Michael Gromiha

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TOP 3
Huang Liang-Tsung; Gromiha M Michael
Reliable prediction of protein thermostability change upon double mutation from amino acid sequence.
Gromiha M Michael
Revisiting "reverse hydrophobic effect": applicable only to coil mutations at the surface.
Gromiha M Michael
Multiple contact network is a key determinant to protein folding rates.

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All Publications

2009: Huang Liang-Tsung; Gromiha M Michael
Reliable prediction of protein thermostability change upon double mutation from amino acid sequence.
Bioinformatics (Oxford, England) 2009;25(17):2181-7.
2009: Gromiha M Michael
Revisiting "reverse hydrophobic effect": applicable only to coil mutations at the surface.
Biopolymers 2009;91(7):591-9.
2009: Gromiha M Michael
Multiple contact network is a key determinant to protein folding rates.
Journal of chemical information and modeling 2009;49(4):1130-5.
2008: Imai Kenichiro; Gromiha M Michael; Horton Paul
Mitochondrial beta-barrel proteins, an exclusive club?
Cell 2008;135(7):1158-9; author reply 1159-60.
2008: Huang Liang-Tsung; Gromiha M Michael
Analysis and prediction of protein folding rates using quadratic response surface models.
Journal of computational chemistry 2008;29(10):1675-83.
2008: Ou Yu-Yen; Gromiha M Michael; Chen Shu-An; Suwa Makiko
TMBETADISC-RBF: Discrimination of beta-barrel membrane proteins using RBF networks and PSSM profiles.
Computational biology and chemistry 2008;32(3):227-31.
2008: Motono Chie; Gromiha M Michael; Kumar Sandeep
Thermodynamic and kinetic determinants of Thermotoga maritima cold shock protein stability: a structural and dynamic analysis.
Proteins 2008;71(2):655-69.
2008: Kumar Manish; Gromiha M Michael; Raghava G P S
Prediction of RNA binding sites in a protein using SVM and PSSM profile.
Proteins 2008;71(1):189-94.
2008: Gromiha M Michael; Suresh M Xavier
Discrimination of mesophilic and thermophilic proteins using machine learning algorithms.
Proteins 2008;70(4):1274-9.
2008: Martis Remila L; Singh Sameer Kumar; Gromiha M Michael; Santhosh C
Role of cation-pi interactions in single chain 'all-alpha' proteins.
Journal of theoretical biology 2008;250(4):655-62.
2008: Istomin Andrei Y; Gromiha M Michael; Vorov Oleg K; Jacobs Donald J; Livesay Dennis R
New insight into long-range nonadditivity within protein double-mutant cycles.
Proteins 2008;70(3):915-24.
2008: Gromiha M Michael; Yabuki Yukimitsu
Functional discrimination of membrane proteins using machine learning techniques.
BMC bioinformatics 2008;9():135.
2007: Gromiha M Michael; Suwa Makiko
Current developments on beta-barrel membrane proteins: sequence and structure analysis, discrimination and prediction.
Current protein & peptide science 2007;8(6):580-99.
2007: Gromiha M Michael; Yabuki Yukimitsu; Suwa Makiko
TMB finding pipeline: novel approach for detecting beta-barrel membrane proteins in genomic sequences.
Journal of chemical information and modeling 2007;47(6):2456-61.
2007: Huang Liang-Tsung; Gromiha M Michael; Ho Shinn-Ying
Sequence analysis and rule development of predicting protein stability change upon mutation using decision tree model.
Journal of molecular modeling 2007;13(8):879-90.
2007: Huang Liang-Tsung; Gromiha M Michael; Ho Shinn-Ying
iPTREE-STAB: interpretable decision tree based method for predicting protein stability changes upon mutations.
Bioinformatics (Oxford, England) 2007;23(10):1292-3.
2007: Huang Liang-Tsung; Saraboji K; Ho Shinn-Ying; Hwang Shiow-Fen; Ponnuswamy M N; Gromiha M Michael
Prediction of protein mutant stability using classification and regression tool.
Biophysical chemistry 2007;125(2-3):462-70.
2007: Gromiha M Michael; Yabuki Yukimitsu; Kundu Srinesh; Suharnan Sivasundaram; Suwa Makiko
TMBETA-GENOME: database for annotated beta-barrel membrane proteins in genomic sequences.
Nucleic acids research 2007;35(Database issue):D314-6.
2007: Parthiban Vijaya; Gromiha M Michael; Hoppe Christian; Schomburg Dietmar
Structural analysis and prediction of protein mutant stability using distance and torsion potentials: role of secondary structure and solvent accessibility.
Proteins 2007;66(1):41-52.
2007: Kumar Manish; Gromiha Michael M; Raghava Gajendra P S
Identification of DNA-binding proteins using support vector machines and evolutionary profiles.
BMC bioinformatics 2007;8():463.
2007: Taguchi Y-h; Gromiha M Michael
Application of amino acid occurrence for discriminating different folding types of globular proteins.
BMC bioinformatics 2007;8():404.
2007: Parthiban Vijaya; Gromiha M Michael; Abhinandan Madenhalli; Schomburg Dietmar
Computational modeling of protein mutant stability: analysis and optimization of statistical potentials and structural features reveal insights into prediction model development.
BMC structural biology 2007;7():54.
2006: Huang Liang-Tsung; Gromiha M Michael; Hwang Shiow-Fen; Ho Shinn-Ying
Knowledge acquisition and development of accurate rules for predicting protein stability changes.
Computational biology and chemistry 2006;30(6):408-15.
2006: Singh Y Hemajit; Gromiha M Michael; Sarai Akinori; Ahmad Shandar
Atom-wise statistics and prediction of solvent accessibility in proteins.
Biophysical chemistry 2006;124(2):145-54.
2006: Chakkaravarthi S; Babu M Madan; Gromiha M Michael; Jayaraman G; Sethumadhavan R
Exploring the environmental preference of weak interactions in (alpha/beta)8 barrel proteins.
Proteins 2006;65(1):75-86.
2006: Gromiha M Michael; Suwa Makiko
Influence of amino acid properties for discriminating outer membrane proteins at better accuracy.
Biochimica et biophysica acta 2006;1764(9):1493-7.
2006: Prabakaran Ponraj; Siebers Jörg G; Ahmad Shandar; Gromiha M Michael; Singarayan Maria G; Sarai Akinori
Classification of protein-DNA complexes based on structural descriptors.
Structure (London, England : 1993) 2006;14(9):1355-67.
2006: Gromiha M Michael; Thangakani A Mary; Selvaraj S
FOLD-RATE: prediction of protein folding rates from amino acid sequence.
Nucleic acids research 2006;34(Web Server issue):W70-4.
2006: Parthiban Vijaya; Gromiha M Michael; Schomburg Dietmar
CUPSAT: prediction of protein stability upon point mutations.
Nucleic acids research 2006;34(Web Server issue):W239-42.
2006: Gromiha M Michael; Suwa Makiko
Discrimination of outer membrane proteins using machine learning algorithms.
Proteins 2006;63(4):1031-7.
2006: Gromiha M Michael; Selvaraj S; Thangakani A Mary
A statistical method for predicting protein unfolding rates from amino acid sequence.
Journal of chemical information and modeling 2006;46(3):1503-8.
2006: Saraboji K; Gromiha M Michael; Ponnuswamy M N
Average assignment method for predicting the stability of protein mutants.
Biopolymers 2006;82(1):80-92.
2006: Kumar M D Shaji; Bava K Abdulla; Gromiha M Michael; Prabakaran Ponraj; Kitajima Koji; Uedaira Hatsuho; Sarai Akinori
ProTherm and ProNIT: thermodynamic databases for proteins and protein-nucleic acid interactions.
Nucleic acids research 2006;34(Database issue):D204-6.
2006: Kumar M D Shaji; Gromiha M Michael
PINT: Protein-protein Interactions Thermodynamic Database.
Nucleic acids research 2006;34(Database issue):D195-8.
2005: Gromiha M Michael; Siebers Joerg G; Selvaraj Samuel; Kono Hidetoshi; Sarai Akinori
Role of inter and intramolecular interactions in protein-DNA recognition.
Gene 2005;364():108-13.
2005: Park Keun-Joon; Gromiha M Michael; Horton Paul; Suwa Makiko
Discrimination of outer membrane proteins using support vector machines.
Bioinformatics (Oxford, England) 2005;21(23):4223-9.
2005: Gromiha M Michael
Motifs in outer membrane protein sequences: applications for discrimination.
Biophysical chemistry 2005;117(1):65-71.
2005: Magyar Csaba; Gromiha M Michael; Pujadas Gerard; Tusnády Gábor E; Simon István
SRide: a server for identifying stabilizing residues in proteins.
Nucleic acids research 2005;33(Web Server issue):W303-5.
2005: Gromiha M Michael; Ahmad Shandar; Suwa Makiko
TMBETA-NET: discrimination and prediction of membrane spanning beta-strands in outer membrane proteins.
Nucleic acids research 2005;33(Web Server issue):W164-7.
2005: Gromiha M Michael
Influence of DNA stiffness in protein-DNA recognition.
Journal of biotechnology 2005;117(2):137-45.
2005: Gromiha M Michael; Ahmad Shandar; Suwa Makiko
Application of residue distribution along the sequence for discriminating outer membrane proteins.
Computational biology and chemistry 2005;29(2):135-42.
2005: Saraboji K; Gromiha M Michael; Ponnuswamy M N
Importance of main-chain hydrophobic free energy to the stability of thermophilic proteins.
International journal of biological macromolecules 2005;35(3-4):211-20.
2005: Gromiha M Michael; Suwa Makiko
A simple statistical method for discriminating outer membrane proteins with better accuracy.
Bioinformatics (Oxford, England) 2005;21(7):961-8.
2005: Gromiha M Michael
A statistical model for predicting protein folding rates from amino acid sequence with structural class information.
Journal of chemical information and modeling 2005;45(2):494-501.
2005: Gromiha M Michael; Suwa Makiko
Structural analysis of residues involving cation-pi interactions in different folding types of membrane proteins.
International journal of biological macromolecules 2005;35(1-2):55-62.
2005: Sarai Akinori; Siebers Jorg; Selvaraj Samuel; Gromiha M Michael; Kono Hidetoshi
Integration of bioinformatics and computational biology to understand protein-DNA recognition mechanism.
Journal of bioinformatics and computational biology 2005;3(1):169-83.
2005: Saraboji K; Gromiha M Michael; Ponnuswamy M N
Relative importance of secondary structure and solvent accessibility to the stability of protein mutants. A case study with amino acid properties and energetics on T4 and human lysozymes.
Computational biology and chemistry 2005;29(1):25-35.
2004: Gromiha M Michael; Parry David A D
Characteristic features of amino acid residues in coiled-coil protein structures.
Biophysical chemistry 2004;111(2):95-103.
2004: Wang Jung-Ying; Ahmad Shandar; Gromiha M Michael; Sarai Akinori
Look-up tables for protein solvent accessibility prediction and nearest neighbor effect analysis.
Biopolymers 2004;75(3):209-16.
2004: Gromiha M Michael; Selvaraj S
Inter-residue interactions in protein folding and stability.
Progress in biophysics and molecular biology 2004;86(2):235-77.
2004: Gromiha M Michael; Santhosh C; Ahmad Shandar
Structural analysis of cation-pi interactions in DNA binding proteins.
International journal of biological macromolecules 2004;34(3):203-11.
2004: Selvaraj S; Gromiha M Michael
Importance of hydrophobic cluster formation through long-range contacts in the folding transition state of two-state proteins.
Proteins 2004;55(4):1023-35.
2004: Gromiha M Michael; Pujadas Gerard; Magyar Csaba; Selvaraj Samuel; Simon Istvan
Locating the stabilizing residues in (alpha/beta)8 barrel proteins based on hydrophobicity, long-range interactions, and sequence conservation.
Proteins 2004;55(2):316-29.
2004: Gromiha M Michael; Ahmad Shandar; Suwa Makiko
Neural network-based prediction of transmembrane beta-strand segments in outer membrane proteins.
Journal of computational chemistry 2004;25(5):762-7.
2004: Ahmad Shandar; Gromiha M Michael; Sarai Akinori
Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information.
Bioinformatics (Oxford, England) 2004;20(4):477-86.
2004: Gromiha M Michael; Selvaraj S
Folding mechanism of all-beta globular proteins.
Preparative biochemistry & biotechnology 2004;34(1):13-23.
2004: Gromiha M Michael; Saraboji K; Ahmad Shandar; Ponnuswamy M N; Suwa Makiko
Role of non-covalent interactions for determining the folding rate of two-state proteins.
Biophysical chemistry 2004;107(3):263-72.
2004: Bava K Abdulla; Gromiha M Michael; Uedaira Hatsuho; Kitajima Koji; Sarai Akinori
ProTherm, version 4.0: thermodynamic database for proteins and mutants.
Nucleic acids research 2004;32(Database issue):D120-1.
2003: Ahmad Shandar; Gromiha M Michael; Sarai Akinori
RVP-net: online prediction of real valued accessible surface area of proteins from single sequences.
Bioinformatics (Oxford, England) 2003;19(14):1849-51.
2003: Gromiha M Michael
Importance of native-state topology for determining the folding rate of two-state proteins.
Journal of chemical information and computer sciences 2003;43(5):1481-5.
2003: Gromiha M Michael; Suwa Makiko
Variation of amino acid properties in all-beta globular and outer membrane protein structures.
International journal of biological macromolecules 2003;32(3-5):93-8.
2003: Ahmad Shandar; Gromiha M Michael
Design and training of a neural network for predicting the solvent accessibility of proteins.
Journal of computational chemistry 2003;24(11):1313-20.
2003: Gromiha M Michael
Influence of cation-pi interactions in different folding types of membrane proteins.
Biophysical chemistry 2003;103(3):251-8.
2003: Selvaraj S; Gromiha M Michael
Role of hydrophobic clusters and long-range contact networks in the folding of (alpha/beta)8 barrel proteins.
Biophysical journal 2003;84(3):1919-25.
2003: Ahmad Shandar; Gromiha M Michael; Sarai Akinori
Real value prediction of solvent accessibility from amino acid sequence.
Proteins 2003;50(4):629-35.
2002: Gromiha M Michael; Thomas Shali; Santhosh C
Role of cation-pi interactions to the stability of thermophilic proteins.
Preparative biochemistry & biotechnology 2002;32(4):355-62.
2002: Kumarevel T S; Gromiha M Michael; Selvaraj S; Gayatri K; Kumar P K R
Influence of medium- and long-range interactions in different folding types of globular proteins.
Biophysical chemistry 2002;99(2):189-98.
2002: Gromiha M Michael; Selvaraj S
Important amino acid properties for determining the transition state structures of two-state protein mutants.
FEBS letters 2002;526(1-3):129-34.
2002: Gromiha M Michael; Oobatake Motohisa; Kono Hidetoshi; Uedaira Hatsuho; Sarai Akinori
Importance of mutant position in Ramachandran plot for predicting protein stability of surface mutations.
Biopolymers 2002;64(4):210-20.
2002: Ahmad Shandar; Gromiha M Michael
NETASA: neural network based prediction of solvent accessibility.
Bioinformatics (Oxford, England) 2002;18(6):819-24.
2002: Gromiha M Michael; Uedaira Hatsuho; An Jianghong; Selvaraj Samuel; Prabakaran Ponraj; Sarai Akinori
ProTherm, Thermodynamic Database for Proteins and Mutants: developments in version 3.0.
Nucleic acids research 2002;30(1):301-2.
2001: Prabakaran P; An J; Gromiha M M; Selvaraj S; Uedaira H; Kono H; Sarai A
Thermodynamic database for protein-nucleic acid interactions (ProNIT).
Bioinformatics (Oxford, England) 2001;17(11):1027-34.
2001: Gromiha M M; Thangakani A M
Role of medium- and long-range interactions to the stability of the mutants of T4 lysozyme.
Preparative biochemistry & biotechnology 2001;31(3):217-27.
2001: Gromiha M M; Selvaraj S
Role of medium--and long-range interactions in discriminating globular and membrane proteins.
International journal of biological macromolecules 2001;29(1):25-34.
2001: Gromiha M M
Important inter-residue contacts for enhancing the thermal stability of thermophilic proteins.
Biophysical chemistry 2001;91(1):71-7.
2001: Kumarevel T S; Gromiha M M; Ponnuswamy M N
Distribution of amino acid residues and residue-residue contacts in molecular chaperones.
Preparative biochemistry & biotechnology 2001;31(2):163-83.
2001: Gromiha M M
Factors influencing the stability of alpha-helices and beta-strands in thermophilic ribonuclease H.
Preparative biochemistry & biotechnology 2001;31(2):103-12.
2001: Kaliannan P; Gromiha M M; Elanthiraiyan M
Solvent accessibility studies on polysaccharides.
International journal of biological macromolecules 2001;28(2):135-41.
2001: Sarai A; Gromiha M M; An J; Prabakaran P; Selvaraj S; Kono H; Oobatake M; Uedaira H
Thermodynamic databases for proteins and protein-nucleic acid interactions.
Biopolymers 2001;61(2):121-6.
2000: Kumarevel T S; Gromiha M M; Ponnuswamy M N
Structural class prediction: an application of residue distribution along the sequence.
Biophysical chemistry 2000;88(1-3):81-101.
2000: Gromiha M M; Oobatake M; Kono H; Uedaira H; Sarai A
Importance of surrounding residues for protein stability of partially buried mutations.
Journal of biomolecular structure & dynamics 2000;18(2):281-95.
2000: Muthusamy R; Gromiha M M; Ponnuswamy P K
On the thermal unfolding character of globular proteins.
Journal of protein chemistry 2000;19(1):1-8.
2000: Gromiha M M; An J; Kono H; Oobatake M; Uedaira H; Prabakaran P; Sarai A
ProTherm, version 2.0: thermodynamic database for proteins and mutants.
Nucleic acids research 2000;28(1):283-5.
1999: Gromiha M M; Oobatake M; Sarai A
Important amino acid properties for enhanced thermostability from mesophilic to thermophilic proteins.
Biophysical chemistry 1999;82(1):51-67.
1999: Gromiha M M; Selvaraj S
Influence of medium and long range interactions in protein folding.
Preparative biochemistry & biotechnology 1999;29(4):339-51.
1999: Gromiha M M; Oobatake M; Kono H; Uedaira H; Sarai A
Relationship between amino acid properties and protein stability: buried mutations.
Journal of protein chemistry 1999;18(5):565-78.
1999: Gromiha M M
A simple method for predicting transmembrane alpha helices with better accuracy.
Protein engineering 1999;12(7):557-61.
1999: Gromiha M M; Oobatake M; Kono H; Uedaira H; Sarai A
Role of structural and sequence information in the prediction of protein stability changes: comparison between buried and partially buried mutations.
Protein engineering 1999;12(7):549-55.
1999: Gromiha M M; Selvaraj S
Importance of long-range interactions in protein folding.
Biophysical chemistry 1999;77(1):49-68.
1999: Gromiha M M; An J; Kono H; Oobatake M; Uedaira H; Sarai A
ProTherm: Thermodynamic Database for Proteins and Mutants.
Nucleic acids research 1999;27(1):286-8.
1998: Kumarevel T S; Gromiha M M; Ponnuswamy M N
Analysis of hydrophobic and charged patches and influence of medium- and long-range interactions in molecular chaperones.
Biophysical chemistry 1998;75(2):105-13.
1998: Selvaraj S; Gromiha M M
Importance of long-range interactions in (alpha/beta)8 barrel fold.
Journal of protein chemistry 1998;17(7):691-7.
1998: Kaliannan P; Gromiha M M; Ramamurthi K; Elanthiraiyan M
Solvent accessibility studies on glycosaminoglycans.
Biophysical chemistry 1998;74(1):11-22.
1998: Selvaraj S; Gromiha M M
An analysis of the amino acid clustering pattern in (alpha/beta)8 barrel proteins.
Journal of protein chemistry 1998;17(5):407-15.
1998: Kumarevel T S; Gromiha M M; Ponnuswamy M N
Solvent accessibility analysis on the mutants of Hsc70 ATPase fragment.
Biophysical chemistry 1998;71(2-3):99-111.
1998: Gromiha M M; Selvaraj S
Protein secondary structure prediction in different structural classes.
Protein engineering 1998;11(4):249-51.
1997: Gromiha M M; Munteanu M G; Simon I; Pongor S
The role of DNA bending in Cro protein-DNA interactions.
Biophysical chemistry 1997;69(2-3):153-60.
1997: Gromiha M M; Majumdar R; Ponnuswamy P K
Identification of membrane spanning beta strands in bacterial porins.
Protein engineering 1997;10(5):497-500.
1996: Gromiha M M; Ponnuswamy P K
Hydrophobic distribution and spatial arrangement of amino acid residues in membrane proteins.
International journal of peptide and protein research 1996;48(5):452-60.
1995: Gromiha M M; Ponnuswamy P K
Prediction of protein secondary structures from their hydrophobic characteristics.
International journal of peptide and protein research 1995;45(3):225-40.
1994: Ponnuswamy P K; Gromiha M M
On the conformational stability of oligonucleotide duplexes and tRNA molecules.
Journal of theoretical biology 1994;169(4):419-32.
1993: Gromiha M M; Ponnuswamy P K
Prediction of transmembrane beta-strands from hydrophobic characteristics of proteins.
International journal of peptide and protein research 1993;42(5):420-31.
1993: Ponnuswamy P K; Gromiha M M
Prediction of transmembrane helices from hydrophobic characteristics of proteins.
International journal of peptide and protein research 1993;42(4):326-41.

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