Enhanced sampling techniques in molecular dynamics simulations of biological systems
Background Molecular dynamics has emerged as an important research methodology
covering systems to the level of millions of atoms. However, insufficient sampling often limits …
covering systems to the level of millions of atoms. However, insufficient sampling often limits …
Three-dimensional protein structure prediction: Methods and computational strategies
A long standing problem in structural bioinformatics is to determine the three-dimensional (3-
D) structure of a protein when only a sequence of amino acid residues is given. Many …
D) structure of a protein when only a sequence of amino acid residues is given. Many …
Improved PEP-FOLD approach for peptide and miniprotein structure prediction
Y Shen, J Maupetit, P Derreumaux… - Journal of chemical …, 2014 - ACS Publications
Peptides and mini proteins have many biological and biomedical implications, which
motivates the development of accurate methods, suitable for large-scale experiments, to …
motivates the development of accurate methods, suitable for large-scale experiments, to …
PEP-FOLD: an updated de novo structure prediction server for both linear and disulfide bonded cyclic peptides
P Thevenet, Y Shen, J Maupetit, F Guyon… - Nucleic acids …, 2012 - academic.oup.com
In the context of the renewed interest of peptides as therapeutics, it is important to have an
on-line resource for 3D structure prediction of peptides with well-defined structures in …
on-line resource for 3D structure prediction of peptides with well-defined structures in …
Incorporation of solvent effect into multi-objective evolutionary algorithm for improved protein structure prediction
The problem of predicting the three-dimensional (3-D) structure of a protein from its one-
dimensional sequence has been called the “holy grail of molecular biology”, and it has …
dimensional sequence has been called the “holy grail of molecular biology”, and it has …
Proteins: sequence to structure and function-current status
SR Shenoy, B Jayaram - Current Protein and Peptide Science, 2010 - ingentaconnect.com
In an era that has been dominated by Structural Biology for the last 30-40 years, a dramatic
change of focus towards sequence analysis has spurred the advent of the genome projects …
change of focus towards sequence analysis has spurred the advent of the genome projects …
ProTSAV: a protein tertiary structure analysis and validation server
Quality assessment of predicted model structures of proteins is as important as the protein
tertiary structure prediction. A highly efficient quality assessment of predicted model …
tertiary structure prediction. A highly efficient quality assessment of predicted model …
Curcumin specifically binds to the human calcium–calmodulin-dependent protein kinase IV: Fluorescence and molecular dynamics simulation studies
Calcium–calmodulin-dependent protein kinase IV (CAMK4) plays significant role in the
regulation of calcium-dependent gene expression, and thus, it is involved in varieties of …
regulation of calcium-dependent gene expression, and thus, it is involved in varieties of …
From drug target to leads-sketching a physicochemical pathway for lead molecule design in silico
SA Shaikh, T Jain, G Sandhu, N Latha… - Current …, 2007 - ingentaconnect.com
The discovery of new pharmaceuticals via computer modeling is one of the key challenges
in modern medicine. The advent of global networks of genomic, proteomic and metabolomic …
in modern medicine. The advent of global networks of genomic, proteomic and metabolomic …
Bhageerath-H: A homology/ab initio hybrid server for predicting tertiary structures of monomeric soluble proteins
Background The advent of human genome sequencing project has led to a spurt in the
number of protein sequences in the databanks. Success of structure based drug discovery …
number of protein sequences in the databanks. Success of structure based drug discovery …