List of works - Shandar Ahmad

A molecular and in silico characterization of Hev b 4, a glycosylated latex allergen

scientific article published in 2008

A new method for determining the constant-pressure heat capacity change associated with the protein denaturation induced by guanidinium chloride (or urea).

scientific article

ASAView: database and tool for solvent accessibility representation in proteins

scientific article

ATP-binding site as a further application of neural networks to residue level prediction

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 of electric moments of RNA-binding proteins: implications for mechanism and prediction

scientific article

Application of residue distribution along the sequence for discriminating outer membrane proteins

Atom-wise statistics and prediction of solvent accessibility in proteins

scientific article published on 24 July 2006

Bioinformatics Approaches for Analysis of Protein-Ligand Interactions

CCRXP: exploring clusters of conserved residues in protein structures

scientific article

Classification of Protein-DNA Complexes Based on Structural Descriptors

Conformational changes in DNA-binding proteins: Relationships with precomplex features and contributions to specificity and stability

scholarly article by Munazah Andrabi published in November 2013

Context dependent reference states of solvent accessibility derived from native protein structures and assessed by predictability analysis

scientific article

Creation of lysine-deficient mutant lymphotoxin-alpha with receptor selectivity by using a phage display system

scientific article

Deconstructing RNA: optical measurement of composition and structure

scientific article

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

scientific article

Dimensionality of amino acid space and solvent accessibility prediction with neural networks

scientific article published on 20 March 2006

Distinct transcriptional regulatory modules underlie STAT3's cell type-independent and cell type-specific functions

scientific article published on 7 January 2013

Enabling full-length evolutionary profiles based deep convolutional neural network for predicting DNA-binding proteins from sequence

scientific article published on 08 July 2019

Exploring the evolutionary rate differences of party hub and date hub proteins in Saccharomyces cerevisiae protein–protein interaction network

article

Feature Selection for Topological Proximity Prediction of Single-Cell Transcriptomic Profiles in <i>Drosophila</i> Embryo Using Genetic Algorithm

scientific article published on 28 December 2020

Human Blood-Brain Differential Gene-Expression Correlates with Dipeptide Frequency of Gene Products

article

Integrated pathway clusters with coherent biological themes for target prioritisation

scientific article

Integrated prediction of one-dimensional structural features and their relationships with conformational flexibility in helical membrane proteins.

scientific article

Lipid recognition propensities of amino acids in membrane proteins from atomic resolution data

scientific article

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

scientific article published in October 2004

Modeling the three-dimensional structures of an unbound single-chain variable fragment (scFv) and its hypothetical complex with a Corynespora cassiicola toxin, cassiicolin

scientific article published on 16 March 2010

Moment-based prediction of DNA-binding proteins

scientific article published in July 2004

Neural network based prediction of protein structure and Function: Comparison with other machine learning methods

scholarly article published June 2008

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

scientific article published in April 2004

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

scientific article published on 20 June 2013

On nucleotide solvent accessibility in RNA structure

scientific article published on 12 May 2010

PROCARB: A Database of Known and Modelled Carbohydrate-Binding Protein Structures with Sequence-Based Prediction Tools.

scientific article

PSSM-based prediction of DNA binding sites in proteins

scientific article

Partner-Aware Prediction of Interacting Residues in Protein-Protein Complexes from Sequence Data ⬇️

scientific article published on December 14, 2011

Pattern Recognition in Bioinformatics

scholarly article by Shandar Ahmad et al published October 2010 in Pattern Recognition Letters

Prediction and evolutionary information analysis of protein solvent accessibility using multiple linear regression

scientific article published in November 2005

Prediction and experimental validation of a putative non-consensus binding site for transcription factor STAT3 in serum amyloid A gene promoter

article

Prediction of dinucleotide-specific RNA-binding sites in proteins

scientific article

Prediction of mono- and di-nucleotide-specific DNA-binding sites in proteins using neural networks

scientific article

Protein Sequence and Structure Databases: A Review

article

Protein-DNA interactions: structural, thermodynamic and clustering patterns of conserved residues in DNA-binding proteins

scientific article published on 18 September 2008

Proteochemometric recognition of stable kinase inhibition complexes using topological autocorrelation and support vector machines

scientific article published in June 2010

Qgrid: clustering tool for detecting charged and hydrophobic regions in proteins

scientific article published on July 2004

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

scientific article published in September 2003

ReadOut: structure-based calculation of direct and indirect readout energies and specificities for protein-DNA recognition

scientific article published on July 2006

Real value prediction of solvent accessibility from amino acid sequence

scientific article published in March 2003

Recognition of drug-target interaction patterns using genetic algorithm-optimized Bayesian-regularized neural networks and support vector machines

Residue propensities, discrimination and binding site prediction of adenine and guanine phosphates

scientific article published on 13 May 2011

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

scientific article published in February 2004

SVM-Cabins: prediction of solvent accessibility using accumulation cutoff set and support vector machine

scientific article

Selective constraints in yeast genes with differential expressivity: codon pair usage and mRNA stability perspectives

scientific article published on 30 April 2011

Sequence and structural features of carbohydrate binding in proteins and assessment of predictability using a neural network

scientific article published on 3 January 2007

Sequence-Based Prediction of Residue-Level Properties in Proteins

Sequence-Dependent Conformational Energy of DNA Derived from Molecular Dynamics Simulations: Toward Understanding the Indirect Readout Mechanism in Protein−DNA Recognition

article

Sequence-dependence and prediction of nucleotide solvent accessibility in double stranded DNA.

scientific article

Solvent accessibility in native and isolated domain environments: general features and implications to interface predictability

Specific 50'CpG island methylation signatures of FHIT and p16 genes and their potential diagnostic relevance in Indian breast cancer patients

scientific article published on September 2008

Structural analysis of cation-pi interactions in DNA binding proteins

scientific article

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

scientific article

uORFs, reinitiation and alternative translation start sites in human mRNAs

scientific article published on 20 March 2008

List of works by Shandar Ahmad

A molecular and in silico characterization of Hev b 4, a glycosylated latex allergen

A new method for determining the constant-pressure heat capacity change associated with the protein denaturation induced by guanidinium chloride (or urea).

ASAView: database and tool for solvent accessibility representation in proteins

ATP-binding site as a further application of neural networks to residue level prediction

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

Analysis of electric moments of RNA-binding proteins: implications for mechanism and prediction

Application of residue distribution along the sequence for discriminating outer membrane proteins

Atom-wise statistics and prediction of solvent accessibility in proteins

Bioinformatics Approaches for Analysis of Protein-Ligand Interactions

CCRXP: exploring clusters of conserved residues in protein structures

Classification of Protein-DNA Complexes Based on Structural Descriptors

Conformational changes in DNA-binding proteins: Relationships with precomplex features and contributions to specificity and stability

Context dependent reference states of solvent accessibility derived from native protein structures and assessed by predictability analysis

Creation of lysine-deficient mutant lymphotoxin-alpha with receptor selectivity by using a phage display system

Deconstructing RNA: optical measurement of composition and structure

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

Dimensionality of amino acid space and solvent accessibility prediction with neural networks

Distinct transcriptional regulatory modules underlie STAT3's cell type-independent and cell type-specific functions

Enabling full-length evolutionary profiles based deep convolutional neural network for predicting DNA-binding proteins from sequence

Exploring the evolutionary rate differences of party hub and date hub proteins in Saccharomyces cerevisiae protein–protein interaction network

Feature Selection for Topological Proximity Prediction of Single-Cell Transcriptomic Profiles in <i>Drosophila</i> Embryo Using Genetic Algorithm

Human Blood-Brain Differential Gene-Expression Correlates with Dipeptide Frequency of Gene Products

Integrated pathway clusters with coherent biological themes for target prioritisation

Integrated prediction of one-dimensional structural features and their relationships with conformational flexibility in helical membrane proteins.

Lipid recognition propensities of amino acids in membrane proteins from atomic resolution data

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

Modeling the three-dimensional structures of an unbound single-chain variable fragment (scFv) and its hypothetical complex with a Corynespora cassiicola toxin, cassiicolin

Moment-based prediction of DNA-binding proteins

Neural network based prediction of protein structure and Function: Comparison with other machine learning methods

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

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

On nucleotide solvent accessibility in RNA structure

PROCARB: A Database of Known and Modelled Carbohydrate-Binding Protein Structures with Sequence-Based Prediction Tools.

PSSM-based prediction of DNA binding sites in proteins

Partner-Aware Prediction of Interacting Residues in Protein-Protein Complexes from Sequence Data ⬇️

Pattern Recognition in Bioinformatics

Prediction and evolutionary information analysis of protein solvent accessibility using multiple linear regression

Prediction and experimental validation of a putative non-consensus binding site for transcription factor STAT3 in serum amyloid A gene promoter

Prediction of dinucleotide-specific RNA-binding sites in proteins

Prediction of mono- and di-nucleotide-specific DNA-binding sites in proteins using neural networks

Protein Sequence and Structure Databases: A Review

Protein-DNA interactions: structural, thermodynamic and clustering patterns of conserved residues in DNA-binding proteins

Proteochemometric recognition of stable kinase inhibition complexes using topological autocorrelation and support vector machines

Qgrid: clustering tool for detecting charged and hydrophobic regions in proteins

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

ReadOut: structure-based calculation of direct and indirect readout energies and specificities for protein-DNA recognition

Real value prediction of solvent accessibility from amino acid sequence

Recognition of drug-target interaction patterns using genetic algorithm-optimized Bayesian-regularized neural networks and support vector machines

Residue propensities, discrimination and binding site prediction of adenine and guanine phosphates

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

SVM-Cabins: prediction of solvent accessibility using accumulation cutoff set and support vector machine

Selective constraints in yeast genes with differential expressivity: codon pair usage and mRNA stability perspectives

Sequence and structural features of carbohydrate binding in proteins and assessment of predictability using a neural network

Sequence-Based Prediction of Residue-Level Properties in Proteins

Sequence-Dependent Conformational Energy of DNA Derived from Molecular Dynamics Simulations: Toward Understanding the Indirect Readout Mechanism in Protein−DNA Recognition

Sequence-dependence and prediction of nucleotide solvent accessibility in double stranded DNA.

Solvent accessibility in native and isolated domain environments: general features and implications to interface predictability

Specific 50'CpG island methylation signatures of FHIT and p16 genes and their potential diagnostic relevance in Indian breast cancer patients

Structural analysis of cation-pi interactions in DNA binding proteins

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

uORFs, reinitiation and alternative translation start sites in human mRNAs