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Soft-core potentials in thermodynamic integration: Comparing one- and two-step transformations

Journal of computational chemistry, 2011-11, Vol.32 (15), p.3253-3263

2011

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A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. III. Determination of scale-consistent backbone-local and correlation potentials in the UNRES force field and force-field calibration and validation

The Journal of chemical physics, 2019-04, Vol.150 (15), p.155104-155104

2019

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Finding multiple reaction pathways via global optimization of action

Nature communications, 2017-05, Vol.8 (1), p.15443-15443, Article 15443

2017

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Exploring the Folding Mechanism of Small Proteins GB1 and LB1

Journal of chemical theory and computation, 2019-06, Vol.15 (6), p.3432-3449

2019

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Non-sequential protein structure alignment by conformational space annealing and local refinement

PloS one, 2019-01, Vol.14 (1), p.e0210177-e0210177

2019

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Contact-assisted protein structure modeling by global optimization in CASP11

Proteins, structure, function, and bioinformatics, 2016-09, Vol.84 (S1), p.189-199

2016

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Data‐assisted protein structure modeling by global optimization in CASP12

Proteins, structure, function, and bioinformatics, 2018-03, Vol.86 (S1), p.240-246

2018

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Protein structure determination by conformational space annealing using NMR geometric restraints

Proteins, structure, function, and bioinformatics, 2015-12, Vol.83 (12), p.2251-2262

2015

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Protein structure modeling and refinement by global optimization in CASP12

Proteins, structure, function, and bioinformatics, 2018-03, Vol.86 (S1), p.122-135

2018

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Sigma-RF: prediction of the variability of spatial restraints in template-based modeling by random forest

BMC bioinformatics, 2015-03, Vol.16 (1), p.94-94, Article 94

2015

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Quantum-Informed Molecular Representation Learning Enhancing ADMET Property Prediction

Journal of chemical information and modeling, 2024-07, Vol.64 (13), p.5028-5040

2024

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Industrializing AI/ML during the end-to-end drug discovery process

Current opinion in structural biology, 2023-04, Vol.79, p.102528-102528, Article 102528

2023

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CHARMM-GUI Glycan Modeler for modeling and simulation of carbohydrates and glycoconjugates

Glycobiology (Oxford), 2019-04, Vol.29 (4), p.320-331

2019

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Application of conformational space annealing to the protein structure modeling using cryo‐EM maps

Journal of computational chemistry, 2023-11, Vol.44 (30), p.2332-2346

2023

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A Simple and Efficient Protein Structure Refinement Method

Journal of chemical theory and computation, 2017-10, Vol.13 (10), p.5146-5162

2017

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Assessment of network module identification across complex diseases

Nature methods, 2019-09, Vol.16 (9), p.843-852

2019

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Conformational Space Annealing explained: A general optimization algorithm, with diverse applications

Computer physics communications, 2018-02, Vol.223, p.28-33

2018

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Folding Mechanisms of Small Proteins GB1 and LB1

Biophysical journal, 2017-02, Vol.112 (3), p.60a-61a

2017

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Finding Multiple Reaction Pathways via Global Optimization of Action

Biophysical journal, 2019-02, Vol.116 (3), p.303a-303a

2019

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DeepFold: enhancing protein structure prediction through optimized loss functions, improved template features, and re-optimized energy function

Bioinformatics (Oxford, England), 2023-12, Vol.39 (12)

2023

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Template based protein structure modeling by global optimization in CASP11

Proteins, structure, function, and bioinformatics, 2016-09, Vol.84 (S1), p.221-232

2016

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Template-free modeling by LEE and LEER in CASP11

Proteins, structure, function, and bioinformatics, 2016-09, Vol.84 (S1), p.118-130

2016

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Finding Dominant Reaction Pathways via Global Optimization of Action

Biophysical journal, 2017-02, Vol.112 (3), p.290a-290a

2017

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Soft-core potentials in thermodynamic integration: Comparing one- and two-step transformation

Journal of computational chemistry, 2011-11, Vol.32 (15), p.3253

2011

Volltextzugriff (PDF)

Template‐free modeling by LEE and LEER in CASP 11

Proteins, structure, function, and bioinformatics, 2016-09, Vol.84 (S1), p.118-130

2016

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Soft-core potentials in thermodynamic integration: Comparing one- and two-step transformations

A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. III. Determination of scale-consistent backbone-local and correlation potentials in the UNRES force field and force-field calibration and validation

Finding multiple reaction pathways via global optimization of action

Exploring the Folding Mechanism of Small Proteins GB1 and LB1

Non-sequential protein structure alignment by conformational space annealing and local refinement

Contact-assisted protein structure modeling by global optimization in CASP11

Data‐assisted protein structure modeling by global optimization in CASP12

Protein structure determination by conformational space annealing using NMR geometric restraints

Protein structure modeling and refinement by global optimization in CASP12

Sigma-RF: prediction of the variability of spatial restraints in template-based modeling by random forest

Quantum-Informed Molecular Representation Learning Enhancing ADMET Property Prediction

Industrializing AI/ML during the end-to-end drug discovery process

CHARMM-GUI Glycan Modeler for modeling and simulation of carbohydrates and glycoconjugates

Application of conformational space annealing to the protein structure modeling using cryo‐EM maps

A Simple and Efficient Protein Structure Refinement Method

Assessment of network module identification across complex diseases

Conformational Space Annealing explained: A general optimization algorithm, with diverse applications

Folding Mechanisms of Small Proteins GB1 and LB1

Finding Multiple Reaction Pathways via Global Optimization of Action

DeepFold: enhancing protein structure prediction through optimized loss functions, improved template features, and re-optimized energy function

Template based protein structure modeling by global optimization in CASP11

Template-free modeling by LEE and LEER in CASP11

Finding Dominant Reaction Pathways via Global Optimization of Action

Soft-core potentials in thermodynamic integration: Comparing one- and two-step transformation

Template‐free modeling by LEE and LEER in CASP 11

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