Adam Liwo

发表

Assessment of chemical‐crosslink‐assisted protein structure modeling in CASP13

Adam Liwo, Juri Rappsilber, J Eduardo Fajardo, 2019, Proteins.

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

Adam Liwo, Jooyoung Lee, Jaroslaw Pillardy, 2002, J. Comput. Chem..

Coarse‐grained model of nucleic acid bases

Adam Liwo, Harold A. Scheraga, Maciej Maciejczyk, 2010, J. Comput. Chem..

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

Adam Liwo, Emilia A Lubecka, A. Liwo, 2019, J. Comput. Chem..

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

Adam Liwo, Dariusz Dyl, Danuta Jeziorek, 1997, J. Comput. Chem..

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

Adam Liwo, Mariusz Makowski, Joanna Makowska, 2005, J. Comput. Chem..

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

Adam Liwo, Harold A. Scheraga, Urszula Kozlowska, 2010, J. Comput. Chem..

In situ data analytics and indexing of protein trajectories

Adam Liwo, Silvia Crivelli, Michela Taufer, 2017, J. Comput. Chem..

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

Adam Liwo, Keehyoung Joo, Cezary Czaplewski, 2015, J. Chem. Inf. Model..

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

Adam Liwo, Stanislaw Oldziej, Piotr Skurski, 1997, Comput. Chem..

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

Adam Liwo, Jaroslaw Kostrowicki, 1984, Comput. Chem..

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

Adam Liwo, Harold A. Scheraga, Shelly Rackovsky, 1997, J. Comput. Chem..

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

Adam Liwo, Yi He, Harold A. Scheraga, 2018, J. Comput. Chem..

Towards Temperature Dependent Coarse-grained Potential of Side-chain Interactions for Protein Folding Simulations

Adam Liwo, Harold A. Scheraga, Cezary Czaplewski, 2010, 2010 IEEE International Conference on BioInformatics and BioEngineering.

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

Adam Liwo, Jaroslaw Kostrowicki, 1984, Comput. Chem..

Improvement of the treatment of loop structures in the UNRES force field by inclusion of coupling between backbone- and side-chain-local conformational states.

Adam Liwo, Harold A. Scheraga, Cezary Czaplewski, 2013, Journal of chemical theory and computation.

Symplectic Algorithms of Molecular Dynamics. An Application to the United-Residue Model

Adam Liwo, Franciszek Rakowski, Harold A. Scheraga, 2006 .

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

Adam Liwo, Zbigniew Grzonka, Anna Tempczyk, 1989, J. Comput. Aided Mol. Des..

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

Adam Liwo, Yi He, Harold A. Scheraga, 2016, Bioinform..

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

Adam Liwo, Harold A. Scheraga, Shelly Rackovsky, 1997, J. Comput. Chem..

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

Adam Liwo, Keehyoung Joo, Jooyoung Lee, 2017, J. Comput. Chem..

Prediction of protein structure using a knowledge-based off-lattice united-residue force field and global optimization methods

Adam Liwo, Cezary Czaplewski, Rajmund Kaźmierkiewicz, 1999 .

UNRES: a united-residue force field for energy-based prediction of protein structure—orgin and significance of multibody terms

Adam Liwo, Jooyoung Lee, Jaroslaw Pillardy, 2000, RECOMB '00.

Reoptimized UNRES Potential for Protein Model Quality Assessment

Adam Liwo, Andrzej Kloczkowski, Pawel Krupa, 2018, Genes.

Surmounting the Multiple-Minima Problem in Protein Folding

Adam Liwo, Jooyoung Lee, Jaroslaw Pillardy, 1999, J. Glob. Optim..

Blind prediction of homo‐ and hetero‐protein complexes: The CASP13‐CAPRI experiment

Elodie Laine, Alessandra Carbone, Adam Liwo, 2019, Proteins.

Energy‐based reconstruction of a protein backbone from its α‐carbon trace by a Monte‐Carlo method

Adam Liwo, Harold A. Scheraga, Rajmund Kazmierkiewicz, 2002, J. Comput. Chem..

Implementation of the ECEPP algorithm, the Monte Carlo minimization method, and the electrostatically driven Monte Carlo method on the Kendall square research KSR1 computer

Adam Liwo, Harold A. Scheraga, Daniel R. Ripoll, 1995, J. Comput. Chem..

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

Monika Tarnowska, Adam Liwo, Zbigniew Grzonka, 1992, Comput. Chem..

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

Adam Liwo, Keehyoung Joo, Cezary Czaplewski, 2020, J. Chem. Inf. Model..

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

Adam Liwo, Keehyoung Joo, Jooyoung Lee, 2016, J. Chem. Inf. Model..

Global Optimization in Protein Folding

Adam Liwo, Harold A. Scheraga, Daniel R. Ripoll, 2009, Encyclopedia of Optimization.

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

Adam Liwo, Paweł Krupa, Anna Hałabis, 2018, J. Chem. Inf. Model..

A Maximum-Likelihood Approach to Force-Field Calibration

Adam Liwo, Cezary Czaplewski, Agnieszka Lewandowska, 2015, J. Chem. Inf. Model..

WeFold: A coopetition for protein structure prediction

Adam Liwo, Yi He, David Baker, 2014, Proteins.

Prediction of protein structure with the coarse‐grained UNRES force field assisted by small X‐ray scattering data and knowledge‐based information

Adam Liwo, Cezary Czaplewski, Agnieszka S Karczyńska, 2018, Proteins.

Hidden protein folding pathways in free-energy landscapes uncovered by network analysis.

Adam Liwo, Yanping Yin, Harold A Scheraga, 2012, Journal of chemical theory and computation.

Efficient parallel algorithms in global optimization of potential energy functions for peptides, proteins, and crystals

Adam Liwo, Daniel R. Ripoll, Yelena A. Arnautova, 2000 .

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

Adam Liwo, Cezary Czaplewski, Adam K. Sieradzan, 2018, Nucleic Acids Res..

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

Adam Liwo, Danuta Jeziorek, Tadeusz Ossowski, 2002, J. Comput. Chem..

A user-friendly interface to computer programs for the determination of the characteristics of equilibrium systems from physicochemical data

Adam Liwo, Piotr Arlukowicz, E. Arłukowicz, 1998 .

A comparative study on some methods for computing equilibrium concentrations

Adam Liwo, Jaroslaw Kostrowicki, Krzysztof Sokolowski, 1988, Comput. Chem..

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

Adam Liwo, Yi He, Yi Xiao, 2009, J. Comput. Chem..

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

Adam Liwo, Harold A. Scheraga, Cezary Czaplewski, 1998, J. Comput. Chem..

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

Adam Liwo, Jaroslaw Kostrowicki, A. Liwo, 1987, Comput. Chem..

Implementation of a Serial Replica Exchange Method in a Physics-Based United-Residue (UNRES) Force Field.

Adam Liwo, Hujun Shen, Cezary Czaplewski, 2008, Journal of chemical theory and computation.

High Performance Computing with Coarse Grained Model of Biological Macromolecules

Adam Liwo, Cezary Czaplewski, Adam K. Sieradzan, 2018, Supercomput. Front. Innov..

An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12

Adam Liwo, Yi He, Jilong Li, 2018, Scientific Reports.

Implementation of molecular dynamics and its extensions with the coarse-grained UNRES force field on massively parallel systems; towards millisecond-scale simulations of protein structure, dynamics, and thermodynamics.

Adam Liwo, Cezary Czaplewski, Philip D. Blood, 2010, Journal of chemical theory and computation.

It-Situ Data Analysis of Protein Folding Trajectories pdf

Adam Liwo, Silvia Crivelli, Michela Taufer, 2015, ArXiv.

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

Adam Liwo, Cezary Czaplewski, Magdalena A. Mozolewska, 2020, Bioinform..

Prediction of the structures of proteins with the UNRES force field, including dynamic formation and breaking of disulfide bonds.

Adam Liwo, Cezary Czaplewski, Stanislaw Oldziej, 2004, Protein engineering, design & selection : PEDS.

Hierarchical energy-based approach to protein-structure prediction: Blind-test evaluation with CASP3 targets

Adam Liwo, Jaroslaw Pillardy, Harold A. Scheraga, 2000 .

CAS MCSCF/CAS MCQDPT2 Study of the Mechanism of Singlet Oxygen Addition to 1,3-Butadiene and Benzene

Adam Liwo, Tadeusz Ossowski, Stanisław Ołdziej, 2000 .

Relation between free energy landscapes of proteins and dynamics.

Adam Liwo, Harold A Scheraga, Gia G Maisuradze, 2010, Journal of chemical theory and computation.

Mechanism of formation of the C‐terminal β‐hairpin of the B3 domain of the immunoglobulin binding protein G from Streptococcus. II. Interplay of local backbone conformational dynamics and long‐range hydrophobic interactions in hairpin formation

Adam Liwo, Stanisław Ołdziej, Harold A Scheraga, 2009, Proteins.

Protein-folding dynamics: overview of molecular simulation techniques.

Adam Liwo, Harold A Scheraga, Mey Khalili, 2007, Annual review of physical chemistry.

Studies of conformational changes of an arginine-binding protein from Thermotoga maritima in the presence and absence of ligand via molecular dynamics simulations with the coarse-grained UNRES force field

Adam Liwo, Adam K. Sieradzan, Magdalena A. Mozolewska, 2015, Journal of Molecular Modeling.

Optimization of the UNRES Force Field by Hierarchical Design of the Potential-Energy Landscape. 2. Off-Lattice Tests of the Method with Single Proteins

Adam Liwo, Jaroslaw Pillardy, Harold A. Scheraga, 2004 .

Combination of SAXS and NMR Techniques as a Tool for the Determination of Peptide Structure in Solution

Adam Liwo, Agnieszka Lewandowska, Stanisław Ołdziej, 2010 .

Determination of the Potentials of Mean Force for Rotation about Cα−Cα Virtual Bonds in Polypeptides from the ab Initio Energy Surfaces of Terminally Blocked Glycine, Alanine, and Proline†

Adam Liwo, Harold A. Scheraga, Stanisław Ołdziej, 2003 .

Mechanism of formation of the C‐terminal β‐hairpin of the B3 domain of the immunoglobulin binding protein G from Streptococcus. I. Importance of hydrophobic interactions in stabilization of β‐hairpin structure

Adam Liwo, Harold A. Scheraga, Joanna Makowska, 2009, Proteins.

An Efficient Deformation-Based Global Optimization Method (Self-Consistent Basin-to-Deformed-Basin Mapping (SCBDBM)). Application to Lennard-Jones Atomic Clusters

Adam Liwo, Jaroslaw Pillardy, Harold A. Scheraga, 1999 .

Accounting for a mirror-image conformation as a subtle effect in protein folding

Adam Liwo, Harold A Scheraga, Gia G Maisuradze, 2014, Proceedings of the National Academy of Sciences.

Recent improvements in prediction of protein structure by global optimization of a potential energy function

Adam Liwo, Harold A. Scheraga, Cezary Czaplewski, 2001, Proceedings of the National Academy of Sciences of the United States of America.

A united residue force‐field for calcium–protein interactions

Adam Liwo, Harold A Scheraga, Mey Khalili, 2004, Protein science : a publication of the Protein Society.

Optimization of the UNRES Force Field by Hierarchical Design of the Potential-Energy Landscape. 1. Tests of the Approach Using Simple Lattice Protein Models

Adam Liwo, Harold A. Scheraga, Cezary Czaplewski, 2004 .

Mechanism of formation of the C‐terminal β‐hairpin of the B3 domain of the immunoglobulin binding protein G from Streptococcus. III. Dynamics of long‐range hydrophobic interactions

Adam Liwo, Agnieszka Lewandowska, Stanisław Ołdziej, 2009, Proteins.

An improved functional form for the temperature scaling factors of the components of the mesoscopic UNRES force field for simulations of protein structure and dynamics.

Adam Liwo, Harold A Scheraga, Hujun Shen, 2009, The journal of physical chemistry. B.

Molecular Simulation Study of the Potentials of Mean Force for the Interactions between Models of Like-Charged and between Charged and Nonpolar Amino Acid Side Chains in Water

Adam Liwo, Harold A. Scheraga, Cezary Czaplewski, 2003 .

Simple physics-based analytical formulas for the potentials of mean force of the interaction of amino-acid side chains in water. V. Like-charged side chains.

Adam Liwo, Mariusz Makowski, Harold A Scheraga, 2011, The journal of physical chemistry. B.

Determination of virtual-bond-angle potentials of mean force for coarse-grained simulations of protein structure and folding from ab initio energy surfaces of terminally-blocked glycine, alanine, and proline

Adam Liwo, Harold A. Scheraga, A. Liwo, 2007 .

Investigation of protein folding by coarse-grained molecular dynamics with the UNRES force field.

Adam Liwo, Cezary Czaplewski, Harold A Scheraga, 2010, The journal of physical chemistry. A.

Microscopic Physics-Based Models of Proteins and Nucleic Acids

Adam Liwo, Mariusz Makowski, Harold A. Scheraga, 2017 .

An Efficient Deformation-Based Global Optimization Method for Off-Lattice Polymer Chains: Self-Consistent Basin-to-Deformed-Basin Mapping (SCBDBM). Application to United-Residue Polypeptide Chains

Adam Liwo, Jaroslaw Pillardy, Harold A. Scheraga, 1999 .

How adequate are one- and two-dimensional free energy landscapes for protein folding dynamics?

Adam Liwo, Harold A Scheraga, Gia G Maisuradze, 2009, Physical review letters.

Improved conformational space annealing method to treat β-structure with the UNRES force-field and to enhance scalability of parallel implementation

Adam Liwo, Jaroslaw Pillardy, Harold A. Scheraga, 2004 .

Towards temperature-dependent coarse-grained potentials of side-chain interactions for protein folding simulations. I: molecular dynamics study of a pair of methane molecules in water at various temperatures.

Adam Liwo, Mariusz Makowski, Cezary Czaplewski, 2009, Protein engineering, design & selection : PEDS.

Simple physics-based analytical formulas for the potentials of mean force for the interaction of amino acid side chains in water. IV. Pairs of different hydrophobic side chains.

Adam Liwo, Mariusz Makowski, Cezary Czaplewski, 2008, The journal of physical chemistry. B.

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

Adam Liwo, Zbigniew Grzonka, Anna Tempczyk, 1989, J. Comput. Aided Mol. Des..

beta-hairpin-forming peptides; models of early stages of protein folding.

Adam Liwo, Agnieszka Lewandowska, Stanisław Ołdziej, 2010, Biophysical chemistry.

Topology of Type II REases revisited; structural classes and the common conserved core

Adam Liwo, Harel Weinstein, Harold A. Scheraga, 2007, Nucleic acids research.

Ab Initio Study of Energetics of Protonation and Hydrogen Bonding of PyridineN-Oxide and Its Derivatives

Adam Liwo, Mariusz Makowski, Lech Chmurzyński, 1999 .

Diffusion Equation and Distance Scaling Methods of Global Optimization: Applications to Crystal Structure Prediction

Adam Liwo, Jaroslaw Pillardy, Harold A. Scheraga, 1998 .

mimicking the mechanism of aspartic proyeases mart 1. molecular mechanics studey

Adam Liwo, Jerzy Ciarkowski, S. Oldziej, 1994 .

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

Adam Liwo, Dariusz Dyl, Danuta Jeziorek, 1997 .

Coarse-grained force field: general folding theory.

Adam Liwo, Harold A Scheraga, A. Liwo, 2011, Physical chemistry chemical physics : PCCP.

Development of Physics-Based Energy Functions that Predict Medium-Resolution Structures for Proteins of the α, β, and α/β Structural Classes

Adam Liwo, Jaroslaw Pillardy, Harold A. Scheraga, 2001 .

Comparison of the low energy conformations of an oncogenic and a non-oncogenic p21 protein, neither of which binds GTP or GDP

Adam Liwo, Harold A. Scheraga, Matthew R. Pincus, 1994, Journal of protein chemistry.

Computational methods to study the structure and dynamics of biomolecules and biomolecular processes : from bioinformatics to molecular quantum mechanics

Adam Liwo, A. Liwo, 2014 .

Molecular dynamics with the United-residue force field: ab initio folding simulations of multichain proteins.

Adam Liwo, Harold A Scheraga, A. Liwo, 2007, The journal of physical chemistry. B.