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Biological and Medicinal Chemistry

Working Paper

The Protein’s Role in Substrate Positioning and Reactivity for Biosynthetic Enzyme Complexes: the Case of SyrB2/SyrB1

Rimsha Mehmood, Helena W. Qi, Adam H. Steeves, Heather Kulik

Version 1 posted 22 October 2018

865

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2

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Theoretical and Computational Chemistry

Working Paper

Calculation of Higher Protonation States and of a New Resting State for Vanadium Chloroperoxidase Using QM/MM, with an Atom-in-Molecules Analysis

Gregory Anderson, Raghu Nath Behera, Ravi V. Gomatam

Version 2 posted 07 January 2020

1,004

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Theoretical and Computational Chemistry

Working Paper

Machine Learning Assisted Free Energy Simulation of Solution–Phase and Enzyme Reactions

Xiaoliang Pan, junjie yang, Richard Van, Evgeny Epifanovsky, Junming Ho, Jing Huang, Jingzhi Pu, Ye Mei, Kwangho Nam, Yihan Shao

Version 1 posted 09 June 2021

725

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1

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Biological and Medicinal Chemistry

Working Paper

Modeling Structure and Absorption Spectra of the Bacteriophytochrome-Based Fluorescent Protein IFP1.4

Igor Polyakov, Bella Grigorenko, Alexander Nemukhin

Version 1 posted 29 November 2019

523

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1

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Theoretical and Computational Chemistry

Working Paper

Computational Modeling Predicts the Stability of Both Pd+ and Pd2+ Ion-Exchanged into H-CHA

Jeroen Van der Mynsbrugge, Martin Head-Gordon, Alexis T. Bell

Version 1 posted 16 November 2020

603

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Biological and Medicinal Chemistry

Working Paper

A Quantum Mechanical Description of Electrostatics Provides a Unified Picture of Catalytic Action Across Methyltransferases

Zhongyue Yang, Fang Liu, Adam H. Steeves, Heather Kulik

Version 1 posted 31 May 2019

564

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Theoretical and Computational Chemistry

Working Paper

Ab Initio Molecular Dynamics Simulations of the Interaction between Organic Phosphates and Goethite

Prasanth Babu Ganta, Oliver Kühn, Ashour A. Ahmed

Version 1 posted 16 November 2020

393

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Theoretical and Computational Chemistry

Working Paper

Structural Factors Determining the Absorption Spectrum of Channelrhodopsins: A Case Study of the Chimera C1C2

Suliman Adam, Christian Wiebeler, Igor Schapiro

Version 1 posted 01 June 2020

485

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Biological and Medicinal Chemistry

Working Paper

The Dual Role of Histidine as General Base and Recruiter of a Third Metal Ion in HIV-1 RNase H

Simon L. Dürr, Olga Bohuszewicz, Reynier Suardiaz, Pablo G. Jambrina, Christine Peter, Yihan Shao, Edina Rosta

Version 1 posted 13 June 2019

797

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2

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Physical Chemistry

Working Paper

Accelerated Computation of Free Energy Profile at Ab Initio QM/MM Accuracy via a Semi-Empirical Reference-Potential. III. Gaussian Smoothing on Density-of-States

Wenxin Hu, Pengfei Li, Jia-Ning Wang, Yuanfei Xue, Yan Mo, Jun Zheng, Xiaoliang Pan, Yihan Shao, Ye Mei

Version 1 posted 29 July 2020

358

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172 results in qm/mm in Keywords: qm/mm

The Protein’s Role in Substrate Positioning and Reactivity for Biosynthetic Enzyme Complexes: the Case of SyrB2/SyrB1

Calculation of Higher Protonation States and of a New Resting State for Vanadium Chloroperoxidase Using QM/MM, with an Atom-in-Molecules Analysis

Machine Learning Assisted Free Energy Simulation of Solution–Phase and Enzyme Reactions

Modeling Structure and Absorption Spectra of the Bacteriophytochrome-Based Fluorescent Protein IFP1.4

Computational Modeling Predicts the Stability of Both Pd+ and Pd2+ Ion-Exchanged into H-CHA

A Quantum Mechanical Description of Electrostatics Provides a Unified Picture of Catalytic Action Across Methyltransferases

Ab Initio Molecular Dynamics Simulations of the Interaction between Organic Phosphates and Goethite

Structural Factors Determining the Absorption Spectrum of Channelrhodopsins: A Case Study of the Chimera C1C2

The Dual Role of Histidine as General Base and Recruiter of a Third Metal Ion in HIV-1 RNase H

Accelerated Computation of Free Energy Profile at Ab Initio QM/MM Accuracy via a Semi-Empirical Reference-Potential. III. Gaussian Smoothing on Density-of-States

172 results in Keywords: qm/mm