Biomolecules
Protein-peptide interactions play essential functional roles in living organisms and their structural characterization is a hot subject of current experimental and theoretical research. Computational modeling of the structure of…
We present a structural data set of the 20 proteinogenic amino acids and their amino-methylated and acetylated (capped) dipeptides. Different protonation states of the backbone (uncharged and zwitterionic) were considered for the amino…
Ion channels are of major interest and form an area of intensive research in the fields of biophysics and medicine since they control many vital physiological functions. The aim of this work is on one hand to propose a fully stochastic and…
DNA G-hairpins are potential key structures participating in folding of human telomeric guanine quadruplexes (GQ). We examined their properties by standard MD simulations starting from the folded state and long T-REMD starting from the…
Non structural protein 3 (NS3) helicase from hepatitis C virus is an enzyme that unwinds and translocates along nucleic acids with an ATP-dependent mechanism and has a key role in the replication of the viral RNA. An inchworm-like mechanism…
Multivariate regression is a widespread computational technique that may give meaningless results if the explanatory variables are too numerous or highly collinear. Tikhonov regularization, or ridge regression, is a popular approach to…
Biology offers a boundless source of adaptation, innovation, and inspiration. A wide range of photosynthetic organisms exist that are capable of harvesting solar light in an exceptionally efficient way, using abundant and low-cost…
We describe a robust, fast, and memory-efficient procedure that can cluster millions of structures derived from molecular dynamics simulations. The essence of the method is based on a peak-picking algorithm applied to three- and…
The direct-coupling analysis is a powerful method for protein contact prediction, and enables us to extract "direct" correlations between distant sites that are latent in "indirect" correlations observed in a protein multiple-sequence…
Protein secondary structure (SS) prediction is important for studying protein structure and function. When only the sequence (profile) information is used as input feature, currently the best predictors can obtain ~80% Q3 accuracy, which…
We previously described the representation of protein 3D structures in spherical coordinates (rho, phi, theta) and two of its applications: separation of the outer layer (OL) from the inner core (IC) of proteins, and assessment of protein…
Ligand burial depth is an indicator of protein flexibility, as the extent of receptor conformational change required to bind a ligand in general varies directly with its depth of burial. In a companion paper (Reyes, V.M. 2015a), we report…
Transformation of protein 3D structures from their all-atom representation (AAR) to the double-centroid reduced representation (DCRR) is a prerequisite to the implementation of both the tetrahedral three-dimensional search motif (3D SM)…
Time kinetics of interaction of natural graphite (GR) to colloidal graphene (G) collagen (C) nanocomposites was studied at ambient conditions, and observed that just one day at ambient conditions is enough to form colloidal graphene…
Protein data bank entries obtain distinct, reproducible flexibility characteristics determined by normal mode analyses of their three dimensional coordinate files. We study the effectiveness and sensitivity of this technique by analyzing…
The adhesion of biological membranes is mediated by the binding of membrane-anchored receptor and ligand proteins. Central questions are how the binding kinetics of these proteins is affected by the membranes and by the membrane anchoring…
Adhesion processes of biological membranes that enclose cells and cellular organelles are essential for immune responses, tissue formation, and signaling. These processes depend sensitively on the binding constant K2D of the…
Validation of research methodology is critical in research design. Correlation between experimental observables must be established before undertaking extensive experiments or propose mechanisms. This article shows that, observables in the…
The identification of low-energy conformers for a given molecule is a fundamental problem in computational chemistry and cheminformatics. We assess here a conformer search that employs a genetic algorithm for sampling the low-energy segment…
The statistics of steps and dwell times in reversible molecular motors differ from those of cycle completion in enzyme kinetics. The reason is that a step is only one of several transitions in the mechanochemical cycle. As a result,…