Assessment of Two Restraint Potentials for Coarse-Grained Chemical-Cross-Link-Assisted Modeling of Protein Structures.

Multi-GPU UNRES for scalable coarse-grained simulations of very large protein systems.

Optimization of parallel implementation of UNRES package for coarse-grained simulations to treat large proteins.

Long-time scale simulations of virus-like particles from three human-norovirus strains.

A coarse-grained approach to NMR-data-assisted modeling of protein structures.

ESCASA: Analytical estimation of atomic coordinates from coarse-grained geometry for nuclear-magnetic-resonance-assisted protein structure modeling. I. Backbone and Hβ protons.

Pseudopotentials for coarse-grained cross-link-assisted modeling of protein structures.

UNRES-Dock - protein-protein and peptide-protein docking by coarse-grained replica-exchange MD simulations.

Improved Consensus-Fragment Selection in Template-Assisted Prediction of Protein Structures with the UNRES Force Field in CASP13.

Introduction of a bounded penalty function in contact-assisted simulations of protein structures to omit false restraints.

High Performance Computing with Coarse Grained Model of Biological Macromolecules.

UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics.

Correction to Maximum Likelihood Calibration of the UNRES Force Field for Simulation of Protein Structure and Dynamics.

A new protein nucleic-acid coarse-grained force field based on the UNRES and NARES-2P force fields.

Maximum Likelihood Calibration of the UNRES Force Field for Simulation of Protein Structure and Dynamics.

Ergodicity and model quality in template-restrained canonical and temperature/Hamiltonian replica exchange coarse-grained molecular dynamics simulations of proteins.

<i>In situ</i> data analytics and indexing of protein trajectories.

Use of Restraints from Consensus Fragments of Multiple Server Models To Enhance Protein-Structure Prediction Capability of the UNRES Force Field.

Performance of protein-structure predictions with the physics-based UNRES force field in CASP11.

A Maximum-Likelihood Approach to Force-Field Calibration.

Prediction of Protein Structure by Template-Based Modeling Combined with the UNRES Force Field.

It-Situ Data Analysis of Protein Folding Trajectories.

Coarse-grained model of nucleic acid bases.

Determination of side-chain-rotamer and side-chain and backbone virtual-bond-stretching potentials of mean force from AM1 energy surfaces of terminally-blocked amino-acid residues, for coarse-grained simulations of protein structure and folding. II. Results, comparison with statistical potentials, and implementation in the UNRES force field.

Determination of side-chain-rotamer and side-chain and backbone virtual-bond-stretching potentials of mean force from AM1 energy surfaces of terminally-blocked amino-acid residues, for coarse-grained simulations of protein structure and folding. I. The method.

Exploring the parameter space of the coarse-grained UNRES force field by random search: Selecting a transferable medium-resolution force field.

Theoretical calculations of homoconjugation equilibrium constants in systems modeling acid-base interactions in side chains of biomolecules using the potential of mean force.

Evolution of physics-based methodology for exploring the conformational energy landscape of proteins.

Energy-based reconstruction of a protein backbone from its -carbon trace by a Monte-Carlo method.

Ab initio study of the mechanism of singlet-dioxygen addition to hydroxyaromatic compounds: Negative evidence for the involvement of peroxa and endoperoxide intermediates.

Surmounting the Multiple-Minima Problem in Protein Folding.

United-residue force field for off-lattice protein-structure simulations: III. Origin of backbone hydrogen-bonding cooperativity in united-residue potentials.

A united-residue force field for off-lattice protein-structure simulations. II. Parameterization of short-range interactions and determination of weights of energy terms by Z-score optimization.

A united-residue force field for off-lattice protein-structure simulations. I. Functional forms and parameters of long-range side-chain interaction potentials from protein crystal data.

MCSCF study of singlet oxygen addition to ethenol - a model of photooxidation reactions of unsaturated and aromatic compounds bearing hydroxy groups.

A New Approach to the Resolution of the Excitation-emission Spectra of Multicomponent Systems.

Implementation of the ECEPP Algorithm, the Monte Carlo Minimization Method, and the Electrostatically Driven Monte Carlo Method on the Kendall Square Research KSR1 Computer.

A molecular mechanics study of the effect of substitution in position 1 on the conformational space of the oxytocin/vasopressin ring.

Modified Free-Wilson Method for the Analysis of Biological Activity Data.

Molecular mechanics calculations on deaminooxytocin and on deamino-arginine-vasopressin and its analogues.

Theoretical studies of the mechanism of the action of the neurohypophyseal hormones. I. Molecular electrostatic potential (MEP) and molecular electrostatic field (MEF) maps of some vasopressin analogues.

A comparative study on some methods for computing equilibrium concentrations.

A general method for the determination of the stoichiometry of unknown species in multicomponent systems from physicochemical measurements.

DECFAM - A new computer oriented algorithm for the determination of equilibrium constants from potentionmetric and/or spectrophotometric measurements - I: Basic principles of the method and calculations of equilibrium concentrations.

DECFAM - A new computer oriented algorithm for the determination of equilibrium constants from potentiometric and/or spectrophotometric measurements - II: Methods based on analytical expressions.