Related papers: A novel method for identification of local conform…
Protein structures can be encoded into binary sequences, these are used to define a Hamming distance in conformational space: the distance between two different molecular conformations is the number of different bits in their sequences.…
The primary structure of a ribonucleic acid (RNA) molecule can be represented as a sequence of nucleotides (bases) over the alphabet {A, C, G, U}. The secondary or tertiary structure of an RNA is a set of base pairs which form bonds between…
How proteins fold remains a central unsolved problem in biology. While the idea of a folding code embedded in the amino acid sequence was introduced more than 6 decades ago, this code remains undefined. While we now have powerful predictive…
Motivation: Thanks to the recent advances in structural biology, nowadays three-dimensional structures of various proteins are solved on a routine basis. A large portion of these contain structural repetitions or internal symmetries. To…
Proteins are dynamic, adopting ensembles of conformations. The nature of this conformational heterogenity is imprinted in the raw electron density measurements obtained from X-ray crystallography experiments. Fitting an ensemble of protein…
Native protein folds often have a high degree of symmetry. We study the relationship between the symmetries of native proteins, and their designabilities -- how many different sequences encode a given native structure. Using a…
COVID-19 has affected the world tremendously. It is critical that biological experiments and clinical designs are informed by computational approaches for time- and cost-effective solutions. Comparative analyses particularly can play a key…
Proteins are responsible for the most diverse set of functions in biology. The ability to extract information from protein sequences and to predict the effects of mutations is extremely valuable in many domains of biology and medicine.…
Protein sequences serve as a natural record of the evolutionary constraints that shape their functional structures. We show that it is possible to use only sequence information to go beyond predicting native structures and global stability…
H-bonds are known to play an important role in the folding of proteins into three-dimensional structures, which in turn determine their diverse functions. The conformations around H-bonds are important, in that they can be non-local along…
Proteins are large biomolecules that regulate all living organisms and consist of one or several chains. The primary structure of a protein chain is a sequence of amino acid residues whose three main atoms (alpha-carbon, nitrogen, and…
The main chain dihedral angles play an important role to decide the protein conformation. The native states of a protein can be regard as an ensemble of a lot of similar conformations, in different conformations the main chain dihedral…
Sequence specific resonance assignment and secondary structure determination of proteins form the basis for variety of structural and functional proteomics studies by NMR. In this context, an efficient standalone method for rapid assignment…
This survey for mathematicians summarizes several works by the author on protein geometry and protein function with applications to viral glycoproteins in general and the spike glycoprotein of the SARS-CoV-2 virus in particular. Background…
Structure-based virtual screening aims to identify high-affinity ligands by estimating binding free energies between proteins and small molecules. However, the conformational flexibility of both proteins and ligands challenges conventional…
Novel numerical techniques, validated by an analysis of barnase and chymotrypsin inhibitor, are used to elucidate the paramount role played by the geometry of the protein backbone in steering the folding to the correct native state. It is…
Protein structures and functions are determined by a contiguous arrangement of amino acid sequences. Designing novel protein sequences and structures with desired geometry and functions is a complex task with large state spaces. Here we…
After the recent ground-breaking advances in protein structure prediction, one of the remaining challenges in protein machine learning is to reliably predict distributions of structural states. Parametric models of fluctuations are…
Methods for alignment of protein sequences typically measure similarity by using substitution matrix with scores for all possible exchanges of one amino acid with another. Although widely used, the matrices derived from homologous sequence…
Word matches are often used in sequence comparison methods, either as a measure of sequence similarity or in the first search steps of algorithms such as BLAST or BLAT. The D2 statistic is the number of matches of words of k letters between…