List of works - M Michael Gromiha

A simple statistical method for discriminating outer membrane proteins with better accuracy

scientific article

A statistical method for predicting protein unfolding rates from amino acid sequence

scientific article published in May 2006

Aggregation prone regions in human proteome: Insights from large-scale data analyses

scientific article

An Analysis of the Amino Acid Clustering Pattern in (α/β)8 Barrel Proteins ⬇️

scientific article published on July 1, 1998

An in-silico method for identifying aggregation rate enhancer and mitigator mutations in proteins

scientific article published on 24 June 2018

Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information

scientific article published on 22 January 2004

Analysis and prediction of protein folding rates using quadratic response surface models

scientific article published in July 2008

Analysis of secondary structural and physicochemical changes in protein-protein complexes

scientific article published on 20 May 2015

Application of amino acid occurrence for discriminating different folding types of globular proteins.

scientific article

Applications of Protein Thermodynamic Database for Understanding Protein Mutant Stability and Designing Stable Mutants

scientific article

Atom-wise statistics and prediction of solvent accessibility in proteins

scientific article

Autoimmune Responses to Soluble Aggregates of Amyloidogenic Proteins Involved in Neurodegenerative Diseases: Overlapping Aggregation Prone and Autoimmunogenic regions

scientific article published on 29 February 2016

Bioinformatics approaches for functional annotation of membrane proteins ⬇️

scientific article published on March 23, 2013

CPAD, Curated Protein Aggregation Database: A Repository of Manually Curated Experimental Data on Protein and Peptide Aggregation

scientific article

CUPSAT: prediction of protein stability upon point mutations.

scientific article

Computational Approaches for Predicting Binding Partners, Interface Residues, and Binding Affinity of Protein-Protein Complexes

scientific article

Computational approaches for predicting the binding sites and understanding the recognition mechanism of protein-DNA complexes

scientific article published on January 2013

Computational modeling of protein mutant stability: analysis and optimization of statistical potentials and structural features reveal insights into prediction model development

scientific article

Contribution of main chain and side chain atoms and their locations to the stability of thermophilic proteins

scientific article published on 11 January 2016

Current developments on beta-barrel membrane proteins: sequence and structure analysis, discrimination and prediction

scientific article published on December 2007

Design and training of a neural network for predicting the solvent accessibility of proteins

scientific article

Development of a machine learning method to predict membrane protein-ligand binding residues using basic sequence information

scientific article

Discrimination of driver and passenger mutations in epidermal growth factor receptor in cancer.

scientific article published on 20 July 2015

Discrimination of mesophilic and thermophilic proteins using machine learning algorithms

scientific article published in March 2008

Discrimination of outer membrane proteins using machine learning algorithms.

scientific article

Discrimination of outer membrane proteins using support vector machines

scientific article published on 4 October 2005

Dissecting and analyzing key residues in protein-DNA complexes

scientific article published on 12 December 2017

Distinct position-specific sequence features of hexa-peptides that form amyloid-fibrils: application to discriminate between amyloid fibril and amorphous β-aggregate forming peptide sequences

scientific article

Drug-Target Interactions: Prediction Methods and Applications

scientific article published on 7 November 2016

Energy based approach for understanding the recognition mechanism in protein-protein complexes

scientific article published in December 2009

Eukaryote-wide sequence analysis of mitochondrial β-barrel outer membrane proteins

scientific article

Exploring the environmental preference of weak interactions in (alpha/beta)8 barrel proteins

scientific article published in October 2006

FOLD-RATE: prediction of protein folding rates from amino acid sequence

scientific article published on July 2006

Feature selection and classification of protein-protein complexes based on their binding affinities using machine learning approaches.

scientific article published on 16 April 2014

Folding RaCe: a robust method for predicting changes in protein folding rates upon point mutations

scientific article published on 16 February 2015

Folding mechanism of all-beta globular proteins

scientific article published in February 2004

Functional discrimination of membrane proteins using machine learning techniques

scientific article

GAP: towards almost 100 percent prediction for β-strand-mediated aggregating peptides with distinct morphologies

scientific article published on 28 March 2014

Guest Editorial for Special Section on the 10th International Conference on Intelligent Computing (ICIC).

scientific article published in January 2016

High throughput computing to improve efficiency of predicting protein stability change upon mutation

scientific article published on January 2014

Hydrophobic environment is a key factor for the stability of thermophilic proteins ⬇️

scientific article published on January 15, 2013

Identification and analysis of binding site residues in protein-carbohydrate complexes using energy based approach

scientific article

Identification of dengue viral RNA-dependent RNA polymerase inhibitor using computational fragment-based approaches and molecular dynamics study

scientific article published on 11 August 2015

Identification of efflux proteins using efficient radial basis function networks with position-specific scoring matrices and biochemical properties

scientific article published on 17 June 2013

Identification of type I and type II inhibitors of c-Yes kinase using in silico and experimental techniques

scientific article

Identifying a potential receptor for the antibacterial peptide of sponge Axinella donnani endosymbiont

scientific article

Importance of hydrophobic cluster formation through long-range contacts in the folding transition state of two-state proteins

scientific article

Importance of long-range interactions in (alpha/beta)8 barrel fold

scientific article published on 01 October 1998

Importance of main-chain hydrophobic free energy to the stability of thermophilic proteins

scientific article published in April 2005

Important amino acid properties for determining the transition state structures of two-state protein mutants

scientific article

Important amino acid residues involved in folding and binding of protein-protein complexes

scientific article published on 17 October 2016

Influence of Medium and Long Range Interactions in (α/β)(8) Barrel Proteins ⬇️

scientific article published on December 1, 1997

Influence of amino acid properties for discriminating outer membrane proteins at better accuracy.

scientific article

Influence of cation–π interactions in different folding types of membrane proteins ⬇️

scientific article published on March 25, 2003

Influence of cation–π interactions in protein–DNA complexes

Influence of medium and long range interactions in different structural classes of globular proteins ⬇️

scientific article published on September 1, 1997

Influence of medium- and long-range interactions in different folding types of globular proteins

scientific article published in October 2002

Insights into the binding specificity of wild type and mutated wheat germ agglutinin towards Neu5Acα(2-3)Gal: a study by in silico mutations and molecular dynamics simulations

scientific article

Integrating computational methods and experimental data for understanding the recognition mechanism and binding affinity of protein-protein complexes

scientific article

Inter-residue interactions in protein folding and stability

scientific article published in October 2004

Introduction: advanced intelligent computing theories and their applications in bioinformatics ⬇️

scientific article published on May 8, 2012

Investigating mutation-specific biological activities of small molecules using quantitative structure-activity relationship for epidermal growth factor receptor in cancer

scientific article

Knowledge acquisition and development of accurate rules for predicting protein stability changes

scientific article published on 26 September 2006

Locating the stabilizing residues in (alpha/beta)8 barrel proteins based on hydrophobicity, long-range interactions, and sequence conservation

scientific article published in May 2004

Look-up tables for protein solvent accessibility prediction and nearest neighbor effect analysis

scientific article published in October 2004

Machine learning algorithms for predicting protein folding rates and stability of mutant proteins: comparison with statistical methods

scientific article published on September 2011

Mammalian Mitochondrial ncRNA Database

scientific article

Mitochondrial beta-barrel proteins, an exclusive club?

Multiple contact network is a key determinant to protein folding rates

scientific article published in April 2009

MutHTP: Mutations in Human Transmembrane Proteins

scientific article published in February 2018

Mutational studies to understand the structure-function relationship in multidrug efflux transporters: applications for distinguishing mutants with high specificity

scientific article published on 23 January 2015

NETASA: neural network based prediction of solvent accessibility

scientific article published in June 2002

Neural network-based prediction of transmembrane beta-strand segments in outer membrane proteins

scientific article published in April 2004

New insight into long-range nonadditivity within protein double-mutant cycles

scientific article

Novel approach for selecting the best predictor for identifying the binding sites in DNA binding proteins

scientific article published on 20 June 2013

On the conformational stability of oligonucleotide duplexes and tRNA molecules

scientific article

PDBparam: Online Resource for Computing Structural Parameters of Proteins

scientific article

PINT: Protein-protein Interactions Thermodynamic Database

scientific article

PROXiMATE: A database of mutant protein-protein complex thermodynamics and kinetics

scientific article

Prediction of RNA binding residues: an extensive analysis based on structure and function to select the best predictor

scientific article

Prediction of change in protein unfolding rates upon point mutations in two state proteins

scientific article

Prediction of membrane spanning segments and topology in beta-barrel membrane proteins at better accuracy

scientific article

Prediction of protein disorder on amino acid substitutions

scientific article published on 5 September 2015

Prediction of protein mutant stability using classification and regression tool

scientific article published on 20 November 2006

ProTherm and ProNIT: thermodynamic databases for proteins and protein-nucleic acid interactions

scientific article

ProTherm, Thermodynamic Database for Proteins and Mutants: developments in version 3.0.

scientific article published on January 2002

ProTherm, version 4.0: thermodynamic database for proteins and mutants

scientific article (publication date: 2004)

Protein-protein binding affinity prediction from amino acid sequence

scientific article published on 28 August 2014

Protein-protein interactions: scoring schemes and binding affinity

scientific article published on 17 November 2016

Quercetin derivatives as non-nucleoside inhibitors for dengue polymerase: molecular docking, molecular dynamics simulation, and binding free energy calculation

scientific article

RVP-net: online prediction of real valued accessible surface area of proteins from single sequences

scientific article published in September 2003

Real value prediction of protein folding rate change upon point mutation ⬇️

scientific article published on March 18, 2012

Real value prediction of solvent accessibility from amino acid sequence

scientific article published in March 2003

Relationship between amino acid properties and functional parameters in olfactory receptors and discrimination of mutants with enhanced specificity ⬇️

scientific article published on May 8, 2012

Reliable prediction of protein thermostability change upon double mutation from amino acid sequence

scientific article published on 17 June 2009

Revisiting "reverse hydrophobic effect": applicable only to coil mutations at the surface.

scientific article

Role of cation-pi interactions in single chain 'all-alpha' proteins

scientific article

Role of cation-pi interactions to the stability of thermophilic proteins

scientific article published in November 2002

Role of hydrophobic clusters and long-range contact networks in the folding of (alpha/beta)8 barrel proteins

scientific article published on March 2003

Role of non-covalent interactions for determining the folding rate of two-state proteins

scientific article published in February 2004

SRide: a server for identifying stabilizing residues in proteins

scientific article

Sequence analysis and rule development of predicting protein stability change upon mutation using decision tree model

scientific article published on 30 March 2007

Sequence and structural features of binding site residues in protein-protein complexes: comparison with protein-nucleic acid complexes ⬇️

scientific article published on October 14, 2011

Structural analysis and prediction of protein mutant stability using distance and torsion potentials: role of secondary structure and solvent accessibility.

scientific article

Structural analysis of cation-pi interactions in DNA binding proteins

scientific article

Structural basis of flavonoids as dengue polymerase inhibitors: insights from QSAR and docking studies

scientific article published on 18 December 2017

Structure based approach for understanding organism specific recognition of protein-RNA complexes

scientific article

Structure based sequence dependent stiffness scale for trinucleotides: a direct method ⬇️

scientific article published on March 1, 2000

TMB finding pipeline: novel approach for detecting beta-barrel membrane proteins in genomic sequences.

scientific article published on 24 October 2007

TMBETA-GENOME: database for annotated beta-barrel membrane proteins in genomic sequences

scientific article

TMBETA-NET: discrimination and prediction of membrane spanning beta-strands in outer membrane proteins

scientific article

TMBETADISC-RBF: Discrimination of beta-barrel membrane proteins using RBF networks and PSSM profiles

scientific article

TMFunction: database for functional residues in membrane proteins

scientific article published on 08 October 2008

The role of stabilization centers in protein thermal stability

scientific article published on February 2016

Theoretical Investigation on the Binding Specificity of Sialyldisaccharides with Hemagglutinins of Influenza A Virus by Molecular Dynamics Simulations ⬇️

scientific article published on July 30, 2012

Theoretical investigation on the glycan-binding specificity of Agrocybe cylindracea galectin using molecular modeling and molecular dynamics simulation studies

scientific article published on 11 March 2015

Thermodynamic and kinetic determinants of Thermotoga maritima cold shock protein stability: a structural and dynamic analysis.

scientific article published in May 2008

Thermodynamic database for proteins: features and applications.

scientific article published in January 2010

Understanding the Recognition Mechanism of Protein-RNA Complexes Using Energy Based Approach ⬇️

scientific article published on November 1, 2010

ccPDB: compilation and creation of data sets from Protein Data Bank ⬇️

scientific article published on December 1, 2011

iPTREE-STAB: interpretable decision tree based method for predicting protein stability changes upon mutations

scientific article published on 22 March 2007

List of works by M Michael Gromiha

A simple statistical method for discriminating outer membrane proteins with better accuracy

A statistical method for predicting protein unfolding rates from amino acid sequence

Aggregation prone regions in human proteome: Insights from large-scale data analyses

An Analysis of the Amino Acid Clustering Pattern in (α/β)8 Barrel Proteins ⬇️

An in-silico method for identifying aggregation rate enhancer and mitigator mutations in proteins

Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information

Analysis and prediction of protein folding rates using quadratic response surface models

Analysis of secondary structural and physicochemical changes in protein-protein complexes

Application of amino acid occurrence for discriminating different folding types of globular proteins.

Applications of Protein Thermodynamic Database for Understanding Protein Mutant Stability and Designing Stable Mutants

Atom-wise statistics and prediction of solvent accessibility in proteins

Autoimmune Responses to Soluble Aggregates of Amyloidogenic Proteins Involved in Neurodegenerative Diseases: Overlapping Aggregation Prone and Autoimmunogenic regions

Bioinformatics approaches for functional annotation of membrane proteins ⬇️

CPAD, Curated Protein Aggregation Database: A Repository of Manually Curated Experimental Data on Protein and Peptide Aggregation

CUPSAT: prediction of protein stability upon point mutations.

Computational Approaches for Predicting Binding Partners, Interface Residues, and Binding Affinity of Protein-Protein Complexes

Computational approaches for predicting the binding sites and understanding the recognition mechanism of protein-DNA complexes

Computational modeling of protein mutant stability: analysis and optimization of statistical potentials and structural features reveal insights into prediction model development

Contribution of main chain and side chain atoms and their locations to the stability of thermophilic proteins

Current developments on beta-barrel membrane proteins: sequence and structure analysis, discrimination and prediction

Design and training of a neural network for predicting the solvent accessibility of proteins

Development of a machine learning method to predict membrane protein-ligand binding residues using basic sequence information

Discrimination of driver and passenger mutations in epidermal growth factor receptor in cancer.

Discrimination of mesophilic and thermophilic proteins using machine learning algorithms

Discrimination of outer membrane proteins using machine learning algorithms.

Discrimination of outer membrane proteins using support vector machines

Dissecting and analyzing key residues in protein-DNA complexes

Distinct position-specific sequence features of hexa-peptides that form amyloid-fibrils: application to discriminate between amyloid fibril and amorphous β-aggregate forming peptide sequences

Drug-Target Interactions: Prediction Methods and Applications

Energy based approach for understanding the recognition mechanism in protein-protein complexes

Eukaryote-wide sequence analysis of mitochondrial β-barrel outer membrane proteins

Exploring the environmental preference of weak interactions in (alpha/beta)8 barrel proteins

FOLD-RATE: prediction of protein folding rates from amino acid sequence

Feature selection and classification of protein-protein complexes based on their binding affinities using machine learning approaches.

Folding RaCe: a robust method for predicting changes in protein folding rates upon point mutations

Folding mechanism of all-beta globular proteins

Functional discrimination of membrane proteins using machine learning techniques

GAP: towards almost 100 percent prediction for β-strand-mediated aggregating peptides with distinct morphologies

Guest Editorial for Special Section on the 10th International Conference on Intelligent Computing (ICIC).

High throughput computing to improve efficiency of predicting protein stability change upon mutation

Hydrophobic environment is a key factor for the stability of thermophilic proteins ⬇️

Identification and analysis of binding site residues in protein-carbohydrate complexes using energy based approach

Identification of dengue viral RNA-dependent RNA polymerase inhibitor using computational fragment-based approaches and molecular dynamics study

Identification of efflux proteins using efficient radial basis function networks with position-specific scoring matrices and biochemical properties

Identification of type I and type II inhibitors of c-Yes kinase using in silico and experimental techniques

Identifying a potential receptor for the antibacterial peptide of sponge Axinella donnani endosymbiont

Importance of hydrophobic cluster formation through long-range contacts in the folding transition state of two-state proteins

Importance of long-range interactions in (alpha/beta)8 barrel fold

Importance of main-chain hydrophobic free energy to the stability of thermophilic proteins

Important amino acid properties for determining the transition state structures of two-state protein mutants

Important amino acid residues involved in folding and binding of protein-protein complexes

Influence of Medium and Long Range Interactions in (α/β)(8) Barrel Proteins ⬇️

Influence of amino acid properties for discriminating outer membrane proteins at better accuracy.

Influence of cation–π interactions in different folding types of membrane proteins ⬇️

Influence of cation–π interactions in protein–DNA complexes

Influence of medium and long range interactions in different structural classes of globular proteins ⬇️

Influence of medium- and long-range interactions in different folding types of globular proteins

Insights into the binding specificity of wild type and mutated wheat germ agglutinin towards Neu5Acα(2-3)Gal: a study by in silico mutations and molecular dynamics simulations

Integrating computational methods and experimental data for understanding the recognition mechanism and binding affinity of protein-protein complexes

Inter-residue interactions in protein folding and stability

Introduction: advanced intelligent computing theories and their applications in bioinformatics ⬇️

Investigating mutation-specific biological activities of small molecules using quantitative structure-activity relationship for epidermal growth factor receptor in cancer

Knowledge acquisition and development of accurate rules for predicting protein stability changes

Locating the stabilizing residues in (alpha/beta)8 barrel proteins based on hydrophobicity, long-range interactions, and sequence conservation

Look-up tables for protein solvent accessibility prediction and nearest neighbor effect analysis

Machine learning algorithms for predicting protein folding rates and stability of mutant proteins: comparison with statistical methods

Mammalian Mitochondrial ncRNA Database

Mitochondrial beta-barrel proteins, an exclusive club?

Multiple contact network is a key determinant to protein folding rates

MutHTP: Mutations in Human Transmembrane Proteins

Mutational studies to understand the structure-function relationship in multidrug efflux transporters: applications for distinguishing mutants with high specificity

NETASA: neural network based prediction of solvent accessibility

Neural network-based prediction of transmembrane beta-strand segments in outer membrane proteins

New insight into long-range nonadditivity within protein double-mutant cycles

Novel approach for selecting the best predictor for identifying the binding sites in DNA binding proteins

On the conformational stability of oligonucleotide duplexes and tRNA molecules

PDBparam: Online Resource for Computing Structural Parameters of Proteins

PINT: Protein-protein Interactions Thermodynamic Database

PROXiMATE: A database of mutant protein-protein complex thermodynamics and kinetics