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The LOTUS initiative for open knowledge management in natural products research

eLife, 2022-05, Vol.11

2022

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Parametrization of 2,2,2-Trifluoroethanol Based on the Generalized Amber Force Field Provides Realistic Agreement between Experimental and Calculated Properties of Pure Liquid as Well as Water-Mixed Solutions

The journal of physical chemistry. B, 2014-09, Vol.118 (35), p.10390-10404

2014

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Iterative Landmark-Based Umbrella Sampling (ILBUS) Protocol for Sampling of Conformational Space of Biomolecules

Journal of chemical information and modeling, 2022-10, Vol.62 (19), p.4783-4798

2022

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Efficient Estimation of Absolute Binding Free Energy for a Homeodomain–DNA Complex from Nonequilibrium Pulling Simulations

Journal of chemical theory and computation, 2020-04, Vol.16 (4), p.2034-2041

2020

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Metadynamics As a Tool for Mapping the Conformational and Free-Energy Space of Peptides  The Alanine Dipeptide Case Study

The journal of physical chemistry. B, 2010-04, Vol.114 (16), p.5632-5642

2010

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Can All-Atom Molecular Dynamics Simulations Quantitatively Describe Homeodomain–DNA Binding Equilibria?

Journal of chemical theory and computation, 2019-04, Vol.15 (4), p.2635-2648

2019

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PAPerFly: Partial Assembly-based Peak Finder for ab initio binding site reconstruction

BMC bioinformatics, 2023-12, Vol.24 (1), p.487-487, Article 487

2023

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Toward Ab Initio Protein Folding: Inherent Secondary Structure Propensity of Short Peptides from the Bioinformatics and Quantum-Chemical Perspective

The journal of physical chemistry. B, 2019-02, Vol.123 (6), p.1215-1227

2019

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AMBER and CHARMM Force Fields Inconsistently Portray the Microscopic Details of Phosphorylation

Journal of chemical theory and computation, 2019-01, Vol.15 (1), p.665-679

2019

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IDSM ChemWebRDF: SPARQLing small-molecule datasets

Journal of cheminformatics, 2021-05, Vol.13 (1), p.38-38, Article 38

2021

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Structure and Stability of the Water−Graphite Complexes

Journal of physical chemistry. C, 2009-05, Vol.113 (19), p.8412-8419

2009

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Effect of TFE on the Helical Content of AK17 and HAL‑1 Peptides: Theoretical Insights into the Mechanism of Helix Stabilization

The journal of physical chemistry. B, 2016-02, Vol.120 (6), p.1048-1059

2016

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Gyration- and Inertia-Tensor-Based Collective Coordinates for Metadynamics. Application on the Conformational Behavior of Polyalanine Peptides and Trp-Cage Folding

The journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory, 2011-10, Vol.115 (41), p.11455-11465

2011

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Noncovalent Interactions in Specific Recognition Motifs of Protein–DNA Complexes

Journal of chemical theory and computation, 2017-02, Vol.13 (2), p.877-885

2017

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A comparison of approaches to accessing existing biological and chemical relational databases via SPARQL

Journal of cheminformatics, 2023-06, Vol.15 (1), p.61-61, Article 61

2023

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Hydrophobic Amino Acids as Universal Elements of Protein-Induced DNA Structure Deformation

International journal of molecular sciences, 2020-06, Vol.21 (11), p.3986

2020

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Critical Assessment of Current Force Fields. Short Peptide Test Case

Journal of chemical theory and computation, 2013-01, Vol.9 (1), p.441-451

2013

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Sequence Versus Composition: What Prescribes IDP Biophysical Properties?

Entropy (Basel, Switzerland), 2019-07, Vol.21 (7), p.654

2019

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Sachem: a chemical cartridge for high-performance substructure search

Journal of cheminformatics, 2018-05, Vol.10 (1), p.27-11, Article 27

2018

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Urea and Guanidinium Induced Denaturation of a Trp-Cage Miniprotein

The journal of physical chemistry. B, 2011-07, Vol.115 (28), p.8910-8924

2011

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Representative Amino Acid Side Chain Interactions in Proteins. A Comparison of Highly Accurate Correlated ab Initio Quantum Chemical and Empirical Potential Procedures

Journal of chemical theory and computation, 2009-04, Vol.5 (4), p.982-992

2009

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Representative Amino Acid Side-Chain Interactions in Protein–DNA Complexes: A Comparison of Highly Accurate Correlated Ab Initio Quantum Mechanical Calculations and Efficient Approaches for Applications to Large Systems

Journal of chemical theory and computation, 2015-09, Vol.11 (9), p.4086-4092

2015

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Interoperable chemical structure search service

Journal of cheminformatics, 2019-06, Vol.11 (1), p.45-7, Article 45

2019

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SmSP2: A serine protease secreted by the blood fluke pathogen Schistosoma mansoni with anti-hemostatic properties

PLoS neglected tropical diseases, 2018-04, Vol.12 (4), p.e0006446-e0006446

2018

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The LOTUS initiative for open knowledge management in natural products research

Parametrization of 2,2,2-Trifluoroethanol Based on the Generalized Amber Force Field Provides Realistic Agreement between Experimental and Calculated Properties of Pure Liquid as Well as Water-Mixed Solutions

Iterative Landmark-Based Umbrella Sampling (ILBUS) Protocol for Sampling of Conformational Space of Biomolecules

Efficient Estimation of Absolute Binding Free Energy for a Homeodomain–DNA Complex from Nonequilibrium Pulling Simulations

Metadynamics As a Tool for Mapping the Conformational and Free-Energy Space of Peptides  The Alanine Dipeptide Case Study

Can All-Atom Molecular Dynamics Simulations Quantitatively Describe Homeodomain–DNA Binding Equilibria?

PAPerFly: Partial Assembly-based Peak Finder for ab initio binding site reconstruction

Toward Ab Initio Protein Folding: Inherent Secondary Structure Propensity of Short Peptides from the Bioinformatics and Quantum-Chemical Perspective

AMBER and CHARMM Force Fields Inconsistently Portray the Microscopic Details of Phosphorylation

IDSM ChemWebRDF: SPARQLing small-molecule datasets

Structure and Stability of the Water−Graphite Complexes

Effect of TFE on the Helical Content of AK17 and HAL‑1 Peptides: Theoretical Insights into the Mechanism of Helix Stabilization

Gyration- and Inertia-Tensor-Based Collective Coordinates for Metadynamics. Application on the Conformational Behavior of Polyalanine Peptides and Trp-Cage Folding

Noncovalent Interactions in Specific Recognition Motifs of Protein–DNA Complexes

A comparison of approaches to accessing existing biological and chemical relational databases via SPARQL

Hydrophobic Amino Acids as Universal Elements of Protein-Induced DNA Structure Deformation

The bio.tools registry of software tools and data resources for the life sciences

Critical Assessment of Current Force Fields. Short Peptide Test Case

Sequence Versus Composition: What Prescribes IDP Biophysical Properties?

Sachem: a chemical cartridge for high-performance substructure search

Urea and Guanidinium Induced Denaturation of a Trp-Cage Miniprotein

Representative Amino Acid Side Chain Interactions in Proteins. A Comparison of Highly Accurate Correlated ab Initio Quantum Chemical and Empirical Potential Procedures

Representative Amino Acid Side-Chain Interactions in Protein–DNA Complexes: A Comparison of Highly Accurate Correlated Ab Initio Quantum Mechanical Calculations and Efficient Approaches for Applications to Large Systems

Interoperable chemical structure search service

SmSP2: A serine protease secreted by the blood fluke pathogen Schistosoma mansoni with anti-hemostatic properties

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