are Modulated by Bond Length Alternation and HOOP Driven Electronic Effects

(2011) Igor Schapiro et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations

(2010) M. Valiev et al.   COMPUTER PHYSICS COMMUNICATIONS

The opsin shift and mechanism of spectral tuning in rhodopsin

(2010) Ramkumar Rajamani et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

The Protonation State of Glu181 in Rhodopsin Revisited: Interpretation of Experimental Data on the Basis of QM/MM Calculations

(2010) Jan S. Frähmcke et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Modeling, Preparation, and Characterization of a Dipole Moment Switch Driven byZ/EPhotoisomerization

(2010) Alfonso Melloni et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Optogenetics

(2010) Karl Deisseroth   NATURE METHODS

Anabaena sensory rhodopsin is a light-driven unidirectional rotor

(2010) A. Strambi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Aborted double bicycle-pedal isomerization with hydrogen bond breaking is the primary event of bacteriorhodopsin proton pumping

(2010) P. Altoe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

QM/MM Methods for Biomolecular Systems

(2009) Hans Martin Senn et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

The Anabaena sensory rhodopsin transducer defines a novel superfamily of prokaryotic small-molecule binding domains

(2009) Robson F De Souza et al.   Biology Direct

The fluorescent protein palette: tools for cellular imaging

(2009) Richard N. Day et al.   CHEMICAL SOCIETY REVIEWS

MOLCAS 7: The Next Generation

(2009) Francesco Aquilante et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Modeling the Fluorescence of Protein-Embedded Tryptophans with ab Initio Multiconfigurational Quantum Chemistry: The Limiting Cases of Parvalbumin and Monellin

(2009) Sara Pistolesi et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Deciphering Intrinsic Deactivation/Isomerization Routes in a Phytochrome Chromophore Model

(2009) Piero Altoè et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A Theoretical Study on the Nature of On- and Off-States of Reversibly Photoswitching Fluorescent Protein Dronpa: Absorption, Emission, Protonation, and Raman

(2009) Xin Li et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Polarization effects in molecular mechanical force fields

(2009) Piotr Cieplak et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

Electrostatic Control of the Photoisomerization Efficiency and Optical Properties in Visual Pigments: On the Role of Counterion Quenching

(2009) Gaia Tomasello et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Engineering an Inward Proton Transport from a Bacterial Sensor Rhodopsin

(2009) Akira Kawanabe et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Color-Tuning Mechanism of Firefly Investigated by Multi-Configurational Perturbation Method

(2009) Isabelle Navizet et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Temporal Control of Immediate Early Gene Induction by Light

(2009) Philipp Schoenenberger et al.   PLoS One

Improved prediction of protein side-chain conformations with SCWRL4

(2009) Georgii G. Krivov et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Photoreactions and Structural Changes of Anabaena Sensory Rhodopsin

(2009) Akira Kawanabe et al.   SENSORS

Density fitting with auxiliary basis sets from Cholesky decompositions

(2009) Thomas Bondo Pedersen et al.   THEORETICAL CHEMISTRY ACCOUNTS

Origin of color tuning in human red, green, and blue cone pigments: SAC-CI and QM/MM study

(2008) Kazuhiro Fujimoto et al.   CHEMICAL PHYSICS LETTERS

The Preference of Tryptophan for Membrane Interfaces

(2008) Haiyan Sun et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Accurate ab initio density fitting for multiconfigurational self-consistent field methods

(2008) Francesco Aquilante et al.   JOURNAL OF CHEMICAL PHYSICS

Three-Layer ONIOM Studies of the Dark State of Rhodopsin: The Protonation State of Glu181

(2008) Katherine F. Hall et al.   JOURNAL OF MOLECULAR BIOLOGY

Origin of the Absorption Maxima of the Photoactive Yellow Protein Resolved via Ab Initio Multiconfigurational Methods

(2008) Pedro B. Coto et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Mechanism of Spectral Tuning Going from Retinal in Vacuo to Bovine Rhodopsin and its Mutants: Multireference ab Initio Quantum Mechanics/Molecular Mechanics Studies

(2008) Ahmet Altun et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Spectral Tuning in Visual Pigments: An ONIOM(QM:MM) Study on Bovine Rhodopsin and its Mutants

(2008) Ahmet Altun et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Effect of Polarization on the Opsin Shift in Rhodopsins. 2. Empirical Polarization Models for Proteins

(2008) Marius Wanko et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Effect of Polarization on the Opsin Shift in Rhodopsins. 1. A Combined QM/QM/MM Model for Bacteriorhodopsin and Pharaonis Sensory Rhodopsin II

(2008) Marius Wanko et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Optical Switches for Remote and Noninvasive Control of Cell Signaling

(2008) P. Gorostiza et al.   SCIENCE