Publications by authors named "Alpeshkumar Malde"

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Molecular Dynamics Identify Variances Between Galectin Carbohydrate-Binding Sites That Impact the Binding Site Conformation and Ligand Binding.
Rob Marc Go, Chandan Kishor, Alpeshkumar K Malde, Helen Blanchard

Proteins· November 2025

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Nipah and Hendra Viruses Use an Adjustable Latch in Receptor Engagement.
Mitchell S von Itzstein, Moritz Winger, Alpeshkumar K Malde, Stephanie Holt, Sarah McAtamney

ACS Infect Dis· October 2025

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Chemical Synthesis of Oligosaccharides Derived from Serotype 35B and D Provides Molecular Insight in l-Ficolin Binding.
Ivan A Gagarinov, Lin Liu, Francesco Torricella, John N Glushka, Alpeshkumar K Malde

J Am Chem Soc· August 2025

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On the Validation of Protein Force Fields Based on Structural Criteria.
Martin Stroet, Martina Setz, Thomas Lee, Alpeshkumar K Malde, Glen van den Bergen

J Phys Chem B· May 2024

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Permeability of Dermatological Solutes through the Short Periodicity Phase of Human Stratum Corneum Lipid Bilayers.
Afshin Zamani Zakaria, Alpeshkumar K Malde, Tim Gould

J Chem Inf Model· January 2024

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Development of a model for granule-bound starch synthase I activity using free-energy calculations.
Shaobo Zhang, Xiaolei Fan, Alpeshkumar K Malde, Robert G Gilbert

Int J Biol Macromol· December 2023

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Probing Disaccharide Binding to Triplatin as Models for Tumor Cell Heparan Sulfate (GAG) Interactions.
Anil K Gorle, Alpeshkumar K Malde, Chih-Wei Chang, Premraj Rajaratnam, Mark von Itzstein

Inorg Chem· August 2023

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Understanding the Binding of Starch Fragments to Granule-Bound Starch Synthase.
Shaobo Zhang, Cheng Li, Robert G Gilbert, Alpeshkumar K Malde

Biomacromolecules· November 2021

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MyD88 TIR domain higher-order assembly interactions revealed by microcrystal electron diffraction and serial femtosecond crystallography.
Max T B Clabbers, Susannah Holmes, Timothy W Muusse, Parimala R Vajjhala, Sara J Thygesen, Alpeshkumar K Malde

Nat Commun· May 2021

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Platinum complexes act as shielding agents against virus infection.
Benjamin Bailly, Anil K Gorle, Larissa Dirr, Alpeshkumar K Malde, Nicholas P Farrell

Chem Commun (Camb)· May 2021

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SARM1 is a metabolic sensor activated by an increased NMN/NAD ratio to trigger axon degeneration.
Matthew D Figley, Weixi Gu, Jeffrey D Nanson, Yun Shi, Yo Sasaki, Alpeshkumar K Malde

Neuron· April 2021

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Bisubstrate Ether-Linked Uridine-Peptide Conjugates as O-GlcNAc Transferase Inhibitors.
Vivek Makwana, Philip Ryan, Alpeshkumar K Malde, Shailendra Anoopkumar-Dukie, Santosh Rudrawar

ChemMedChem· February 2021

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Simplified Novel Muraymycin Analogues; using a Serine Template Strategy for Linking Key Pharmacophores.
Bhautikkumar Patel, Rachel V Kerr, Alpeshkumar K Malde, Matthew Zunk, Timothy D H Bugg

ChemMedChem· August 2020

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Crystal Structures of Protein-Bound Cyclic Peptides.
Alpeshkumar K Malde, Timothy A Hill, Abishek Iyer, David P Fairlie

Chem Rev· September 2019

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Automated Topology Builder Version 3.0: Prediction of Solvation Free Enthalpies in Water and Hexane.
Martin Stroet, Bertrand Caron, Koen M Visscher, Daan P Geerke, Alpeshkumar K Malde

J Chem Theory Comput· November 2018

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Predicting the Prevalence of Alternative Warfarin Tautomers in Solution.
Alpeshkumar K Malde, Martin Stroet, Bertrand Caron, Koen M Visscher, Alan E Mark

J Chem Theory Comput· August 2018

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Effect of Binding on Enantioselectivity of Epoxide Hydrolase.
Julian Zaugg, Yosephine Gumulya, Mikael Bodén, Alan E Mark, Alpeshkumar K Malde

J Chem Inf Model· March 2018

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Optimization of Empirical Force Fields by Parameter Space Mapping: A Single-Step Perturbation Approach.
Martin Stroet, Katarzyna B Koziara, Alpeshkumar K Malde, Alan E Mark

J Chem Theory Comput· December 2017

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Learning epistatic interactions from sequence-activity data to predict enantioselectivity.
Julian Zaugg, Yosephine Gumulya, Alpeshkumar K Malde, Mikael Bodén

J Comput Aided Mol Des· December 2017

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Elucidating the Spatial Arrangement of Emitter Molecules in Organic Light-Emitting Diode Films.
Claire Tonnelé, Martin Stroet, Bertrand Caron, Andrew J Clulow, Ravi C R Nagiri, Alpeshkumar K Malde

Angew Chem Int Ed Engl· July 2017

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Molecular dynamics simulations reveal structural insights into inhibitor binding modes and functionality in human Group IIA phospholipase A.
Ryung Rae Kim, Alpeshkumar K Malde, Alireza Nematollahi, Kieran F Scott, W Bret Church

Proteins· May 2017

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The characterization of modified starch branching enzymes: toward the control of starch chain-length distributions.
Cheng Li, Alex Chi Wu, Rob Marc Go, Jacob Malouf, Mark S Turner, Alpeshkumar K Malde

PLoS One· April 2016

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Binding of Starch Fragments to the Starch Branching Enzyme: Implications for Developing Slower-Digesting Starch.
Rob Marc Go, Alan E Mark, Alpeshkumar K Malde, Robert G Gilbert

Biomacromolecules· August 2015

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Testing and validation of the Automated Topology Builder (ATB) version 2.0: prediction of hydration free enthalpies.
Katarzyna B Koziara, Martin Stroet, Alpeshkumar K Malde, Alan E Mark

J Comput Aided Mol Des· March 2014

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Comparative Occupancy Analysis (CoOAn) - A Straightforward and Directly Applicable 3D-QSAR Formalism to Extract Molecular Features Obligatory for Designing Potent Leads.
Jitender Verma, Alpeshkumar Malde, Santosh Khedkar, Evans Coutinho

Mol Inform· July 2012

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