Lista de obras -

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

artículo científico publicado en 2004

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

artículo científico publicado en 2006

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

artículo científico publicado en 2017

An analysis of the amino acid clustering pattern in (alpha/beta)8 barrel proteins

article

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

artículo científico publicado en 2018

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

artículo científico publicado en 2004

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

artículo científico publicado en 2008

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

artículo científico publicado en 2015

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

artículo científico publicado en 2007

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

artículo científico publicado en 2016

Atom-wise statistics and prediction of solvent accessibility in proteins

artículo científico publicado en 2006

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

artículo científico

Bioinformatics approaches for functional annotation of membrane proteins

artículo científico publicado en 2014

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

artículo científico publicado en 2016

CUPSAT: prediction of protein stability upon point mutations.

artículo científico publicado en 2006

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

artículo científico publicado en 2017

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

artículo científico

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

artículo científico publicado en 2007

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

artículo científico publicado en 2016

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

artículo científico publicado en 2007

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

artículo científico publicado en 2003

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

artículo científico publicado en 2015

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

artículo científico publicado en 2015

Discrimination of mesophilic and thermophilic proteins using machine learning algorithms

artículo científico publicado en 2008

Discrimination of outer membrane proteins using machine learning algorithms.

artículo científico publicado en 2006

Discrimination of outer membrane proteins using support vector machines

artículo científico publicado en 2005

Dissecting and analyzing key residues in protein-DNA complexes

artículo científico publicado en 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

artículo científico publicado en 2013

Drug-Target Interactions: Prediction Methods and Applications

artículo científico publicado en 2016

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

artículo científico publicado en 2009

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

artículo científico publicado en 2011

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

artículo científico publicado en 2006

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

artículo científico publicado en 2006

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

artículo científico publicado en 2014

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

artículo científico publicado en 2015

Folding mechanism of all-beta globular proteins

artículo científico publicado en 2004

Functional discrimination of membrane proteins using machine learning techniques

artículo científico publicado en 2008

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

artículo científico publicado en 2014

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

artículo científico publicado en 2016

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

artículo científico publicado en 2014

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

artículo científico publicado en 2013

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

artículo científico publicado en 2014

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

artículo científico publicado en 2015

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

artículo científico publicado en 2013

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

artículo científico publicado en 2017

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

artículo científico publicado en 2015

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

artículo científico publicado en 2004

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

artículo científico publicado en 1998

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

artículo científico publicado en 2005

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

artículo científico publicado en 2002

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

artículo científico publicado en 2016

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

artículo científico publicado en 1997

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

artículo científico publicado en 2006

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

artículo científico publicado el 25 de marzo de 2003

Influence of cation–π interactions in protein–DNA complexes

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

artículo científico publicado en 1997

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

artículo científico publicado en 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

artículo científico publicado en 2014

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

artículo científico publicado en 2017

Inter-residue interactions in protein folding and stability

artículo científico publicado en 2004

Introduction: Advanced intelligent computing theories and their applications in bioinformatics

artículo científico publicado en 2012

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

artículo científico publicado en 2017

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

artículo científico publicado en 2006

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

artículo científico publicado en 2004

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

artículo científico publicado en 2004

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

artículo científico publicado en 2011

Mammalian Mitochondrial ncRNA Database

artículo científico publicado en 2015

Mitochondrial beta-barrel proteins, an exclusive club?

Multiple contact network is a key determinant to protein folding rates

artículo científico publicado en 2009

MutHTP: Mutations in Human Transmembrane Proteins.

artículo científico publicado en 2018

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

artículo científico

NETASA: neural network based prediction of solvent accessibility

artículo científico publicado en 2002

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

artículo científico publicado en 2004

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

artículo científico publicado en 2008

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

artículo científico publicado en 2013

On the conformational stability of oligonucleotide duplexes and tRNA molecules

artículo científico publicado en 1994

PDBparam: Online Resource for Computing Structural Parameters of Proteins

artículo científico publicado en 2016

PINT: Protein-protein Interactions Thermodynamic Database

artículo científico publicado en 2006

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

artículo científico publicado en 2017

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

artículo científico publicado en 2014

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

artículo científico publicado en 2016

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

artículo científico publicado en 2010

Prediction of protein disorder on amino acid substitutions

artículo científico publicado en 2015

Prediction of protein mutant stability using classification and regression tool

artículo científico publicado en 2006

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

artículo científico publicado en 2006

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

artículo científico publicado en 2002

ProTherm, version 4.0: thermodynamic database for proteins and mutants

artículo científico publicado en 2004

Protein-protein binding affinity prediction from amino acid sequence

artículo científico publicado en 2014

Protein-protein interactions: scoring schemes and binding affinity

artículo científico publicado en 2016

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

artículo científico publicado en 2016

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

artículo científico publicado en 2003

Real value prediction of protein folding rate change upon point mutation

artículo científico publicado en 2012

Real value prediction of solvent accessibility from amino acid sequence

artículo científico publicado en 2003

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

artículo científico publicado en 2012

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

artículo científico publicado en 2009

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

artículo científico publicado en 2009

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

artículo científico publicado en 2008

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

artículo científico publicado en 2002

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

artículo científico publicado en 2003

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

artículo científico publicado en 2004

SRide: a server for identifying stabilizing residues in proteins

artículo científico publicado en 2005

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

artículo científico publicado en 2007

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

artículo científico publicado el 14 de octubre de 2011

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

artículo científico publicado en 2007

Structural analysis of cation-pi interactions in DNA binding proteins

artículo científico publicado en 2004

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

artículo científico publicado en 2017

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

artículo científico publicado en 2015

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

artículo científico publicado en 2000

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

artículo científico publicado en 2007

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

artículo científico publicado en 2006

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

artículo científico publicado en 2005

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

artículo científico publicado en 2008

TMFunction: database for functional residues in membrane proteins

artículo científico publicado en 2008

The role of stabilization centers in protein thermal stability

artículo científico publicado en 2016

Theoretical investigation on the binding specificity of sialyldisaccharides with hemagglutinins of influenza A virus by molecular dynamics simulations

artículo científico publicado en 2012

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

artículo científico

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

artículo científico publicado en 2008

Thermodynamic database for proteins: features and applications.

artículo científico publicado en 2010

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

artículo científico publicado el 1 de noviembre de 2010

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

artículo científico publicado el 1 de diciembre de 2011

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

artículo científico publicado en 2007

Lista de obras de

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 (alpha/beta)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