2,698 research outputs found
Protein folding using contact maps
We present the development of the idea to use dynamics in the space of
contact maps as a computational approach to the protein folding problem. We
first introduce two important technical ingredients, the reconstruction of a
three dimensional conformation from a contact map and the Monte Carlo dynamics
in contact map space. We then discuss two approximations to the free energy of
the contact maps and a method to derive energy parameters based on perceptron
learning. Finally we present results, first for predictions based on threading
and then for energy minimization of crambin and of a set of 6 immunoglobulins.
The main result is that we proved that the two simple approximations we studied
for the free energy are not suitable for protein folding. Perspectives are
discussed in the last section.Comment: 29 pages, 10 figure
ABC likelihood-freee methods for model choice in Gibbs random fields
Gibbs random fields (GRF) are polymorphous statistical models that can be
used to analyse different types of dependence, in particular for spatially
correlated data. However, when those models are faced with the challenge of
selecting a dependence structure from many, the use of standard model choice
methods is hampered by the unavailability of the normalising constant in the
Gibbs likelihood. In particular, from a Bayesian perspective, the computation
of the posterior probabilities of the models under competition requires special
likelihood-free simulation techniques like the Approximate Bayesian Computation
(ABC) algorithm that is intensively used in population genetics. We show in
this paper how to implement an ABC algorithm geared towards model choice in the
general setting of Gibbs random fields, demonstrating in particular that there
exists a sufficient statistic across models. The accuracy of the approximation
to the posterior probabilities can be further improved by importance sampling
on the distribution of the models. The practical aspects of the method are
detailed through two applications, the test of an iid Bernoulli model versus a
first-order Markov chain, and the choice of a folding structure for two
proteins.Comment: 19 pages, 5 figures, to appear in Bayesian Analysi
On the optimal contact potential of proteins
We analytically derive the lower bound of the total conformational energy of
a protein structure by assuming that the total conformational energy is well
approximated by the sum of sequence-dependent pairwise contact energies. The
condition for the native structure achieving the lower bound leads to the
contact energy matrix that is a scalar multiple of the native contact matrix,
i.e., the so-called Go potential. We also derive spectral relations between
contact matrix and energy matrix, and approximations related to one-dimensional
protein structures. Implications for protein structure prediction are
discussed.Comment: 5 pages, text onl
Protein secondary structure: Entropy, correlations and prediction
Is protein secondary structure primarily determined by local interactions
between residues closely spaced along the amino acid backbone, or by non-local
tertiary interactions? To answer this question we have measured the entropy
densities of primary structure and secondary structure sequences, and the local
inter-sequence mutual information density. We find that the important
inter-sequence interactions are short ranged, that correlations between
neighboring amino acids are essentially uninformative, and that only 1/4 of the
total information needed to determine the secondary structure is available from
local inter-sequence correlations. Since the remaining information must come
from non-local interactions, this observation supports the view that the
majority of most proteins fold via a cooperative process where secondary and
tertiary structure form concurrently. To provide a more direct comparison to
existing secondary structure prediction methods, we construct a simple hidden
Markov model (HMM) of the sequences. This HMM achieves a prediction accuracy
comparable to other single sequence secondary structure prediction algorithms,
and can extract almost all of the inter-sequence mutual information. This
suggests that these algorithms are almost optimal, and that we should not
expect a dramatic improvement in prediction accuracy. However, local
correlations between secondary and primary structure are probably of
under-appreciated importance in many tertiary structure prediction methods,
such as threading.Comment: 8 pages, 5 figure
Through the Eye of the Needle: Recent Advances in Understanding Biopolymer Translocation
In recent years polymer translocation, i.e., transport of polymeric molecules
through nanometer-sized pores and channels embedded in membranes, has witnessed
strong advances. It is now possible to observe single-molecule polymer dynamics
during the motion through channels with unprecedented spatial and temporal
resolution. These striking experimental studies have stimulated many
theoretical developments. In this short theory-experiment review, we discuss
recent progress in this field with a strong focus on non-equilibrium aspects of
polymer dynamics during the translocation process.Comment: 29 pages, 6 figures, 3 tables, to appear in J. Phys.: Condens. Matter
as a Topical Revie
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