Revisiting structural organization of proteins at high temperature from a network perspective

Current structure predictors are not learning the physics of protein folding

(2022) Carlos Outeiral et al.   BIOINFORMATICS

Charge reversal mutations in mesophilic-thermophilic orthologous protein pairs and their role in enhancing coulombic interaction energy

(2022) Suman Hait et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Rational Design of Pepsin for Enhanced Thermostability via Exploiting the Guide of Structural Weakness on Stability

(2021) Yue Zhao et al.   Frontiers in Physics

Systematically Scrutinizing the Impact of Substitution Sites on Thermostability and Detergent Tolerance for Bacillus subtilis Lipase A

(2020) Christina Nutschel et al.   Journal of Chemical Information and Modeling

Finding the generalized molecular principles of protein thermal stability

(2019) Suman Hait et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Principles of Protein Stability and Their Application in Computational Design

(2018) Adi Goldenzweig et al.   Annual Review of Biochemistry

Translational regulation of ribosomal protein S15 drives characteristic patterns of protein-mRNA epistasis

(2018) Saurav Mallik et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Topology and Oligomerization of Mono- and Oligomeric Proteins Regulate Their Half-Lives in the Cell

(2018) Saurav Mallik et al.   STRUCTURE

Modular Organization of Residue-Level Contacts Shapes the Selection Pressure on Individual Amino Acid Sites of Ribosomal Proteins

(2017) Saurav Mallik et al.   Genome Biology and Evolution

All-Atom Simulations Reveal Protein Charge Decoration in the Folded and Unfolded Ensemble Is Key in Thermophilic Adaptation

(2017) Lucas Sawle et al.   Journal of Chemical Theory and Computation

Coevolutionary constraints in the sequence-space of macromolecular complexes reflect their self-assembly pathways

(2017) Saurav Mallik et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Diverse activation pathways in class A GPCRs converge near the G-protein-coupling region

(2016) A. J. Venkatakrishnan et al.   NATURE

Protein contact network topology: a natural language for allostery

(2015) Luisa Di Paola et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Temperature dependence of amino acid hydrophobicities

(2015) Richard Wolfenden et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Defining the loop structures in proteins based on composite β-turn mimics

(2015) Jesmita Dhar et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Predicting protein folding rate change upon point mutation using residue-level coevolutionary information

(2015) Saurav Mallik et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The stability ofTaqDNA polymerase results from a reduced entropic folding penalty; identification of other thermophilic proteins with similar folding thermodynamics

(2013) Chin-Chi Liu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Role of long- and short-range hydrophobic, hydrophilic and charged residues contact network in protein’s structural organization

(2012) Dhriti Sengupta et al.   BMC BIOINFORMATICS

Do topological parameters of amino acids within protein contact networks depend on their physico-chemical properties?

(2012) Dhriti Sengupta et al.   PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS

How Do Thermophilic Proteins and Proteomes Withstand High Temperature?

(2011) Lucas Sawle et al.   BIOPHYSICAL JOURNAL

Thermodynamic Analysis of Ligand-Induced Changes in Protein Thermal Unfolding Applied to High-Throughput Determination of Ligand Affinities with Extrinsic Fluorescent Dyes

(2010) Curtis J. Layton et al.   BIOCHEMISTRY

Protein design automation

(2010) Bassil I. Dahiyat et al.   PROTEIN SCIENCE

A Quantitative Model of Thermal Stabilization and Destabilization of Proteins by Ligands

(2008) Piotras Cimmperman et al.   BIOPHYSICAL JOURNAL