Binding of an antiviral agent to a sensitive and a resistant human rhinovirus. Computer simulation studies with sampling of amino acid side-chain conformations

1992 ◽  
Vol 225 (3) ◽  
pp. 697-712 ◽  
Author(s):  
Rebecca C. Wade ◽  
J.Andrew McCammon
Keyword(s):  
Computer Simulation ◽  
Amino Acid ◽  
Antiviral Agent ◽  
Human Rhinovirus ◽  
Side Chain ◽  
Amino Acid Side Chain ◽  
Simulation Studies ◽  
Computer Simulation Studies ◽  
Chain Conformations

scholarly journals DLPacker: Deep Learning for Prediction of Amino Acid Side Chain Conformations in Proteins

2021 ◽  
Author(s):  
Mikita Misiura ◽  
Raghav Shroff ◽  
Ross Thyer ◽  
Anatoly Kolomeisky
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Protein Design ◽  
Structure Prediction ◽  
Deep Neural Networks ◽  
Side Chain ◽  
Amino Acid Side Chain ◽  
Image Transformation ◽  
Hydrophobic Amino Acids ◽  
Chain Conformations

Prediction of side chain conformations of amino acids in proteins (also termed 'packing') is an important and challenging part of protein structure prediction with many interesting applications in protein design. A variety of methods for packing have been developed but more accurate ones are still needed. Machine learning (ML) methods have recently become a powerful tool for solving various problems in diverse areas of science, including structural biology. In this work we evaluate the potential of Deep Neural Networks (DNNs) for prediction of amino acid side chain conformations. We formulate the problem as image-to-image transformation and train a U-net style DNN to solve the problem. We show that our method outperforms other physics-based methods by a significant margin: reconstruction RMSDs for most amino acids are about 20% smaller compared to SCWRL4 and Rosetta Packer with RMSDs for bulky hydrophobic amino acids Phe, Tyr and Trp being up to 50% smaller.

scholarly journals Computer Simulation Studies of Mammalian Pyruvate Kinase

1967 ◽  
Vol 242 (9) ◽  
pp. 2124-2133 ◽  
Author(s):  
Lawrence A. Kerson ◽  
David Garfinkel ◽  
Albert S. Mildvan
Keyword(s):  
Computer Simulation ◽  
Pyruvate Kinase ◽  
Simulation Studies ◽  
Computer Simulation Studies

Amino acid side-chain populations in aqueous and saline solution: Bis-penicillamine enkephalin

Biopolymers ◽  
1992 ◽  
Vol 32 (12) ◽  
pp. 1623-1629 ◽  
Author(s):  
Paul E. Smith ◽  
B. Montgomery Pettitt
Keyword(s):  
Amino Acid ◽  
Saline Solution ◽  
Side Chain ◽  
Amino Acid Side Chain
Sign in / Sign up

Export Citation Format

Share Document