Comparative Analysis of Bacteriophytochrome Agp2 and Its Engineered Photoactivatable NIR Fluorescent Proteins PAiRFP1 and PAiRFP2

Mechanism of pH-induced conformational changes in MurE ligase obtained from Salmonella enterica serovar Typhi

(2020) Faez Iqbal Khan et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

A Thermolabile Phospholipase B from Talaromyces marneffei GD-0079: Biochemical Characterization and Structure Dynamics Study

(2020) Rabia Durrani et al.   Biomolecules

Mechanistic insights into the urea-induced denaturation of a non-seleno thiol specific antioxidant human peroxiredoxin 6

(2020) Sana Qausain et al.   INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES

Mechanistic insights into the urea-induced denaturation of human sphingosine kinase 1

(2020) Faez Iqbal Khan et al.   INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES

DeepDDG: Predicting the Stability Change of Protein Point Mutations Using Neural Networks

(2019) Huali Cao et al.   Journal of Chemical Information and Modeling

Identifying novel sphingosine kinase 1 inhibitors as therapeutics against breast cancer

(2019) Faez Iqbal Khan et al.   JOURNAL OF ENZYME INHIBITION AND MEDICINAL CHEMISTRY

Effects of reverse genetic mutations on the spectral and photochemical behavior of a photoactivatable fluorescent protein PAiRFP1

(2019) Fakhrul Hassan et al.   SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY

Functional implications of pH-induced conformational changes in the Sphingosine kinase 1

(2019) Preeti Gupta et al.   SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY

Recent Studies of Mitochondrial SLC25: Integration of Experimental and Computational Approaches

(2018) Yan-Jing Wang et al.   CURRENT PROTEIN & PEPTIDE SCIENCE

Mechanistic insights into the urea-induced denaturation of kinase domain of human integrin linked kinase

(2018) Sunayana Begum Syed et al.   INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES

On the (un)coupling of the chromophore, tongue interactions, and overall conformation in a bacterial phytochrome

(2018) Heikki Takala et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

DynaMut: predicting the impact of mutations on protein conformation, flexibility and stability

(2018) Carlos HM Rodrigues et al.   NUCLEIC ACIDS RESEARCH

Coordination of the biliverdin D-ring in bacteriophytochromes

(2018) Nils Lenngren et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

High throughput screening, docking and molecular dynamics studies to identify potential inhibitors of human calcium/calmodulin-dependent protein kinase IV

(2018) Anam Beg et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Structural snapshot of a bacterial phytochrome in its functional intermediate state

(2018) Andrea Schmidt et al.   Nature Communications

Phytochromes from Agrobacterium fabrum

(2017) Tilman Lamparter et al.   PHOTOCHEMISTRY AND PHOTOBIOLOGY

Designing brighter near-infrared fluorescent proteins: insights from structural and biochemical studies

(2017) Mikhail Baloban et al.   Chemical Science

Bacteriophytochrome Photoisomerization Proceeds Homogeneously Despite Heterogeneity in Ground State

(2016) Cheng Wang et al.   BIOPHYSICAL JOURNAL

Molecular mechanism of Ras-related protein Rab-5A and effect of mutations in the catalytically active phosphate-binding loop

(2016) Faez Iqbal Khan et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Structure prediction and functional analyses of a thermostable lipase obtained from Shewanella putrefaciens

(2016) Faez Iqbal Khan et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Phytochrome B integrates light and temperature signals in Arabidopsis

(2016) Martina Legris et al.   SCIENCE

Phytochromes function as thermosensors in Arabidopsis

(2016) Jae-Hoon Jung et al.   SCIENCE

Bright monomeric near-infrared fluorescent proteins as tags and biosensors for multiscale imaging

(2016) Daria M. Shcherbakova et al.   Nature Communications

Thermostable chitinase II from Thermomyces lanuginosus SSBP: Cloning, structure prediction and molecular dynamics simulations

(2015) Faez Iqbal Khan et al.   JOURNAL OF THEORETICAL BIOLOGY

Flexibility and small pockets at protein–protein interfaces: New insights into druggability

(2015) Harry Jubb et al.   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

Rational design of a monomeric and photostable far-red fluorescent protein for fluorescence imagingin vivo

(2015) Dan Yu et al.   PROTEIN SCIENCE

WEBnm@ v2.0: Web server and services for comparing protein flexibility

(2014) Sandhya P Tiwari et al.   BMC BIOINFORMATICS

In Vivo image Analysis Using iRFP Transgenic Mice

(2014) Mai Thi Nhu Tran et al.   EXPERIMENTAL ANIMALS

Creation of thermostable and alkaline stable xylanase variants by DNA shuffling

(2014) Dawn Elizabeth Stephens et al.   JOURNAL OF BIOTECHNOLOGY

Structure-Based Virtual Screening Approach for Discovery of Covalently Bound Ligands

(2014) Dora Toledo Warshaviak et al.   Journal of Chemical Information and Modeling

Docking Covalent Inhibitors: A Parameter Free Approach To Pose Prediction and Scoring

(2014) Kai Zhu et al.   Journal of Chemical Information and Modeling

iMODS: internal coordinates normal mode analysis server

(2014) José Ramón López-Blanco et al.   NUCLEIC ACIDS RESEARCH

An improved monomeric infrared fluorescent protein for neuronal and tumour brain imaging

(2014) Dan Yu et al.   Nature Communications

A Coarse-Grained Elastic Network Atom Contact Model and Its Use in the Simulation of Protein Dynamics and the Prediction of the Effect of Mutations

(2014) Vincent Frappier et al.   PLoS Computational Biology

Near-infrared fluorescent proteins for multicolor in vivo imaging

(2013) Daria M Shcherbakova et al.   NATURE METHODS

Far-red light photoactivatable near-infrared fluorescent proteins engineered from a bacterial phytochrome

(2013) Kiryl D. Piatkevich et al.   Nature Communications

Extended Stokes Shift in Fluorescent Proteins: Chromophore–Protein Interactions in a Near-Infrared TagRFP675 Variant

(2013) Kiryl D. Piatkevich et al.   Scientific Reports

Real-Time Tracking of Phytochrome’s Orientational Changes During Pr Photoisomerization

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

Assessing Predictors of Changes in Protein Stability upon Mutation Using Self-Consistency

(2012) Grant Thiltgen et al.   PLoS One

Bacteriophytochrome controls carotenoid-independent response to photodynamic stress in a non-photosynthetic rhizobacterium, Azospirillum brasilense Sp7

(2012) Santosh Kumar et al.   Scientific Reports

Bacterial phytochromes: More than meets the light

(2011) Michele E. Auldridge et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

Structure-guided Engineering Enhances a Phytochrome-based Infrared Fluorescent Protein

(2011) Michele E. Auldridge et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Bright and stable near-infrared fluorescent protein for in vivo imaging

(2011) Grigory S Filonov et al.   NATURE BIOTECHNOLOGY

Determination of Ensemble-Average Pairwise Root Mean-Square Deviation from Experimental B-Factors

(2010) Antonija Kuzmanic et al.   BIOPHYSICAL JOURNAL

A Brief History of Phytochromes

(2010) Nathan C. Rockwell et al.   CHEMPHYSCHEM

Performance of protein stability predictors

(2010) Sofia Khan et al.   HUMAN MUTATION

FlexServ: an integrated tool for the analysis of protein flexibility

(2009) J. Camps et al.   BIOINFORMATICS

A single circularly permuted GFP sensor for inositol-1,3,4,5-tetrakisphosphate based on a split PH domain

(2009) Reiko Sakaguchi et al.   BIOORGANIC & MEDICINAL CHEMISTRY

In Vivo Fluorescent Detection of Fe-S Clusters Coordinated by Human GRX2

(2009) Kevin G. Hoff et al.   CHEMISTRY & BIOLOGY

Assessing computational methods for predicting protein stability upon mutation: good on average but not in the details

(2009) V. Potapov et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Mutational Analysis ofDeinococcus radioduransBacteriophytochrome Reveals Key Amino Acids Necessary for the Photochromicity and Proton Exchange Cycle of Phytochromes

(2008) Jeremiah R. Wagner et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

SCWRL and MolIDE: computer programs for side-chain conformation prediction and homology modeling

(2008) Qiang Wang et al.   Nature Protocols

Design of a highly specific and noninvasive biosensor suitable for real-time in vivo imaging of mercury (II) uptake

(2008) Richard R. Chapleau et al.   PROTEIN SCIENCE