Search Results - "Journal of chemical information and modeling"

AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings by Eberhardt, Jerome, Santos-Martins, Diogo, Tillack, Andreas F, Forli, Stefano

“…AutoDock Vina is arguably one of the fastest and most widely used open-source programs for molecular docking. However, compared to other programs in the…”
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New Basis Set Exchange: An Open, Up-to-Date Resource for the Molecular Sciences Community by Pritchard, Benjamin P, Altarawy, Doaa, Didier, Brett, Gibson, Tara D, Windus, Theresa L

“…The Basis Set Exchange (BSE) has been a prominent fixture in the quantum chemistry community. First publicly available in 2007, it is recognized by both users…”
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Omicron Variant (B.1.1.529): Infectivity, Vaccine Breakthrough, and Antibody Resistance by Chen, Jiahui, Wang, Rui, Gilby, Nancy Benovich, Wei, Guo-Wei

“…The latest severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant Omicron (B.1.1.529) has ushered panic responses around the world due to its…”
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Analyzing Learned Molecular Representations for Property Prediction by Yang, Kevin, Swanson, Kyle, Jin, Wengong, Coley, Connor, Eiden, Philipp, Gao, Hua, Guzman-Perez, Angel, Hopper, Timothy, Kelley, Brian, Mathea, Miriam, Palmer, Andrew, Settels, Volker, Jaakkola, Tommi, Jensen, Klavs, Barzilay, Regina

“…Advancements in neural machinery have led to a wide range of algorithmic solutions for molecular property prediction. Two classes of models in particular have…”
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AmberTools by Case, David A., Aktulga, Hasan Metin, Belfon, Kellon, Cerutti, David S., Cisneros, G. Andrés, Cruzeiro, Vinícius Wilian D., Forouzesh, Negin, Giese, Timothy J., Götz, Andreas W., Gohlke, Holger, Izadi, Saeed, Kasavajhala, Koushik, Kaymak, Mehmet C., King, Edward, Kurtzman, Tom, Lee, Tai-Sung, Li, Pengfei, Liu, Jian, Luchko, Tyler, Luo, Ray, Manathunga, Madushanka, Machado, Matias R., Nguyen, Hai Minh, O’Hearn, Kurt A., Onufriev, Alexey V., Pan, Feng, Pantano, Sergio, Qi, Ruxi, Rahnamoun, Ali, Risheh, Ali, Schott-Verdugo, Stephan, Shajan, Akhil, Swails, Jason, Wang, Junmei, Wei, Haixin, Wu, Xiongwu, Wu, Yongxian, Zhang, Shi, Zhao, Shiji, Zhu, Qiang, Cheatham, Thomas E., Roe, Daniel R., Roitberg, Adrian, Simmerling, Carlos, York, Darrin M., Nagan, Maria C., Merz, Kenneth M.

“…AmberTools is a free and open-source collection of programs used to set up, run, and analyze molecular simulations. The newer features contained within…”
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ZINC20A Free Ultralarge-Scale Chemical Database for Ligand Discovery by Irwin, John J, Tang, Khanh G, Young, Jennifer, Dandarchuluun, Chinzorig, Wong, Benjamin R, Khurelbaatar, Munkhzul, Moroz, Yurii S, Mayfield, John, Sayle, Roger A

“…Identifying and purchasing new small molecules to test in biological assays are enabling for ligand discovery, but as purchasable chemical space continues to…”
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GuacaMol: Benchmarking Models for de Novo Molecular Design by Brown, Nathan, Fiscato, Marco, Segler, Marwin H.S, Vaucher, Alain C

“…De novo design seeks to generate molecules with required property profiles by virtual design-make-test cycles. With the emergence of deep learning and neural…”
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MolGPT: Molecular Generation Using a Transformer-Decoder Model by Bagal, Viraj, Aggarwal, Rishal, Vinod, P K, Priyakumar, U Deva

“…Application of deep learning techniques for generation of molecules, termed as inverse molecular design, has been gaining enormous traction in drug design. The…”
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Fast Identification of Possible Drug Treatment of Coronavirus Disease-19 (COVID-19) through Computational Drug Repurposing Study by Wang, Junmei

“…The recent outbreak of novel coronavirus disease-19 (COVID-19) calls for and welcomes possible treatment strategies using drugs on the market. It is very…”
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Deep Learning in Chemistry by Mater, Adam C, Coote, Michelle L

“…Machine learning enables computers to address problems by learning from data. Deep learning is a type of machine learning that uses a hierarchical…”
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KDEEP: Protein-Ligand Absolute Binding Affinity Prediction via 3D-Convolutional Neural Networks by Jiménez, José, Škalič, Miha, Martínez-Rosell, Gerard, De Fabritiis, Gianni

“…Accurately predicting protein-ligand binding affinities is an important problem in computational chemistry since it can substantially accelerate drug discovery…”
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ZINC 15 – Ligand Discovery for Everyone by Sterling, Teague, Irwin, John J

“…Many questions about the biological activity and availability of small molecules remain inaccessible to investigators who could most benefit from their…”
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Relative Binding Free Energy Calculations in Drug Discovery: Recent Advances and Practical Considerations by Cournia, Zoe, Allen, Bryce, Sherman, Woody

“…Accurate in silico prediction of protein–ligand binding affinities has been a primary objective of structure-based drug design for decades due to the putative…”
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Comparative Assessment of Scoring Functions: The CASF-2016 Update by Su, Minyi, Yang, Qifan, Du, Yu, Feng, Guoqin, Liu, Zhihai, Li, Yan, Wang, Renxiao

“…In structure-based drug design, scoring functions are often employed to evaluate protein–ligand interactions. A variety of scoring functions have been…”
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Protein–Ligand Scoring with Convolutional Neural Networks by Ragoza, Matthew, Hochuli, Joshua, Idrobo, Elisa, Sunseri, Jocelyn, Koes, David Ryan

“…Computational approaches to drug discovery can reduce the time and cost associated with experimental assays and enable the screening of novel chemotypes…”
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Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery by Lee, Tai-Sung, Allen, Bryce K, Giese, Timothy J, Guo, Zhenyu, Li, Pengfei, Lin, Charles, McGee, T. Dwight, Pearlman, David A, Radak, Brian K, Tao, Yujun, Tsai, Hsu-Chun, Xu, Huafeng, Sherman, Woody, York, Darrin M

“…Predicting protein–ligand binding affinities and the associated thermodynamics of biomolecular recognition is a primary objective of structure-based drug…”
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The Synthesizability of Molecules Proposed by Generative Models by Gao, Wenhao, Coley, Connor W

“…The discovery of functional molecules is an expensive and time-consuming process, exemplified by the rising costs of small molecule therapeutic discovery. One…”
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Graph Convolutional Neural Networks for Predicting Drug-Target Interactions by Torng, Wen, Altman, Russ B

“…Accurate determination of target-ligand interactions is crucial in the drug discovery process. In this paper, we propose a graph-convolutional (Graph-CNN)…”
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Large-Scale Assessment of Binding Free Energy Calculations in Active Drug Discovery Projects by Schindler, Christina E. M, Baumann, Hannah, Blum, Andreas, Böse, Dietrich, Buchstaller, Hans-Peter, Burgdorf, Lars, Cappel, Daniel, Chekler, Eugene, Czodrowski, Paul, Dorsch, Dieter, Eguida, Merveille K. I, Follows, Bruce, Fuchß, Thomas, Grädler, Ulrich, Gunera, Jakub, Johnson, Theresa, Jorand Lebrun, Catherine, Karra, Srinivasa, Klein, Markus, Knehans, Tim, Koetzner, Lisa, Krier, Mireille, Leiendecker, Matthias, Leuthner, Birgitta, Li, Liwei, Mochalkin, Igor, Musil, Djordje, Neagu, Constantin, Rippmann, Friedrich, Schiemann, Kai, Schulz, Robert, Steinbrecher, Thomas, Tanzer, Eva-Maria, Unzue Lopez, Andrea, Viacava Follis, Ariele, Wegener, Ansgar, Kuhn, Daniel

“…Accurate ranking of compounds with regards to their binding affinity to a protein using computational methods is of great interest to pharmaceutical research…”
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Autodock Vina Adopts More Accurate Binding Poses but Autodock4 Forms Better Binding Affinity by Nguyen, Nguyen Thanh, Nguyen, Trung Hai, Pham, T. Ngoc Han, Huy, Nguyen Truong, Bay, Mai Van, Pham, Minh Quan, Nam, Pham Cam, Vu, Van V, Ngo, Son Tung

“…The binding pose and affinity between a ligand and enzyme are very important pieces of information for computer-aided drug design. In the initial stage of a…”
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