As was noted in our recent review, 1 the protein folding field underwent a cyclic development.
Initially, protein folding was viewed as a strictly experimental field belonging to the realm of …

… (N Dokholyan, L Li, E Shakhnovich, manuscript submitted) … (N Dokholyan, L Li, E Shakhnovich,
manuscript submitted) did … ; N Dokholyan, L Li, E Shakhnovich, manuscript submitted) can …

Recently, protein-folding models have advanced to the point where folding simulations of
protein-like chains of reasonable length (up to 125 amino acids) are feasible, and the major …

… The total energy of a conformation is the sum of contact energies: E=YA(fi, r)B, where r are
the positions of monomers i, B, are the contact energies for pairs of monomers i, j, and A(r, r) is …

The statistical mechanics of protein folding implies that the best-folding proteins are those that
have the native conformation as a pronounced energy minimum. We show that this can be …

… To this end, using the same design procedure (Shakhnovich & Gutin, 1993a,b), we selected
a set of sequences having a different total energy for the 8 nucleus contacts but a similar …

EXPERIMENTAL 1–6 and simulation 7 studies show that small mono-meric proteins fold in
one kinetic step, which entails overcoming the free-energy barrier between the unfolded and …

… we use the residue-residue contact energies e, listed in Table V of Miyazawa & Jernigan (1985).
Their expression for the total energy difference between the soivated extended and …

To understand the kinetics of protein folding, we introduce the concept of a “transition coordinate”
which is defined to be the coordinate along which the system progresses most slowly. …

… N 1/2/ N e’ where Ne is the well-known parameter of the reptation model [4, 5]. It follows
from the condition Ne > 1 that for the realistic chain lengths N 1/2/ N e 1. Therefore the …