Predicting the final folded structure of protein molecules and simulating their folding pathways is of crucial importance for designing viral drugs and studying diseases such as Alzheimer's at the molecular level. To this end, this paper investigates the problem of protein conformation prediction under the constraint of avoiding high-entropyloss routes during folding. Using the well-established kinetostatic compliance (KCM)-based nonlinear dynamics of a protein molecule, this paper formulates the protein conformation prediction as a pointwise optimal control synthesis problem cast as a quadratic program (QP). It is shown that the KCM torques in the protein folding literature can be utilized for defining a reference vector field for the QP-based control generation problem. The resulting kinetostatic control torque inputs will be close to the KCM-based reference vector field and guaranteed to be constrained by a predetermined bound; hence, high-entropy-loss routes during folding are avoided while the energy of the molecule is decreased. I. INTRODUCTION Computer-aided prediction of the folded structure of a protein molecule lies at the heart of protein engineering, drug discovery, and investigating diseases such as Alzheimer's at the molecular and cellular levels [1]. The 3D structure of a protein molecule, known as the protein conformation, is mainly determined by its linear amino acid (AA) sequence [2]. The protein folding problem is concerned with determining the final folded structure of a protein molecule given its linear AA sequence. Studying the folding pathways is also important for designing viral drugs that cause misfolding in virus proteins [3]. Knowledge-based and physics-based methods are the two prominent computational approaches for solving the protein folding problem. Knowledge-based methods, which also include the approach of Google's DeepMind AlphaFold [4], rely on using previously determined types of folds to solve the protein folding problem [5]. In physicsbased methods, on the other hand, protein folding simulations are carried out using the first principles [6]. Physicsbased methods enjoy several advantages over their knowledge-based counterparts such as the ability to model the protein-nucleic acid interactions and to simulate protein folding pathways. However, physics-based methods relying on standard molecular dynamics (MD) suffer from numerical instabilities [7]. To address the inherent challenges of MD-based protein folding solutions, Kazerounian and collaborators [8]-[11] introduced the kinetostatic compliance